Contacts of the strand formed by residues 351 - 358 (chain B) in PDB entry 3IW4


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 GLY 351 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347B  LYS*     3.4     1.5    -      -       -      -
    348B  GLY      2.6    39.8    +      -       -      -
    349B  SER      3.0     4.8    +      -       -      -
    350B  PHE*     1.3    82.5    -      -       -      +
    352B  LYS*     1.3    59.9    +      -       -      -
    368B  LYS*     4.6     0.2    -      -       -      -
    370B  LEU*     4.1    20.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 352 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344B  VAL*     4.3    15.7    -      -       +      -
    346B  GLY      3.5     8.3    -      -       -      +
    347B  LYS*     3.1    37.0    -      -       +      +
    350B  PHE      4.0     0.6    +      -       -      -
    351B  GLY*     1.3    71.6    -      -       -      -
    353B  VAL*     1.3    62.1    +      -       -      +
    354B  MET*     4.1    25.1    -      -       +      -
    367B  ILE      3.5     2.3    -      -       -      +
    368B  LYS*     3.6     0.4    -      -       -      -
    369B  ILE*     3.0    48.3    +      -       +      +
    637B  LEU*     6.3     2.0    -      -       +      -
    638B  TPO      5.6     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 353 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344B  VAL*     3.5     4.7    -      -       -      +
    345B  LEU*     2.7    29.0    +      -       +      -
    346B  GLY      2.9    18.2    +      -       -      +
    350B  PHE*     3.5    28.9    -      -       +      +
    352B  LYS*     1.3    74.8    -      -       -      +
    354B  MET*     1.3    58.6    +      -       -      +
    366B  ALA*     3.7    27.8    -      -       +      -
    367B  ILE      3.5    11.0    -      -       -      +
    368B  LYS*     4.3     7.4    -      -       +      +
    901B  LW4      3.8    51.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 354 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341B  PHE*     3.7    30.1    -      -       +      -
    343B  MET      3.4    26.0    -      -       -      +
    344B  VAL*     3.9     9.2    -      -       +      -
    345B  LEU*     4.2     4.0    -      -       -      -
    352B  LYS*     4.1    20.4    -      -       +      -
    353B  VAL*     1.3    76.3    -      -       -      +
    355B  LEU*     1.3    72.6    +      -       -      +
    356B  ALA*     3.6     0.7    +      -       +      -
    366B  ALA*     3.4     4.2    -      -       -      -
    367B  ILE*     2.9    39.9    +      -       +      +
    369B  ILE*     3.9    24.5    -      -       +      -
    635B  PRO*     3.7    27.8    -      -       +      -
    636B  VAL      5.9     1.8    -      -       -      +
    637B  LEU*     5.6     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341B  PHE*     3.7     2.9    -      -       -      -
    342B  LEU*     2.8    41.7    +      -       +      -
    343B  MET*     2.5    52.4    +      -       +      +
    345B  LEU*     3.8    15.8    -      -       +      +
    354B  MET*     1.3    72.6    -      -       -      +
    356B  ALA*     1.3    68.2    +      -       -      +
    364B  LEU*     4.2    15.0    -      -       +      -
    365B  TYR      3.5     9.9    -      -       -      +
    419B  TYR*     3.9    47.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339B  PHE*     4.3     7.9    -      -       +      -
    340B  ASN      3.3    13.5    -      -       -      +
    341B  PHE*     4.3     9.6    -      -       +      -
    342B  LEU*     4.0     5.4    -      -       -      -
    354B  MET      4.5     0.7    -      -       -      +
    355B  LEU*     1.3    77.6    -      -       -      +
    357B  ASP*     1.3    59.7    +      -       -      +
    364B  LEU*     3.3     3.2    -      -       -      +
    365B  TYR*     2.7    45.8    +      -       -      +
    367B  ILE*     3.6    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 357 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339B  PHE*     3.5     5.5    -      -       -      -
    340B  ASN*     3.0    51.1    +      -       -      +
    342B  LEU*     3.7    17.2    -      -       +      +
    356B  ALA*     1.3    74.1    -      -       -      +
    358B  ARG*     1.3    82.5    +      -       -      +
    359B  LYS*     4.3     3.0    +      -       -      -
    360B  GLY      4.9     0.9    +      -       -      -
    361B  THR      3.9     5.2    -      -       -      +
    362B  GLU*     4.7     4.0    -      -       -      +
    363B  GLU      3.1    15.0    -      -       -      +
    364B  LEU*     3.2    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 358 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332B  ASP*     4.1    25.8    +      -       -      +
    333B  ARG      4.5     3.6    +      -       -      -
    334B  VAL*     3.5    30.6    -      -       -      +
    338B  ASP*     3.6    15.1    -      -       +      +
    339B  PHE*     4.0    13.6    -      -       +      -
    356B  ALA      4.3     0.4    +      -       -      -
    357B  ASP*     1.3    79.3    -      -       -      +
    359B  LYS*     1.3    68.9    +      -       -      +
    360B  GLY      3.3     0.5    +      -       -      -
    361B  THR*     2.7    44.4    -      -       +      +
    363B  GLU*     3.1    30.8    +      -       +      -
    365B  TYR*     4.0    22.2    +      -       +      -
    404B  HIS*     5.2     3.7    +      -       -      -
    665B  HIS*     5.7     2.4    -      -       -      -
----------------------------------------------------------
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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