Contacts of the strand formed by residues 26 - 38 (chain A) in PDB entry 1XWD


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 26 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     3.6    34.8    -      -       +      +
     13A  GLN*     3.0    15.7    -      -       -      +
     14A  GLU*     4.4     4.9    -      -       +      +
     24A  PRO*     4.1    18.2    -      -       +      +
     25A  ILE*     1.3    78.3    -      -       -      +
     27A  GLN*     1.3    63.5    +      -       -      +
     77A  GLU      4.0     1.4    -      -       -      +
     78A  ASN*     2.7    11.4    +      -       -      +
     79A  HIS*     3.2    37.6    +      -       -      +
     94A  NAG      4.0    30.1    -      -       -      +
     38B  VAL*     3.7     8.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  THR      3.4     2.8    -      -       -      +
     12A  LEU*     4.3     2.7    -      -       -      -
     13A  GLN*     2.5    36.8    +      -       -      +
     15A  ASN*     3.0    26.5    +      -       +      +
     16A  PRO*     5.4     1.0    -      -       -      +
     17A  PHE*     5.8     1.0    -      -       -      -
     26A  LEU*     1.3    77.6    -      -       -      +
     28A  CYS*     1.3    64.3    +      -       -      +
     29A  MET*     3.2    30.0    +      -       +      +
     79A  HIS*     3.2     5.1    -      -       -      +
     35B  ARG*     4.4     4.5    +      -       -      +
     36B  ASP      3.1    29.3    +      -       -      +
     37B  LEU*     3.6    12.5    -      -       -      +
     38B  VAL*     3.6    15.7    -      -       +      +
    403B  SO4      3.3    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  GLN*     1.3    70.1    -      -       -      +
     29A  MET*     1.3    58.7    +      -       -      +
     60A  CYS*     3.9     9.0    -      -       -      -
     61A  VAL      3.7    14.4    -      -       -      -
     62A  ALA*     3.6    20.0    -      -       -      -
     79A  HIS*     2.9    21.5    +      -       -      +
     81A  ALA      3.7     2.9    -      -       -      -
     82A  CYS*     2.0    57.4    -      -       +      -
     35B  ARG*     3.2     1.4    -      -       -      +
     36B  ASP*     2.6    37.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  GLU      4.0     1.6    -      -       -      +
     11A  THR*     3.1    24.7    +      -       -      +
     13A  GLN*     3.7    32.4    +      -       +      +
     14A  GLU      5.3     4.7    -      -       -      +
     15A  ASN*     5.7     0.4    -      -       -      -
     16A  PRO*     6.0     2.7    -      -       +      -
     27A  GLN*     3.2    49.8    -      -       +      +
     28A  CYS*     1.3    75.6    -      -       -      +
     30A  GLY*     1.3    57.5    +      -       -      +
     60A  CYS*     3.6     5.1    -      -       -      -
     33B  TYR*     3.1    30.7    -      -       +      +
     34B  THR      3.3     7.4    -      -       -      -
     35B  ARG*     3.7    17.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PRO*     3.5    13.0    -      -       -      -
      9A  GLU      3.9     1.6    -      -       -      -
     10A  CYS*     3.8     8.1    -      -       -      -
     29A  MET*     1.3    76.6    -      -       -      +
     31A  CYS*     1.3    65.1    +      -       -      -
     60A  CYS*     3.8     3.3    -      -       -      -
     32B  CYS      3.7     0.2    -      -       -      +
     33B  TYR*     3.3    15.6    -      -       -      -
     34B  THR*     2.9    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  CYS*     2.0    58.1    -      -       +      +
      8A  PRO*     2.8    24.6    +      -       -      +
      9A  GLU*     4.2     3.9    -      -       -      -
     10A  CYS      3.5    14.6    +      -       -      +
     30A  GLY*     1.3    77.0    -      -       -      -
     32A  CYS*     1.3    65.0    +      -       -      +
     84A  CYS*     4.0     3.3    -      -       -      -
     31B  TYR*     3.9    16.8    -      -       +      -
     32B  CYS      3.3     4.5    -      -       -      +
     33B  TYR*     3.8    15.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  CYS*     1.3    75.6    -      -       -      +
     33A  PHE*     1.3    62.2    +      -       -      +
     34A  SER*     4.4     1.7    +      -       -      -
     58A  THR*     3.2    26.9    -      -       +      +
     59A  CYS      3.6     0.2    -      -       -      -
     60A  CYS*     3.4    32.3    -      -       -      -
     84A  CYS*     2.0    47.8    -      -       -      -
