Contacts of the strand formed by residues 240 - 245 (chain R) 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 HIS 240 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234R  TRP*     3.6     7.9    -      -       -      -
    235R  ILE*     2.8    55.9    +      -       +      +
    238R  GLY      3.5     0.4    -      -       -      -
    239R  SER*     1.3   104.9    +      -       -      +
    241R  LEU*     1.3    56.3    +      -       -      +
    242R  ALA      4.2     0.2    -      -       -      -
    252R  ILE*     3.9    20.9    -      -       +      +
    253R  TYR      3.1    16.2    +      -       -      +
    254R  ASP*     3.5    34.2    +      -       +      -
    255R  VAL*     4.6     0.7    -      -       -      -
    261R  ILE*     4.3    14.0    -      -       +      +
    276R  TRP*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 241 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202R  ALA*     3.9    25.8    -      -       +      -
    209R  ILE*     4.0    22.2    -      -       +      -
    211R  LEU*     4.3     7.2    -      -       +      -
    222R  LEU*     5.1     4.5    -      -       +      -
    232R  LEU*     4.1     8.5    -      -       +      -
    233R  SER      3.7    32.1    -      -       -      +
    234R  TRP*     3.8    20.0    -      -       +      +
    240R  HIS*     1.3    73.5    -      -       -      +
    242R  ALA*     1.3    65.4    +      -       -      +
    243R  VAL*     3.9    13.3    +      -       +      +
    251R  GLU      3.8     0.7    -      -       -      +
    252R  ILE*     3.5     3.7    -      -       -      -
    253R  TYR*     2.8    42.0    +      -       +      +
    255R  VAL*     4.2    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 242 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232R  LEU*     3.2     7.3    -      -       -      +
    233R  SER*     3.0    38.8    +      -       -      +
    240R  HIS      4.2     0.8    +      -       -      -
    241R  LEU*     1.3    71.7    -      -       -      +
    243R  VAL*     1.3    64.0    +      -       -      +
    250R  VAL*     5.2     0.4    -      -       +      -
    251R  GLU      3.5     5.8    -      -       -      +
    252R  ILE*     4.5     3.1    -      -       +      +
    274R  LEU*     4.0    10.8    -      -       +      -
    276R  TRP*     3.7    25.6    -      -       +      +
    281R  LEU*     3.9    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 243 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209R  ILE*     3.4    22.7    -      -       +      -
    223R  CYS*     5.2     0.2    -      -       -      -
    229R  TYR*     3.1    42.8    -      -       +      -
    231R  SER      3.5     7.0    -      -       -      +
    232R  LEU*     4.8     2.2    -      -       +      -
    241R  LEU*     4.0    22.2    -      -       +      +
    242R  ALA*     1.3    81.6    -      -       -      +
    244R  GLY*     1.3    63.3    +      -       -      +
    249R  LEU      3.9     0.2    -      -       -      +
    250R  VAL*     3.3     3.4    -      -       -      +
    251R  GLU*     2.8    46.8    +      -       +      +
    253R  TYR*     4.1    19.5    -      -       +      -
    274R  LEU*     4.2     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 244 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229R  TYR*     3.6     5.2    -      -       -      -
    230R  THR*     3.0    23.8    +      -       -      -
    231R  SER*     3.0    26.7    +      -       -      +
    243R  VAL*     1.3    74.0    -      -       -      +
    245R  GLN*     1.3    66.8    +      -       -      +
    249R  LEU      3.3     7.4    -      -       -      -
    250R  VAL*     4.3     2.7    -      -       -      -
    271R  VAL*     4.3    11.0    -      -       -      -
    274R  LEU*     3.9     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 245 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225R  THR*     2.8    26.7    +      -       -      +
    227R  ASN*     3.6    10.1    -      -       -      +
    228R  GLU      3.3    10.3    -      -       -      +
    229R  TYR*     3.8    19.7    -      -       +      -
    230R  THR*     3.7     6.3    -      -       -      -
    243R  VAL*     5.1     0.4    -      -       +      -
    244R  GLY*     1.3    79.5    -      -       -      +
    246R  ALA*     1.3    66.4    +      -       -      +
    247R  ASN*     3.1    22.5    +      -       -      +
    248R  GLY*     3.0    12.1    +      -       -      -
    249R  LEU*     2.9    24.8    +      -       -      +
    251R  GLU*     3.3    40.0    +      -       -      +
    271R  VAL*     3.2    15.6    +      -       -      +
----------------------------------------------------------
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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