Contacts of the strand formed by residues 952 - 969 (chain A) in PDB entry 2XDP


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LEU 952 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    927A  VAL*     4.0    22.4    -      -       +      -
    944A  GLN*     5.4     7.4    -      -       +      -
    945A  VAL      3.4     2.7    -      -       -      +
    946A  LYS*     3.6    31.2    -      -       +      -
    950A  GLY      3.7    12.3    -      -       -      +
    951A  LYS*     1.3    73.1    -      -       -      +
    953A  TYR*     1.3    70.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 953 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    912A  PHE*     3.8    32.8    -      +       +      -
    944A  GLN*     3.4     6.2    -      -       -      -
    945A  VAL*     2.8    41.9    +      -       +      +
    947A  TRP*     3.7    21.7    -      +       +      -
    951A  LYS*     2.9    60.6    +      -       +      +
    952A  LEU*     1.3    80.2    -      -       -      +
    954A  GLY*     1.3    62.5    +      -       -      +
    955A  ALA      3.8     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 954 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    912A  PHE*     3.6     6.8    -      -       -      +
    913A  ASP*     3.1    41.4    +      -       -      +
    942A  VAL*     5.9     2.5    -      -       -      -
    943A  VAL      3.6     6.7    -      -       -      -
    944A  GLN*     4.7     3.4    -      -       -      -
    953A  TYR*     1.3    73.7    -      -       -      +
    955A  ALA*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 955 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    910A  VAL*     4.1     8.7    -      -       +      -
    911A  MET      3.2    17.9    -      -       -      +
    912A  PHE*     3.9    17.5    -      -       +      -
    913A  ASP*     3.7     9.2    +      -       -      +
    942A  VAL*     3.5     9.1    -      -       -      +
    943A  VAL*     2.9    31.3    +      -       +      +
    945A  VAL*     3.9    19.7    -      -       +      -
    954A  GLY*     1.3    74.4    -      -       -      +
    956A  LYS*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 956 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    910A  VAL*     3.3     7.1    -      -       -      -
    911A  MET*     2.9    34.2    +      -       +      +
    913A  ASP*     5.6     2.9    -      -       -      +
    940A  GLY*     3.2    25.6    -      -       -      +
    941A  GLU      3.2     7.4    -      -       -      +
    942A  VAL*     4.1    13.9    -      -       +      -
    943A  VAL*     4.4     0.7    -      -       -      -
    955A  ALA*     1.3    78.1    -      -       -      +
    957A  TYR*     1.3    62.4    +      -       -      +
    958A  PHE*     3.1    38.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 957 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    908A  TYR*     3.5    31.8    -      +       +      -
    909A  GLU      3.9     6.7    -      -       -      -
    910A  VAL*     4.2     7.6    -      -       +      -
    926A  ILE*     5.7     0.9    -      -       +      -
    936A  PRO*     3.6    18.9    -      -       +      +
    937A  PRO*     3.3    45.5    -      -       +      -
    938A  ALA      3.4    18.2    -      -       -      +
    939A  GLU*     4.0    10.1    -      -       +      -
    940A  GLY      2.6    32.9    +      -       -      -
    941A  GLU      2.8    14.0    +      -       -      +
    943A  VAL*     4.2     7.6    -      -       +      +
    956A  LYS*     1.3    70.8    -      -       -      +
    958A  PHE*     1.3    60.7    +      -       -      +
    959A  GLY*     3.1    43.7    -      -       -      -
    960A  SER*     3.6    12.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 958 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    909A  GLU*     2.9    19.5    +      -       -      +
    911A  MET*     3.7    29.8    -      -       +      -
    917A  PHE*     4.5    15.7    -      +       +      -
    939A  GLU*     3.0    21.4    -      -       +      +
    940A  GLY*     3.1    28.3    -      -       -      +
    956A  LYS*     3.1    55.0    -      -       +      -
    957A  TYR*     1.3    83.3    -      -       -      +
    959A  GLY*     1.3    58.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 959 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    909A  GLU*     2.8    30.0    +      -       -      -
    939A  GLU*     4.1     9.2    -      -       -      -
    957A  TYR*     3.1    32.2    -      -       -      -
    958A  PHE*     1.3    80.8    -      -       -      +
    960A  SER*     1.3    58.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 960 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    906A  THR*     4.2    12.3    -      -       -      +
    907A  PHE      3.2    13.9    -      -       -      -
    908A  TYR*     3.9    10.8    -      -       -      +
    909A  GLU*     4.1     6.5    -      -       -      +
    936A  PRO*     6.1     0.4    -      -       -      +
    957A  TYR*     3.6    12.0    +      -       -      -
    959A  GLY*     1.3    75.5    -      -       -      -
    961A  ASN*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 961 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    906A  THR*     3.4     6.3    -      -       -      +
    907A  PHE*     2.8    44.6    +      -       -      +
    909A  GLU*     2.8    29.7    +      -       -      +
