Contacts of the strand formed by residues 309 - 314 (chain B) in PDB entry 4U7C


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 ALA 309 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  ILE*     4.0    22.4    -      -       +      -
    107B  ASP      3.7     9.4    -      -       -      +
    108B  MET*     3.8    21.8    -      -       -      -
    109B  ASP*     3.4     7.4    -      -       -      +
    298B  ARG*     3.0    32.3    +      -       +      +
    301B  ILE*     4.4    12.9    -      -       +      +
    307B  LEU      4.1     0.6    +      -       -      -
    308B  THR*     1.3    74.1    -      -       -      +
    310B  SER*     1.3    61.0    +      -       -      +
    330B  ASN*     3.6     9.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  ILE*     3.4     4.7    -      -       -      +
    107B  ASP*     2.9    32.1    +      -       -      +
    109B  ASP*     3.1    10.8    +      -       -      -
    309B  ALA*     1.3    75.3    -      -       -      +
    311B  ALA*     1.3    61.5    +      -       -      +
    324B  SER*     3.4    22.0    -      -       -      -
    327B  ASN      3.3    11.3    +      -       -      -
    328B  LYS*     3.4    16.5    -      -       -      -
    330B  ASN      3.1    22.3    +      -       -      -
    331B  GLY      3.2     9.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  VAL*     4.5     7.9    -      -       +      -
    105B  HIS      3.1    10.8    -      -       -      +
    106B  ILE*     4.3    10.8    -      -       +      -
    294B  VAL*     3.6    30.3    -      -       +      -
    298B  ARG*     4.1     8.3    -      -       -      -
    310B  SER*     1.3    76.9    -      -       -      +
    312B  GLY*     1.3    59.6    +      -       -      +
    323B  CYS      4.4     0.5    -      -       -      +
    324B  SER*     3.4    13.6    +      -       -      -
    327B  ASN*     5.8     0.2    -      -       -      +
    331B  GLY      3.1     7.5    +      -       -      +
    332B  GLN*     3.3    23.3    -      -       +      -
    333B  TYR      3.4     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  ILE      3.5     1.0    -      -       -      +
    104B  VAL*     3.1     7.6    -      -       -      +
    105B  HIS      2.9    31.7    +      -       -      -
    311B  ALA*     1.3    74.5    -      -       -      +
    313B  ILE*     1.3    64.5    +      -       -      +
    320B  ALA*     3.6    10.7    -      -       -      +
    323B  CYS*     3.6     3.1    -      -       -      -
    324B  SER*     3.5    20.4    -      -       -      -
    333B  TYR      3.6     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  THR*     3.8    26.5    -      -       +      -
    103B  ILE      3.4     3.8    -      -       -      +
    104B  VAL*     4.4     5.8    -      -       +      -
    290B  ALA*     4.2     8.7    -      -       +      -
    291B  GLN*     3.9    23.8    -      -       -      +
    294B  VAL*     3.6    36.8    -      -       +      -
    311B  ALA      5.1     0.2    -      -       -      -
    312B  GLY*     1.3    78.0    -      -       -      +
    314B  ALA*     1.3    60.2    +      -       -      +
    323B  CYS*     4.0     2.4    -      -       -      +
    332B  GLN*     4.1     9.4    -      -       +      +
    333B  TYR      2.8    15.8    +      -       -      +
    334B  GLN*     3.1    28.7    -      -       +      +
    335B  ILE      2.6    33.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  ASN      4.6     0.4    -      -       -      -
    102B  THR*     5.0     1.6    -      -       -      -
    103B  ILE*     2.9    32.9    +      -       -      +
    312B  GLY      4.2     0.2    -      -       -      -
    313B  ILE*     1.3    78.8    -      -       -      +
    315B  PRO*     1.3    76.2    -      -       +      +
    316B  ASN      3.2     1.5    +      -       -      -
    319B  LEU*     3.5    14.1    -      -       +      -
    320B  ALA*     3.4    28.9    -      -       -      +
    323B  CYS*     4.2     2.2    -      -       -      -
    335B  ILE*     3.8    12.1    -      -       +      -
----------------------------------------------------------
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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