Contacts of the strand formed by residues 93 - 99 (chain L) in PDB entry 5A31


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 LYS 93 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92L  SER*     1.3    79.3    -      -       -      +
     94L  ILE*     1.3    64.6    +      -       -      +
     95L  SER      3.5     0.2    +      -       -      -
    110L  GLN*     4.6    22.2    -      -       -      +
    111L  LEU      3.6     4.3    -      -       -      +
    112L  GLU*     3.4    17.7    -      -       +      +
    142L  LEU*     3.1    43.9    +      -       +      +
    143L  ALA*     3.3    27.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 94 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77L  LEU*     6.3     0.4    -      -       +      -
     79L  ILE*     3.9    33.0    -      -       +      -
     91L  PRO*     3.9    20.4    -      -       +      -
     92L  SER      3.7     0.4    -      -       -      -
     93L  LYS*     1.3    77.6    -      -       -      +
     95L  SER*     1.3    60.5    +      -       -      +
     96L  VAL*     4.3    15.0    -      -       +      -
    110L  GLN*     3.4     4.2    -      -       -      +
    111L  LEU*     2.8    52.1    +      -       +      +
    113L  LEU*     3.6    27.3    -      -       +      +
    122L  VAL*     6.0     2.7    -      -       +      -
    139L  ILE*     4.3    17.5    -      -       +      -
    140L  ALA      3.3     9.4    -      -       -      +
    141L  VAL*     4.2    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 95 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93L  LYS      3.5     0.2    +      -       -      -
     94L  ILE*     1.3    75.3    -      -       -      +
     96L  VAL*     1.3    63.8    +      -       -      +
     97L  ARG*     3.2    19.9    +      -       -      +
    107L  GLU*     2.8    32.2    +      -       -      +
    110L  GLN*     3.9     8.1    -      -       -      -
    138L  GLN      3.6     1.7    -      -       -      +
    139L  ILE*     3.6     1.6    -      -       -      -
    140L  ALA*     2.8    35.1    +      -       -      +
    142L  LEU*     4.0    25.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77L  LEU*     4.1    19.3    -      -       +      -
     94L  ILE*     4.3    15.5    -      -       +      -
     95L  SER*     1.3    78.5    +      -       -      +
     97L  ARG*     1.3    64.7    -      -       -      +
     98L  VAL*     4.2     7.4    -      -       +      -
    107L  GLU*     3.5     3.6    -      -       -      +
    108L  ILE*     2.9    46.6    +      -       +      +
    109L  ARG      3.2    19.2    +      -       -      +
    110L  GLN*     5.7     0.4    -      -       -      -
    111L  LEU*     6.2     0.4    -      -       +      -
    122L  VAL*     4.9     9.9    -      -       +      -
    124L  LEU*     4.1    17.3    -      -       +      -
    137L  ILE*     4.2    13.0    -      -       +      -
    138L  GLN      3.5     7.0    -      -       -      +
    139L  ILE*     4.4     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 97 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61L  PRO*     4.9     5.9    -      -       -      +
     63L  LEU*     4.7     3.0    -      -       -      +
     95L  SER*     3.2    18.8    +      -       -      +
     96L  VAL*     1.3    82.2    -      -       -      +
     98L  VAL*     1.3    62.4    -      -       -      +
    105L  LEU*     3.9    19.7    -      -       +      +
    106L  GLN      3.3    15.9    -      -       -      +
    107L  GLU*     4.1    12.3    +      -       +      +
    137L  ILE      3.5     0.3    -      -       -      -
    138L  GLN*     2.7    74.6    +      -       -      +
    140L  ALA*     3.8    14.8    -      -       -      +
    142L  LEU*     3.7    28.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 98 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96L  VAL*     4.2     5.6    -      -       +      -
     97L  ARG*     1.3    81.7    -      -       -      +
     99L  GLY*     1.3    59.0    +      -       -      +
    104L  ASN      4.4     0.2    -      -       -      +
    105L  LEU*     3.8     4.9    -      -       -      -
    106L  GLN*     3.1    26.1    +      -       -      +
    108L  ILE*     3.3    44.9    -      -       +      -
    124L  LEU*     5.8     0.4    -      -       +      -
    132L  THR*     4.0    16.2    -      -       +      +
    134L  THR*     3.7    20.4    -      -       +      +
    136L  MET      3.2    11.2    -      -       -      +
    137L  ILE*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 99 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98L  VAL*     1.3    75.0    -      -       -      +
    100L  ASN*     1.3    71.6    +      -       -      -
    101L  ASN      3.4     2.0    -      -       -      -
    104L  ASN*     3.9    10.3    -      -       -      -
    105L  LEU*     3.4    12.0    -      -       -      +
    134L  THR*     3.0    12.9    +      -       -      -
    135L  PHE      4.0     0.2    +      -       -      -
    136L  MET*     3.2    28.9    +      -       -      +
----------------------------------------------------------
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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