    919A  ARG*     3.2    27.4    +      -       -      +
    960A  SER*     1.3    76.3    -      -       -      +
    962A  ILE*     1.3    75.3    +      -       -      +
    963A  ALA*     3.9     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 962 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    904A  SER*     4.0    21.3    -      -       -      +
    905A  GLN      3.4     7.2    -      -       -      +
    906A  THR*     4.3    14.6    -      -       +      +
    961A  ASN*     1.3    83.5    -      -       -      +
    963A  ALA*     1.3    72.5    +      -       -      +
    964A  HIS*     5.9     1.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 963 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    904A  SER*     3.3     6.8    -      -       -      -
    905A  GLN      2.7    30.7    +      -       -      -
    907A  PHE*     3.6    22.4    -      -       +      -
    961A  ASN*     3.9     7.3    +      -       -      +
    962A  ILE*     1.3    75.5    -      -       -      +
    964A  HIS*     1.3    71.5    +      -       -      +
   1995A  SO4      3.7    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 964 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    902A  VAL*     3.8    27.4    -      -       +      -
    903A  THR*     3.0    22.2    -      -       -      +
    904A  SER*     4.2    10.3    +      -       -      -
    905A  GLN*     4.5     0.4    -      -       -      -
    907A  PHE*     3.8    12.4    -      -       -      -
    962A  ILE*     6.2     0.8    -      -       +      +
    963A  ALA*     1.3    85.0    -      -       -      +
    965A  MET*     1.3    68.2    +      -       -      +
    966A  TYR*     4.0    13.5    +      -       +      +
    980A  ARG      4.6     4.9    +      -       -      -
   1995A  SO4      2.7    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 965 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    901A  ALA      3.9     0.3    -      -       -      +
    902A  VAL*     3.4     5.2    -      -       -      +
    903A  THR*     2.9    44.7    +      -       -      +
    905A  GLN*     3.6    31.4    -      -       +      +
    907A  PHE*     3.7    20.6    -      -       -      -
    922A  PHE*     3.8    24.7    -      -       +      -
    964A  HIS*     1.3    75.3    -      -       -      +
    966A  TYR*     1.3    63.5    +      -       -      +
    967A  GLN      4.1     0.4    +      -       -      -
    977A  ALA*     3.5    34.1    -      -       +      +
    978A  MET      3.5    29.4    -      -       -      +
    979A  LYS*     3.8     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 966 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    899A  VAL*     4.3    13.5    -      -       +      -
    901A  ALA      3.5     3.1    -      -       -      +
    902A  VAL*     3.7    32.3    -      -       +      +
    964A  HIS*     4.0    15.8    +      -       +      +
    965A  MET*     1.3    75.3    -      -       -      +
    967A  GLN*     1.3    63.2    +      -       -      +
    968A  VAL*     3.5    11.7    +      -       +      +
    976A  ILE      3.7     0.2    -      -       -      +
    977A  ALA*     4.3     1.6    -      -       -      -
    978A  MET      2.8    38.4    +      -       -      +
    980A  ARG*     3.8    25.5    +      -       +      -
    983A  ILE*     3.4    32.3    -      -       +      -
   1995A  SO4      2.6    37.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 967 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    899A  VAL*     3.6     3.6    -      -       -      -
    900A  MET*     2.7    40.0    +      -       +      -
    901A  ALA*     2.9    29.6    +      -       +      +
    903A  THR*     6.3     0.7    -      -       +      -
    965A  MET      4.1     1.4    +      -       -      -
    966A  TYR*     1.3    69.9    -      -       -      +
    968A  VAL*     1.3    55.6    +      -       -      +
    975A  GLN*     3.1    42.2    +      -       -      +
    976A  ILE*     3.7    11.7    -      -       -      +
    977A  ALA*     3.6    21.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 968 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    897A  CYS*     3.8    16.8    -      -       +      -
    898A  ARG      3.2    10.1    -      -       -      +
    899A  VAL*     4.5    12.6    -      -       +      -
    900A  MET*     4.2     2.7    -      -       -      -
    966A  TYR*     3.7    18.6    -      -       +      +
    967A  GLN*     1.3    79.3    -      -       -      +
    969A  GLU*     1.3    61.1    +      -       -      +
    970A  PHE*     3.8    15.2    -      -       +      -
    975A  GLN*     3.1     8.1    -      -       -      +
    976A  ILE*     2.9    51.1    +      -       +      +
    978A  MET*     3.6    22.7    -      -       +      -
    983A  ILE*     4.9     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 969 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    897A  CYS*     3.3     5.3    -      -       -      -
    898A  ARG*     2.9    41.8    +      -       +      +
    900A  MET*     3.7    34.3    -      -       +      +
    968A  VAL*     1.3    74.9    -      -       -      +
    970A  PHE*     1.3    74.1    +      -       -      +
    973A  GLY*     4.1    12.6    -      -       -      +
    974A  SER      3.4    10.1    -      -       -      +
    975A  GLN*     3.2    23.7    +      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il