Contacts of the strand formed by residues 4349 - 4353 (chain B) in PDB entry 6W4H


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 TYR4349 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6881A  ALA*     2.5    32.0    +      -       +      -
   6884A  ARG*     3.0    22.1    -      -       +      +
   6885A  GLN*     2.9    20.9    +      -       +      -
   6904A  ASP*     5.4     2.2    -      -       -      -
   4297B  MET*     3.8    30.5    -      -       +      -
   4308B  ILE*     3.3     6.1    -      -       -      +
   4309B  THR      2.8    34.4    +      -       -      +
   4310B  VAL      3.3    27.1    -      -       -      -
   4311B  THR*     3.7     9.2    -      -       -      +
   4312B  PRO*     3.8    30.5    -      -       +      -
   4320B  SER*     5.0     1.1    -      -       -      -
   4321B  PHE      3.2    15.9    -      -       -      +
   4322B  GLY*     3.9     8.3    -      -       -      -
   4323B  GLY*     5.0     0.4    -      -       -      -
   4345B  LEU*     5.7     0.2    -      -       -      -
   4348B  LYS*     1.3    79.0    -      -       -      +
   4350B  VAL*     1.3    60.1    +      -       -      +
   4351B  GLN*     3.6     7.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL4350 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4307B  ALA      3.3     9.9    -      -       -      +
   4308B  ILE*     4.5     1.1    -      -       +      +
   4319B  GLU      3.7     0.9    -      -       -      +
   4320B  SER*     3.5     1.2    -      -       -      -
   4321B  PHE*     2.9    38.8    +      -       +      +
   4323B  GLY*     4.6     4.1    -      -       -      +
   4326B  CYS*     3.6    38.6    -      -       +      -
   4345B  LEU*     3.9    19.7    -      -       +      -
   4349B  TYR*     1.3    73.8    -      -       -      +
   4351B  GLN*     1.3    64.9    +      -       -      +
   4352B  ILE*     3.7    23.6    +      -       +      -
   4364B  THR*     3.8     9.0    -      -       +      -
   4376B  TRP*     3.8    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN4351 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4306B  GLN      2.8    33.3    +      -       -      +
   4307B  ALA*     2.8    17.4    +      -       -      +
   4309B  THR*     3.0    23.0    +      -       -      +
   4312B  PRO*     3.7     2.1    -      -       -      +
   4313B  GLU      2.9    19.0    +      -       -      -
   4314B  ALA*     3.4    26.9    -      -       -      +
   4318B  GLN*     3.6    19.1    -      -       -      +
   4319B  GLU      3.4     3.6    -      -       -      -
   4320B  SER*     2.6    26.5    +      -       -      +
   4349B  TYR*     3.6     6.0    +      -       -      +
   4350B  VAL*     1.3    73.4    -      -       -      +
   4352B  ILE*     1.3    63.8    +      -       -      +
   4353B  PRO*     4.6     0.2    -      -       -      -
   4376B  TRP*     2.8    31.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE4352 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4318B  GLN*     3.2     3.2    -      -       -      -
   4319B  GLU*     2.8    33.0    +      -       -      +
   4321B  PHE*     3.7    31.0    -      -       +      -
   4350B  VAL*     3.7    23.6    -      -       +      +
   4351B  GLN*     1.3    82.4    -      -       -      +
   4353B  PRO*     1.4    86.7    -      -       +      +
   4356B  CYS*     3.7    24.2    -      -       +      +
   4357B  ALA*     3.8     6.1    -      -       -      -
   4360B  PRO*     4.0    15.5    -      -       +      +
   4363B  PHE*     3.7    23.3    -      -       +      -
   4364B  THR*     4.0    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO4353 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4317B  ASP      3.5    10.8    -      -       -      +
   4318B  GLN*     4.2     8.7    -      -       +      +
   4351B  GLN      4.3     2.5    -      -       -      +
   4352B  ILE*     1.4    87.9    -      -       +      +
   4354B  THR*     1.3    61.8    +      -       -      +
   4355B  THR*     4.0    14.1    -      -       -      +
   4356B  CYS*     2.8    23.8    +      -       -      -
   4357B  ALA      3.1     9.2    +      -       -      -
   4363B  PHE*     3.4    28.3    -      -       +      -
   4376B  TRP*     4.9     3.1    -      -       +      -
   4379B  TYR*     3.6    38.6    -      -       +      +
----------------------------------------------------------
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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