Contacts of the strand formed by residues 131 - 136 (chain 4) in PDB entry 1O18


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 131 (chain 4).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1024  PRO*     3.2    12.6    -      -       +      +
    1034  THR      2.9    21.8    +      -       -      -
    1244  PHE*     3.8     3.4    -      -       -      -
    1294  VAL*     3.4     6.0    -      -       -      +
    1304  PRO*     1.3    83.1    -      -       +      +
    1324  MET*     1.3    64.2    +      -       -      +
    3564  TRP*     4.0    22.4    -      -       +      -
    3574  ILE      3.0    20.9    -      -       -      +
    3584  THR*     3.9     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 132 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1034  THR*     3.2    18.6    -      -       -      +
    1054  LEU*     3.7    15.9    -      -       +      -
    1194  MET      4.0     0.4    -      -       -      +
    1204  THR*     3.8    29.6    -      -       -      +
    1234  MET*     3.6    36.1    -      -       +      -
    1244  PHE*     3.4    33.0    -      -       +      -
    1294  VAL*     4.2     6.7    -      -       +      -
    1314  ALA*     1.3    75.8    -      -       -      +
    1334  TYR*     1.3    65.2    +      -       -      +
    1344  VAL*     4.1     9.9    -      -       +      -
    3564  TRP*     3.4     6.3    -      -       -      -
    3574  ILE*     2.8    30.6    +      -       -      +
    3704  VAL*     4.3    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 133 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1034  THR      3.3     2.5    +      -       -      +
    1044  LEU*     3.5    15.7    -      -       +      +
    1054  LEU*     2.8    28.2    +      -       -      +
    1324  MET*     1.3    81.0    -      -       -      +
    1344  VAL*     1.3    74.7    +      -       -      +
    1354  ALA*     4.2    12.8    -      -       +      -
    3464  LEU*     4.5     4.7    -      -       +      +
    3524  PHE*     3.3    32.5    -      +       +      -
    3554  MET*     3.5    41.6    -      -       +      +
    3564  TRP*     3.9    16.6    -      -       +      -
    3574  ILE*     5.1     2.9    -      -       +      -
    3704  VAL*     4.7     4.5    -      -       +      -
    3724  ARG*     2.9    43.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1054  LEU*     3.4     5.2    -      -       +      -
    1064  THR      4.4     2.5    -      -       -      -
    1074  GLU*     3.6    48.2    -      -       +      +
    1164  ARG*     3.2    43.6    +      -       +      +
    1194  MET*     4.3    19.3    -      -       +      -
    1204  THR*     4.5     5.8    -      -       -      +
    1324  MET*     4.1    20.6    -      -       +      -
    1334  TYR*     1.3    87.3    -      -       -      +
    1354  ALA*     1.3    55.7    +      -       -      +
    3704  VAL*     4.6     9.0    -      -       +      +
    3724  ARG*     4.5     3.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1044  LEU*     4.2     7.4    -      -       +      -
    1054  LEU      2.9    11.1    +      -       -      +
    1064  THR*     3.3     4.3    -      -       -      -
    1074  GLU*     3.0    23.4    +      -       -      +
    1334  TYR*     4.0    17.1    -      -       +      -
    1344  VAL*     1.3    73.6    -      -       -      +
    1364  ILE*     1.3    62.7    +      -       -      +
    1394  VAL*     6.1     1.6    -      -       +      -
    1404  LEU*     3.6    37.5    -      -       +      -
    3464  LEU*     4.7     1.3    -      -       +      -
    3724  ARG*     5.9     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 136 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1074  GLU*     3.7    26.2    -      -       +      +
    1084  ALA      4.6     2.2    -      -       -      +
    1094  PRO*     4.2    32.1    -      -       +      +
    1164  ARG*     4.0    14.8    -      -       -      +
    1344  VAL      4.3     0.2    +      -       -      -
    1354  ALA*     1.3    71.9    -      -       -      +
    1374  GLN*     1.3    69.0    +      -       -      +
    1384  ALA*     4.2     7.9    -      -       +      +
    1394  VAL*     3.2    38.9    +      -       +      +
    1404  LEU*     3.2    11.0    +      -       -      +
    1634  VAL*     5.1     1.3    -      -       +      -
    1704  ALA*     4.8    15.0    -      -       +      -
    1754  ILE*     6.5     0.2    -      -       +      -
----------------------------------------------------------
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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