Contacts of the strand formed by residues 556 - 565 (chain B) in PDB entry 1PG4


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 556 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362B  ARG*     3.5    16.5    -      -       -      +
    388B  GLU*     4.3     4.3    -      -       -      -
    521B  ASN      4.3     1.8    -      -       -      -
    551B  PRO*     3.7     5.7    -      -       -      +
    552B  HIS      3.0    30.3    +      -       -      +
    554B  ILE      3.3     3.4    +      -       -      -
    555B  LYS*     1.3    75.2    -      -       -      +
    557B  GLN*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 557 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    519B  VAL      4.6     1.4    -      -       -      +
    520B  LEU*     3.5    14.3    -      -       +      +
    521B  ASN*     2.9    45.3    +      -       +      +
    522B  VAL*     3.5    26.9    -      -       +      +
    549B  GLY*     3.7    28.1    +      -       -      -
    550B  ILE*     3.1    11.6    -      -       -      +
    551B  PRO*     5.2     0.4    -      -       +      -
    552B  HIS*     4.1     3.8    -      -       -      -
    555B  LYS*     2.9    11.8    +      -       -      +
    556B  GLY*     1.3    80.4    -      -       -      +
    558B  ALA*     1.3    62.7    +      -       -      +
    616B  ARG*     5.8     4.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 558 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    522B  VAL*     5.1     0.4    -      -       -      -
    549B  GLY*     3.4     6.6    -      -       -      -
    550B  ILE*     2.8    50.3    +      -       +      +
    552B  HIS*     4.0    24.8    -      -       +      +
    555B  LYS*     4.8     2.2    -      -       +      -
    557B  GLN*     1.3    74.9    -      -       -      +
    559B  ILE*     1.3    64.8    +      -       -      +
    594B  ASP*     3.3    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 559 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520B  LEU*     4.4     5.8    -      -       +      -
    522B  VAL*     3.7    27.8    -      -       +      -
    527B  LEU*     4.1     0.9    -      -       +      -
    532B  ILE*     4.1    13.5    -      -       +      -
    547B  VAL*     3.8    25.1    -      -       +      -
    548B  VAL      4.0     2.5    -      -       -      -
    549B  GLY*     5.0     0.4    -      -       -      -
    550B  ILE*     5.5     0.2    -      -       -      -
    558B  ALA*     1.3    70.1    -      -       -      +
    560B  TYR*     1.3    62.1    +      -       -      +
    561B  ALA*     5.1     0.2    -      -       +      -
    590B  LEU      3.8     9.0    -      -       -      +
    591B  ALA*     3.4    36.8    -      -       -      +
    592B  THR      3.7     6.1    -      -       -      +
    593B  PRO*     3.7    27.1    -      -       +      +
    594B  ASP*     2.8    39.2    +      -       -      +
    595B  VAL*     3.1     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 560 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546B  ALA      3.9     0.5    -      -       -      +
    547B  VAL*     3.6     1.6    -      -       -      -
    548B  VAL*     2.9    42.1    +      -       +      +
    550B  ILE*     3.8    31.2    -      -       +      -
    558B  ALA      3.5     0.6    +      -       -      -
    559B  ILE*     1.3    73.5    -      -       -      +
    561B  ALA*     1.3    61.1    +      -       -      +
    562B  TYR*     3.5    35.1    +      +       -      -
    595B  VAL*     3.5    30.9    -      -       +      +
    597B  HIS*     2.9    41.1    +      -       +      +
    619B  ALA*     3.8    16.4    -      -       +      -
    645B  LYS*     3.3    34.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 561 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536B  LEU*     3.9    27.8    -      -       +      -
    546B  ALA      3.7     3.4    -      -       -      +
    547B  VAL*     4.0     9.6    -      -       +      -
    559B  ILE*     4.1     0.8    -      -       +      -
    560B  TYR*     1.3    75.6    -      -       -      +
    562B  TYR*     1.3    63.6    +      -       -      +
    563B  VAL*     3.6     3.5    +      -       +      +
    593B  PRO*     4.2     9.4    -      -       +      -
    595B  VAL      2.9    15.1    +      -       -      +
    596B  LEU*     3.5    16.3    -      -       +      -
    597B  HIS      2.9    25.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 562 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545B  ALA*     3.2     6.1    -      -       -      +
    546B  ALA*     2.9    44.6    +      -       +      +
    548B  VAL*     4.0     7.6    -      -       +      -
    560B  TYR*     3.5    24.1    -      +       -      -
    561B  ALA*     1.3    71.1    -      -       -      +
    563B  VAL*     1.3    59.7    +      -       -      +
    597B  HIS*     3.3    42.2    -      +       -      -
    599B  THR*     4.1     4.7    -      -       +      -
    602B  LEU*     3.7    19.8    -      -       +      +
    615B  LEU*     2.6    67.6    +      -       +      -
    618B  ILE*     3.8     8.3    -      -       +      +
    619B  ALA*     3.4    15.2    +      -       -      +
    641B  LEU*     4.2    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 563 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536B  LEU*     4.5    15.0    -      -       +      -
    542B  ILE*     3.7    39.5    -      -       +      -
    544B  GLU      3.7     1.6    -      -       -      -
    545B  ALA*     4.6     1.6    -      -       +      -
    561B  ALA*     3.8    20.6    -      -       +      +
    562B  TYR*     1.3    79.7    -      -       -      +
    564B  THR*     1.3    68.7    +      -       -      +
    565B  LEU*     3.9     2.9    +      -       +      +
    579B  VAL*     5.0     0.4    -      -       +      -
    596B  LEU*     4.3    14.8    -      -       +      -
    597B  HIS      2.9    11.0    +      -       -      +
    598B  TRP*     3.4    31.4    -      -       +      +
    599B  THR*     3.0    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 564 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542B  ILE*     3.8     3.1    -      -       -      +
    543B  ALA*     2.9    33.1    +      -       +      -
    544B  GLU*     2.9    27.2    +      -       +      +
    563B  VAL*     1.3    72.5    -      -       -      +
    565B  LEU*     1.3    65.8    +      -       -      +
    599B  THR      2.9    15.1    +      -       -      +
    600B  ASP*     3.4    27.7    -      -       +      +
    602B  LEU*     3.6    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 565 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541B  LYS*     3.5    16.4    -      -       +      +
    542B  ILE*     4.1    16.6    -      -       +      -
    543B  ALA*     4.4     2.5    -      -       -      +
    563B  VAL*     3.9     2.8    +      -       +      +
    564B  THR*     1.3    83.5    -      -       -      +
    566B  ASN*     1.3    70.2    +      -       -      +
    567B  HIS*     3.8     6.1    +      -       -      -
    569B  GLU*     3.8    15.5    -      -       +      +
    571B  PRO*     3.8    20.2    -      -       +      -
    575B  LEU*     3.5    32.3    -      -       +      -
    598B  TRP*     3.6    39.3    -      -       +      -
    599B  THR      4.5     0.6    +      -       -      -
    600B  ASP*     4.3     6.8    +      -       -      +
----------------------------------------------------------
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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