Contacts of the strand formed by residues 319 - 325 (chain B) in PDB entry 3OOT


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 319 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181B  TYR*     3.3    59.7    -      -       +      +
    182B  ILE      3.4    16.8    -      -       -      +
    183B  ASN*     3.6    18.3    -      -       -      +
    184B  LEU*     4.1     3.3    -      -       -      +
    190B  TRP*     3.8     2.8    -      -       -      -
    314B  ASP*     3.0    60.3    +      -       -      +
    317B  ASN*     3.5    32.5    +      -       +      +
    318B  ASN*     1.3    72.9    -      -       -      +
    320B  ILE*     1.3    67.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  HIS      4.0     1.0    -      -       -      +
    181B  TYR*     3.3     3.5    -      -       -      -
    182B  ILE*     2.8    38.3    +      -       +      +
    184B  LEU*     3.7    22.2    -      -       +      -
    190B  TRP*     3.7    27.8    -      -       +      -
    192B  ILE*     4.0    11.2    -      -       +      -
    214B  VAL*     3.8    27.8    -      -       +      -
    311B  THR*     3.7    19.7    -      -       +      -
    312B  GLU      3.4     4.0    -      -       -      +
    313B  PHE*     4.0     7.9    -      -       +      -
    319B  ARG*     1.3    76.0    -      -       -      +
    321B  GLY*     1.3    60.3    -      -       -      +
    322B  PHE*     3.6    32.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 321 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  PHE*     3.7     9.3    -      -       -      -
    180B  HIS      3.5     4.5    -      -       -      -
    181B  TYR*     3.4    28.3    -      -       -      -
    310B  TYR      3.7     0.5    -      -       -      +
    311B  THR*     3.4     5.7    -      -       -      +
    312B  GLU*     2.8    41.0    +      -       -      -
    320B  ILE*     1.3    73.2    -      -       -      +
    322B  PHE*     1.3    63.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  ASN      4.0     1.6    -      -       -      +
    179B  PHE*     3.4     5.4    -      -       -      -
    180B  HIS*     3.0    29.0    +      -       -      +
    182B  ILE*     3.6    32.1    -      -       +      -
    192B  ILE*     4.3     5.4    -      -       +      -
    214B  VAL*     4.0    20.9    -      -       +      -
    262B  LEU*     4.1    13.9    -      -       +      -
    267B  TYR*     3.7    33.0    +      +       +      +
    301B  LEU*     4.7     1.8    -      -       +      -
    305B  PHE*     3.6    28.9    -      +       -      -
    309B  PHE*     4.1     9.2    -      -       +      -
    310B  TYR      3.5     1.6    -      -       -      -
    311B  THR*     3.4    35.9    -      -       +      -
    320B  ILE*     3.6    17.9    -      -       +      -
    321B  GLY*     1.3    77.4    -      -       -      -
    323B  ALA*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  TYR*     3.9    26.0    -      -       +      -
    176B  GLU      4.1     6.5    -      -       -      +
    178B  ASN      4.2    12.1    -      -       -      +
    179B  PHE*     3.7    22.2    -      -       +      -
    267B  TYR*     6.0     0.2    -      -       -      -
    309B  PHE*     3.3     8.8    -      -       -      -
    310B  TYR*     2.7    36.7    +      -       -      +
    322B  PHE*     1.3    74.4    -      -       -      +
    324B  LEU*     1.3    60.3    +      -       -      +
    325B  ALA      3.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  TYR*     3.2     4.2    -      -       -      -
    176B  GLU*     2.9    67.3    +      -       +      +
    308B  LYS*     3.7    34.1    -      -       +      +
    309B  PHE*     3.9    22.2    -      -       +      -
    323B  ALA*     1.3    68.8    -      -       -      +
    325B  ALA*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  TYR*     4.4    13.0    -      -       +      -
    157B  ARG*     4.4    11.8    +      -       -      +
    174B  HIS      3.3    11.4    -      -       -      +
    175B  TYR*     4.3     0.2    -      -       -      +
    176B  GLU*     4.5     4.2    -      -       -      +
    306B  ILE      4.7     1.1    -      -       -      +
    307B  ARG      3.6    17.9    -      -       -      +
    308B  LYS      2.9    21.3    +      -       -      +
    309B  PHE      4.4     0.4    -      -       -      -
    310B  TYR*     3.7    17.5    -      -       +      +
    323B  ALA      3.2     2.7    +      -       -      -
    324B  LEU*     1.3    80.1    -      -       -      +
    326B  ARG*     1.4    62.7    +      -       -      +
----------------------------------------------------------
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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