Contacts of the strand formed by residues 316 - 323 (chain A) in PDB entry 4R54


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 316 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  TYR*     3.5    21.1    -      -       -      -
    258A  ILE      3.3     9.2    -      -       -      -
    259A  GLU*     3.8     2.3    -      -       -      +
    309A  LYS*     3.6     5.5    -      -       -      +
    310A  ASP*     2.9    24.6    +      -       -      +
    313A  ALA      3.0    12.2    +      -       -      +
    314A  GLU      3.3     2.3    -      -       -      +
    315A  LYS*     1.3    75.2    -      -       -      +
    317A  ILE*     1.3    69.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  VAL*     5.3     0.2    -      -       +      -
    256A  VAL      3.8     0.5    -      -       -      +
    257A  TYR*     3.4     6.3    -      -       -      -
    258A  ILE*     2.9    43.5    +      -       +      +
    260A  THR*     4.3    15.0    -      -       +      +
    264A  ALA*     3.9    37.0    -      -       +      +
    266A  ILE*     4.1    19.1    -      -       +      -
    269A  VAL*     4.0    13.5    -      -       +      -
    307A  ILE*     4.3     5.8    -      -       +      -
    308A  ARG      3.4    10.3    -      -       -      +
    309A  LYS*     4.8     1.6    -      -       +      -
    310A  ASP      4.3     0.4    -      -       -      +
    315A  LYS      4.4     4.5    -      -       -      +
    316A  GLY*     1.3    80.2    -      -       -      +
    318A  HIS*     1.3    74.7    +      -       -      +
    319A  MET*     4.2    19.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  SER*     5.5     1.8    +      -       -      -
    256A  VAL      3.3     6.4    +      -       -      +
    257A  TYR*     3.3    25.3    -      +       -      +
    306A  ARG      3.3     2.6    -      -       -      +
    307A  ILE*     3.3     0.5    -      -       -      -
    308A  ARG*     2.8    56.4    +      -       -      +
    310A  ASP*     2.9    35.8    +      -       -      -
    317A  ILE*     1.3    80.5    -      -       -      +
    319A  MET*     1.3    66.0    +      -       -      +
    150B  ILE*     4.0    19.4    -      -       +      +
    217B  TYR*     3.4    19.7    -      -       -      -
    240B  SER*     3.6    19.9    -      -       -      -
    241B  ALA      5.2     0.9    -      -       -      -
    242B  THR*     4.2    13.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ALA*     4.4     4.5    -      -       -      -
    137A  LEU*     3.8    30.7    -      -       +      -
    140A  VAL*     4.7     5.8    -      -       +      -
    255A  SER*     3.7     5.7    +      -       -      -
    256A  VAL*     3.0    47.1    +      -       +      +
    258A  ILE*     4.2    10.8    -      -       +      -
    269A  VAL*     4.7     3.1    -      -       +      -
    273A  ILE*     4.4    15.9    -      -       +      -
    304A  VAL*     3.9    18.8    -      -       +      -
    305A  GLY      3.5    12.3    -      -       -      +
    306A  ARG*     3.7     6.3    -      -       -      -
    307A  ILE*     3.8    10.8    -      -       +      -
    308A  ARG*     5.0     1.6    -      -       -      -
    317A  ILE*     4.2    21.8    -      -       +      +
    318A  HIS*     1.3    78.1    -      -       -      +
    320A  TRP*     1.3    62.0    +      -       -      +
    321A  VAL*     4.1    11.4    -      -       +      -
    242B  THR*     5.5     2.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  TYR*     3.7    26.9    -      +       -      -
    253A  SER*     3.3    30.1    -      -       -      -
    254A  GLU      3.4    19.7    -      -       -      -
    255A  SER*     3.9    13.0    -      -       -      -
    291A  PRO*     3.0    43.0    +      -       +      +
    292A  GLN*     5.1     0.2    -      -       -      +
    303A  PHE      3.7     0.5    -      -       -      +
    304A  VAL*     3.3     5.9    -      -       -      +
    305A  GLY      2.8    37.3    +      -       -      +
    306A  ARG*     3.8    14.4    -      -       +      -
    319A  MET*     1.3    72.9    -      -       -      +
    321A  VAL*     1.3    61.2    +      -       -      +
    322A  VAL*     3.6     7.8    -      -       +      +
    205B  ALA*     3.9    18.3    +      -       +      -
    207B  PRO*     3.4    26.6    -      -       +      +
    242B  THR*     4.6     6.3    -      -       +      -
    244B  VAL*     3.7    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  GLN*     3.1    41.3    +      -       +      +
    133A  MET*     5.4     0.7    -      -       -      -
    136A  ALA*     3.8    22.0    -      -       +      -
    137A  LEU*     6.3     0.2    -      -       +      -
    253A  SER*     3.3     1.7    -      -       -      -
    254A  GLU*     2.9    41.4    +      -       -      +
    256A  VAL*     3.9    20.9    -      -       +      -
    302A  THR*     3.7    16.2    -      -       +      -
    303A  PHE      3.3     3.8    -      -       -      +
    304A  VAL*     4.2     2.7    -      -       +      -
    319A  MET*     4.1    13.2    -      -       +      -
    320A  TRP*     1.3    79.6    -      -       -      +
    322A  VAL*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  GLN*     4.0     2.2    -      -       -      -
    251A  ALA*     4.3     2.2    -      -       +      -
    252A  HIS      3.3     9.6    -      -       -      +
    253A  SER*     3.6    17.5    -      -       -      +
    291A  PRO*     3.6    22.7    -      -       +      -
    292A  GLN      3.9     2.0    -      -       -      +
    293A  ALA*     3.7    21.8    -      -       -      +
    296A  ALA*     3.6    24.0    -      -       +      -
    302A  THR*     3.6     1.6    -      -       -      +
    303A  PHE*     2.8    42.4    +      -       +      -
    320A  TRP*     3.6    23.3    -      -       -      +
    321A  VAL*     1.3    80.5    -      -       -      +
    323A  SER*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  GLN*     3.5    25.2    +      -       -      +
    251A  ALA*     4.0     5.2    -      -       -      -
    252A  HIS      3.0    27.9    +      -       -      +
    296A  ALA*     4.5     2.7    -      -       -      -
    299A  SER      4.9     0.5    +      -       -      -
    301A  ASP      3.1    20.1    +      -       -      -
    302A  THR*     3.4    18.4    +      -       -      -
    322A  VAL*     1.3    79.8    -      -       -      +
    324A  ASP*     1.3    65.6    +      -       -      +
    325A  ASN      3.1     0.7    +      -       -      -
    328A  LYS*     3.6    16.7    +      -       -      +
    329A  GLY*     5.5     1.8    -      -       -      -
----------------------------------------------------------
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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