Contacts of the strand formed by residues 542 - 552 (chain B) in PDB entry 2P2F


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 ILE 542 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536B  LEU*     3.3    37.2    -      -       +      +
    537B  VAL*     3.5    23.1    -      -       +      +
    539B  HIS*     3.3    20.3    +      -       +      +
    540B  PRO      3.5     0.4    -      -       -      -
    541B  LYS*     1.3    80.1    -      -       -      +
    543B  ALA*     1.3    62.3    +      -       -      +
    544B  GLU      3.7    26.2    -      -       -      +
    545B  ALA*     4.6     2.2    -      -       +      -
    563B  VAL*     3.4    22.7    -      -       +      -
    564B  THR      3.7     4.5    -      -       -      +
    565B  LEU*     4.1     7.2    -      -       +      -
    566B  ASN*     3.8     7.9    +      -       -      +
    579B  VAL*     3.7    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 543 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537B  VAL*     4.1    12.4    -      -       -      +
    542B  ILE*     1.3    75.6    -      -       -      +
    544B  GLU*     1.3    67.8    +      -       +      +
    564B  THR*     2.8    20.2    +      -       +      +
    565B  LEU      3.5    12.8    -      -       -      +
    566B  ASN*     3.2    22.6    +      -       -      +
    567B  HIS*     6.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 544 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537B  VAL*     3.8     9.2    -      -       +      -
    542B  ILE*     3.7     4.6    -      -       -      +
    543B  ALA*     1.3    84.1    -      -       +      +
    545B  ALA*     1.3    61.8    +      -       -      +
    563B  VAL*     3.7     0.5    -      -       -      -
    564B  THR*     2.7    53.0    +      -       +      +
    602B  LEU*     3.7    19.8    -      -       +      +
    604B  LYS*     3.2    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 545 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533B  GLU*     3.4    21.1    -      -       -      +
    536B  LEU*     3.7    40.2    -      -       +      -
    537B  VAL*     3.8    11.0    -      -       +      +
    542B  ILE*     4.6     2.0    -      -       +      -
    544B  GLU*     1.3    79.4    -      -       -      +
    546B  ALA*     1.3    61.9    +      -       -      +
    562B  TYR      3.0    13.0    -      -       -      +
    563B  VAL*     4.5     4.0    -      -       +      -
    602B  LEU*     4.2     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 546 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533B  GLU*     3.3     9.4    -      -       -      +
    545B  ALA*     1.3    75.0    -      -       -      +
    547B  VAL*     1.3    62.1    +      -       -      +
    548B  VAL*     5.7     0.7    -      -       +      -
    561B  ALA*     3.5     0.5    -      -       -      -
    562B  TYR*     2.7    46.8    +      -       -      +
    602B  LEU*     4.4    12.0    -      -       +      +
    610B  ILE*     4.7    14.1    -      -       +      -
    612B  ARG*     5.6     5.2    -      -       +      -
    615B  LEU*     3.7    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 547 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520B  LEU*     4.3     2.9    -      -       +      -
    529B  THR*     3.5    32.9    -      -       +      +
    532B  ILE*     3.6    36.1    -      -       +      -
    533B  GLU*     3.0    26.7    +      -       +      +
    536B  LEU*     3.8    16.2    -      -       +      -
    546B  ALA*     1.3    75.6    -      -       -      +
    548B  VAL*     1.3    76.5    +      -       -      +
    559B  ILE*     3.8    26.0    -      -       +      -
    560B  TYR      3.5     4.3    -      -       -      +
    561B  ALA*     3.9     7.2    -      -       +      -
    612B  ARG*     5.0     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 548 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520B  LEU*     4.0     7.8    -      -       -      +
    529B  THR*     4.6     4.0    -      -       -      -
    546B  ALA*     5.2     0.9    -      -       +      -
    547B  VAL*     1.3    83.0    -      -       -      +
    549B  GLY*     1.3    70.2    +      -       -      +
    558B  ALA      3.7     0.9    -      -       -      +
    559B  ILE*     4.0     2.6    -      -       -      -
    560B  TYR*     2.9    40.2    +      -       +      +
    562B  TYR*     4.4     6.5    -      -       +      -
    612B  ARG*     4.4    15.5    -      -       +      +
    615B  LEU*     3.9    20.4    -      -       +      +
    616B  ARG*     3.9    42.4    -      -       +      +
    619B  ALA*     4.0    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 549 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520B  LEU*     3.6    25.8    -      -       -      +
    548B  VAL*     1.3    83.5    -      -       -      +
    550B  ILE*     1.3    66.1    +      -       -      +
    551B  PRO*     4.9     0.5    -      -       -      +
    557B  GLN*     3.9    15.5    +      -       -      -
    558B  ALA      3.5     7.6    -      -       -      -
    616B  ARG*     4.2    15.3    -      -       -      +
    620B  ALA*     5.6     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 550 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549B  GLY*     1.3    79.7    -      -       -      +
    551B  PRO*     1.3    81.7    -      -       +      +
    557B  GLN*     3.0     8.6    -      -       -      -
    558B  ALA*     2.7    55.9    +      -       +      +
    560B  TYR*     4.0    23.8    -      -       +      -
    594B  ASP*     6.5     0.2    -      -       +      -
    595B  VAL*     5.3     7.4    -      -       +      -
    619B  ALA*     3.7    45.3    -      -       +      +
    620B  ALA*     3.9     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 551 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549B  GLY      4.9     0.4    -      -       -      +
    550B  ILE*     1.3   101.2    -      -       +      +
    552B  HIS*     1.3    59.8    +      -       -      +
    556B  GLY      3.5     9.4    -      -       -      +
    557B  GLN*     5.3     1.1    -      -       +      -
    620B  ALA*     4.6    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 552 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362B  ARG*     5.1     0.2    +      -       -      -
    550B  ILE      3.4     0.2    +      -       -      -
    551B  PRO*     1.3    75.6    +      -       -      +
    553B  ALA*     1.3    64.5    +      -       -      +
    554B  ILE*     3.1    27.1    +      -       -      +
    555B  LYS*     3.1    50.5    -      -       +      +
    556B  GLY*     3.0    27.2    +      -       -      +
    557B  GLN      3.9    22.0    -      -       -      +
    558B  ALA*     3.9    15.0    -      -       +      +
    594B  ASP*     5.2     3.1    +      -       -      -
----------------------------------------------------------
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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