Contacts of the strand formed by residues 115 - 122 (chain B) in PDB entry 1X2W


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 ALA 115 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  PRO*     3.4     9.7    -      -       -      +
     21B  LYS      3.1    25.6    +      -       -      +
     63B  ILE*     4.0    26.0    -      -       +      +
     64B  PHE*     4.9     0.7    -      -       -      -
     65B  TRP*     3.8    27.4    -      -       +      +
     98B  TYR*     5.6     1.3    -      -       +      -
    109B  ARG*     4.7     2.0    -      -       -      -
    114B  MET*     1.3    80.3    -      -       -      +
    116B  GLN*     1.3    72.1    +      -       -      +
    117B  PHE*     3.9     2.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  PHE      3.4     9.8    +      -       -      +
     18B  SER*     3.6    25.1    -      -       -      +
     20B  PRO*     4.7     6.2    -      -       +      +
     59B  PHE*     3.2    29.2    -      -       -      +
     62B  SER*     2.9    24.9    +      -       -      +
     63B  ILE*     3.0    13.6    +      -       +      +
     64B  PHE*     3.1    29.8    -      -       +      -
     65B  TRP*     2.8    20.1    +      -       -      -
    115B  ALA*     1.3    77.0    -      -       -      +
    117B  PHE*     1.3    68.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  PRO*     3.2     2.6    -      -       -      +
     17B  PHE*     2.7    54.6    +      -       +      +
     19B  GLU*     3.3    23.8    -      -       +      -
     21B  LYS*     3.8    19.7    -      -       +      -
     26B  ALA*     3.8    15.9    -      -       +      -
     29B  PHE*     3.5    27.4    -      +       -      -
     30B  CYS*     3.7    19.3    -      -       -      -
     39B  LEU*     3.7     7.4    -      -       +      -
     64B  PHE*     3.5    12.0    -      -       -      -
     65B  TRP*     3.7    20.2    -      -       +      +
    115B  ALA      3.9     7.2    -      -       -      -
    116B  GLN*     1.3    83.7    -      -       -      +
    118B  VAL*     1.3    61.4    +      -       -      +
    119B  CYS*     3.6    21.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  TYR*     4.2     8.1    -      -       +      -
     15B  LYS      3.4    17.3    -      -       -      +
     16B  PRO*     3.9    17.9    -      -       +      -
     39B  LEU*     3.5    11.0    -      -       -      +
     40B  VAL*     3.0    43.1    +      -       +      +
     51B  VAL*     4.1    14.6    -      -       +      +
     54B  LEU*     5.4     2.2    -      -       +      -
     55B  ALA*     4.6     4.3    -      -       +      +
     64B  PHE*     4.1     7.2    -      -       +      -
     65B  TRP      3.9     4.6    +      -       -      -
     99B  PHE*     4.0    24.7    -      -       +      -
    117B  PHE*     1.3    79.9    -      -       -      +
    119B  CYS*     1.3    74.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  TRP*     3.7    19.7    -      -       +      -
     14B  TYR*     3.3     4.9    -      -       -      -
     15B  LYS      2.7    32.5    +      -       -      +
     17B  PHE*     3.7    15.5    -      -       +      -
     29B  PHE*     4.5     0.9    -      -       -      -
     30B  CYS*     2.0    53.8    -      -       +      +
     33B  GLN*     4.6     1.3    -      -       -      -
     38B  HIS      3.4     5.4    -      -       -      +
    117B  PHE*     3.6    17.7    -      -       -      -
    118B  VAL*     1.3    77.5    -      -       -      +
    120B  GLU*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  ASP*     4.6     4.3    -      -       -      +
      6B  TRP*     3.9     3.9    -      -       -      -
     12B  HIS*     3.3    28.5    +      -       -      +
     13B  CYS      3.2    11.9    -      -       -      +
     14B  TYR*     3.4    28.5    +      -       +      -
     36B  GLY      3.7     1.9    -      -       -      +
     37B  GLY*     3.4     2.3    -      -       -      -
     38B  HIS*     2.7    33.8    +      -       -      +
     39B  LEU      4.4     1.1    -      -       -      +
     40B  VAL*     3.2    12.7    -      -       -      +
     41B  SER*     3.0    36.8    +      -       -      +
     47B  GLU*     3.8     5.9    -      -       -      +
    119B  CYS*     1.3    77.9    -      -       -      +
    121B  PHE*     1.3    73.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  ASP      5.7     0.7    -      -       -      -
      2B  CYS*     5.7     0.2    -      -       -      -
      3B  PRO*     3.6    13.5    -      -       +      -
      6B  TRP*     3.5    40.2    -      +       -      -
     12B  HIS*     3.4     8.3    +      -       -      -
     13B  CYS*     2.8    69.8    +      -       +      -
     34B  HIS*     3.4    52.0    -      +       +      -
     35B  ALA      3.8    11.0    -      -       -      +
     36B  GLY      3.8    17.3    -      -       -      +
     37B  GLY*     4.2     2.0    -      -       -      -
    120B  GLU*     1.3    77.0    -      -       -      +
    122B  GLN*     1.3    72.8    +      -       -      +
    123B  ALA*     4.1     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  GLY      4.2     1.3    -      -       -      +
     12B  HIS*     3.4    29.3    +      -       +      -
     34B  HIS*     5.7     0.3    -      -       -      -
     36B  GLY      4.9     1.8    +      -       -      -
    121B  PHE*     1.3    84.5    -      -       -      +
    123B  ALA*     1.3    96.7    +      -       +      +
----------------------------------------------------------
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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