Contacts of the strand formed by residues 263 - 267 (chain B) in PDB entry 4M83


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 HIS 263 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  TRP*     4.9     4.7    -      +       -      -
    227B  PRO*     4.7    22.8    -      -       +      +
    230B  ALA*     4.4    15.0    -      -       +      +
    232B  LYS      2.8    11.4    +      -       -      +
    233B  VAL*     3.2    10.6    -      -       +      +
    234B  VAL*     3.0    26.6    +      -       -      +
    256B  PHE*     5.8     0.7    -      -       -      -
    261B  GLY      4.6     0.2    -      -       -      +
    262B  TRP*     1.3    76.5    -      -       -      +
    264B  LEU*     1.3    76.5    +      -       -      +
    265B  VAL*     4.0     7.3    -      -       +      +
    282B  ASP      4.6     3.7    +      -       -      -
    283B  ASN*     3.3    35.0    +      -       +      +
    284B  VAL      4.3     0.4    +      -       -      -
    285B  GLU*     2.9    37.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  VAL*     3.6    26.0    -      -       +      +
    236B  VAL*     3.6    28.3    -      -       +      -
    252B  CYS      3.6    22.2    -      -       -      +
    253B  VAL*     4.1     5.4    -      -       -      -
    256B  PHE*     4.0    15.5    -      -       +      -
    263B  HIS*     1.3    81.3    -      -       -      +
    265B  VAL*     1.3    74.2    -      -       -      +
    266B  LEU*     3.8    17.7    -      -       +      -
    283B  ASN*     2.8     7.5    +      -       -      +
    284B  VAL*     3.6    36.4    -      -       +      -
    285B  GLU      3.2    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  TRP*     3.6    33.0    -      -       +      -
    233B  VAL*     4.4     6.5    -      -       +      -
    234B  VAL      2.8    15.8    +      -       -      +
    235B  LEU*     3.5    22.3    -      -       +      +
    236B  VAL      2.9    27.5    +      -       -      -
    263B  HIS*     4.0     4.7    -      -       -      +
    264B  LEU*     1.3    81.2    -      -       -      +
    266B  LEU*     1.3    62.7    +      -       -      +
    285B  GLU*     3.5    11.2    -      -       +      +
    287B  HIS*     3.8    26.9    -      -       +      +
    290B  VAL*     5.1     2.0    -      -       +      -
    295B  ILE*     4.0    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  VAL*     3.7    30.1    -      -       +      -
    249B  TYR*     4.3    10.3    -      -       +      +
    252B  CYS*     3.8    20.9    -      -       +      -
    253B  VAL*     3.4    32.5    -      -       +      -
    264B  LEU*     3.8    14.8    -      -       +      -
    265B  VAL*     1.3    74.1    -      -       -      +
    267B  GLN*     1.3    59.2    +      -       -      +
    268B  ILE*     3.8     7.4    -      -       +      -
    277B  LEU*     3.8     9.0    -      -       +      -
    284B  VAL*     4.2     4.3    -      -       +      -
    285B  GLU      2.9     8.7    +      -       -      -
    286B  VAL*     3.5    31.1    -      -       +      +
    287B  HIS*     2.9    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 267 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235B  LEU*     4.7     2.5    -      -       +      -
    236B  VAL*     2.9    23.7    +      -       -      +
    237B  SER*     2.9    25.0    +      -       -      +
    238B  LEU*     3.9     2.4    -      -       -      +
    239B  GLY      2.4    33.5    +      -       -      +
    240B  SER*     5.7     0.2    -      -       -      -
    243B  THR*     5.3     1.6    +      -       -      -
    249B  TYR*     3.7    13.1    +      -       -      -
    266B  LEU*     1.3    73.2    -      -       -      +
    268B  ILE*     1.3    59.4    +      -       -      +
    269B  GLY*     2.8    21.8    +      -       -      -
    287B  HIS      3.7     3.1    -      -       -      -
    288B  ASP      3.0     8.3    -      -       -      +
    290B  VAL*     3.5    20.4    -      -       +      -
    502B  UDP      2.9    29.3    -      -       +      +
----------------------------------------------------------
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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