Contacts of the strand formed by residues 310 - 314 (chain B) in PDB entry 4OE5


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 ARG 310 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200B  LEU*     3.7    20.6    -      -       +      +
    280B  CYS      3.0    13.0    +      -       -      +
    281B  GLY*     3.1     2.4    -      -       -      -
    282B  ILE      2.9    26.2    +      -       -      +
    308B  PHE      4.0     9.4    +      -       -      +
    309B  PRO*     1.3    75.6    -      -       -      +
    311B  LEU*     1.3    61.7    +      -       -      +
    312B  ALA      4.2     0.2    -      -       -      -
    539B  LEU      4.3     0.2    +      -       -      -
    540B  ARG*     2.8    48.8    +      -       +      +
    541B  TRP*     4.3     9.6    -      -       +      -
    542B  THR      3.0    20.0    +      -       -      -
    543B  SER*     3.6    27.3    +      -       -      +
    544B  PRO*     5.5     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  TRP*     4.0    20.6    -      -       +      -
    282B  ILE*     3.8    34.5    -      -       +      -
    291B  PHE*     4.1    19.2    -      -       +      -
    294B  LEU*     6.1     0.2    -      -       +      -
    295B  TRP*     3.9    45.3    -      -       +      +
    298B  VAL*     4.0    13.0    -      -       +      -
    309B  PRO*     3.9    12.5    +      -       +      +
    310B  ARG*     1.3    82.2    -      -       -      +
    312B  ALA*     1.3    53.0    +      -       -      +
    313B  GLY      4.2     0.8    +      -       -      -
    540B  ARG*     2.4    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282B  ILE      2.9    14.2    +      -       -      +
    283B  ASN*     3.4    21.8    -      -       -      +
    284B  PHE*     2.7    36.4    +      -       -      +
    291B  PHE*     3.8     2.8    -      -       -      -
    311B  LEU*     1.3    71.2    -      -       -      +
    313B  GLY*     1.3    56.1    +      -       -      +
    535B  PRO*     3.5    13.7    -      -       -      +
    536B  HIS*     5.1     2.2    -      -       +      -
    540B  ARG*     3.2    17.5    -      -       -      +
    541B  TRP*     3.8    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308A  PHE*     5.4     4.2    -      -       -      -
    284B  PHE*     3.5     4.0    -      -       -      -
    291B  PHE*     3.5    34.3    -      -       -      -
    311B  LEU      4.3     0.4    +      -       -      -
    312B  ALA*     1.3    74.3    -      -       -      +
    314B  GLU*     1.3    60.9    +      -       -      -
    315B  CYS*     3.9     7.2    +      -       -      -
    535B  PRO*     3.9    23.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  LEU*     5.5     2.0    -      -       +      +
    284B  PHE      3.0     9.9    +      -       -      +
    285B  THR*     3.3    32.5    +      -       +      +
    286B  GLY      3.1    24.4    +      -       -      +
    313B  GLY*     1.3    72.9    -      -       -      -
    315B  CYS*     1.3    59.3    +      -       -      +
    348B  CYS*     5.3    12.8    -      -       -      +
    478B  LEU*     5.3    16.2    -      -       +      +
    529B  ASN*     4.5    22.6    -      -       +      +
    535B  PRO*     5.5     3.6    -      -       +      -
----------------------------------------------------------
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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