     30B  GLY      3.7     0.3    -      -       -      +
     31B  TYR*     3.3    27.8    -      -       -      -
     32B  CYS*     3.3    13.0    +      -       -      +
     34B  THR*     4.6     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  CYS*     1.3    73.7    -      -       -      +
     34A  SER*     1.3    78.3    +      -       -      +
     35A  ARG*     4.0    20.6    -      -       +      -
     56A  GLU*     5.7     0.7    -      -       -      -
     57A  SER      4.3     0.2    -      -       -      -
     58A  THR*     3.5    28.3    +      -       +      +
     84A  CYS*     5.0     0.2    -      -       -      -
     29B  ALA*     4.0    15.3    -      -       +      -
     30B  GLY*     3.3    35.9    -      -       -      -
     31B  TYR*     3.7    28.7    -      +       +      +
----------------------------------------------------------
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Residues in contact with SER 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  CYS      4.4     2.6    +      -       -      -
     33A  PHE*     1.3    85.3    -      -       -      +
     35A  ARG*     1.3    67.8    +      -       -      +
     56A  GLU      3.4    11.0    -      -       -      -
     57A  SER*     3.7     5.6    -      -       -      +
     58A  THR      4.4     2.5    -      -       -      -
     29B  ALA*     3.5     0.7    -      -       -      -
     30B  GLY      3.0    28.4    +      -       -      +
     32B  CYS*     4.4     5.2    -      -       -      +
     50B  THR*     3.4    24.0    +      -       -      -
     51B  CYS*     3.0    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  PHE*     4.0    19.4    -      -       +      -
     34A  SER*     1.3    77.8    -      -       -      +
     36A  ALA*     1.3    61.8    +      -       -      +
     37A  TYR*     3.9    10.2    -      -       +      -
     54A  THR      4.1     0.2    -      -       -      +
     55A  SER*     3.3     2.6    -      -       -      -
     56A  GLU*     2.9    76.6    +      -       -      +
      8B  ILE*     5.9     3.8    -      -       -      +
     28B  CYS      3.3    16.4    -      -       -      +
     29B  ALA*     3.8    10.8    -      -       +      +
     51B  CYS*     4.1     9.3    +      -       -      -
    100B  GLY*     4.4     2.8    -      -       -      -
    101B  PRO*     3.6    25.9    -      -       -      +
    402B  SO4      3.1    39.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ARG*     1.3    75.5    -      -       -      +
     37A  TYR*     1.3    67.6    +      -       -      +
     53A  VAL*     4.4     4.5    -      -       +      -
     54A  THR      3.2     9.6    -      -       -      +
     55A  SER*     4.5     4.3    -      -       -      -
      8B  ILE*     4.8     0.3    -      -       -      +
     27B  TRP*     3.3    35.7    -      -       +      +
     28B  CYS*     3.1    20.8    +      -       +      +
     51B  CYS      4.4     0.2    -      -       -      +
     52B  THR*     4.1    29.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ARG*     3.9    13.9    -      -       -      -
     36A  ALA*     1.3    80.2    -      -       -      +
     38A  PRO*     1.3    89.0    -      -       +      +
     40A  PRO*     4.0     9.4    -      -       +      -
     53A  VAL*     4.3     2.7    -      -       -      +
     54A  THR*     2.8    45.3    +      -       +      +
     56A  GLU*     2.6    44.0    +      -       +      -
      8B  ILE*     3.7    17.7    -      -       +      -
     27B  TRP*     3.8     9.4    -      -       -      -
     98B  GLY*     3.4    11.8    -      -       -      -
     99B  LEU      3.7     0.2    +      -       -      -
    100B  GLY*     3.0    36.8    +      -       -      -
    101B  PRO*     3.5    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  TYR*     1.3    95.6    -      -       +      +
     39A  THR*     1.3    68.0    +      -       -      +
     40A  PRO*     3.2    10.6    -      -       -      +
     52A  ASN      3.6     8.5    -      -       -      +
     53A  VAL*     4.6     0.2    -      -       -      -
     10B  ILE*     3.7    38.3    -      -       +      +
     27B  TRP*     3.2    33.3    -      -       +      +
     74B  TYR*     5.9     2.9    -      -       -      +
     76B  TYR*     5.3     0.9    -      -       +      -
     77B  PRO*     3.7    26.2    -      -       +      +
    101B  PRO*     4.7     4.2    -      -       -      +
----------------------------------------------------------
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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