Contacts of the strand formed by residues 62 - 68 (chain A) in PDB entry 3OFN


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 LYS 62 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  LEU*     4.3    20.6    -      -       +      -
     55A  VAL      3.3    11.2    -      -       -      +
     56A  GLU*     3.6    28.1    +      -       -      -
     57A  PHE*     4.6     4.3    -      -       -      -
     60A  GLY      3.8     7.7    +      -       -      +
     61A  VAL*     1.3    84.1    -      -       -      +
     63A  GLY*     1.3    53.8    +      -       -      +
     77A  LEU*     3.6     1.7    -      -       -      +
     78A  PHE*     2.6    56.0    +      -       +      +
     93A  THR*     5.3     6.3    -      -       +      -
    113A  LEU*     5.6     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  LEU*     3.4     6.8    -      -       -      +
     55A  VAL*     2.7    34.5    +      -       -      +
     57A  PHE*     4.2     2.3    -      -       -      -
     62A  LYS*     1.3    74.7    -      -       -      +
     64A  MET*     1.3    62.0    +      -       -      -
     75A  ILE*     3.8    13.9    -      -       -      -
     76A  VAL      3.1    15.0    -      -       -      -
     77A  LEU*     4.1     2.0    -      -       -      -
     78A  PHE*     4.1     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  GLU*     3.3    36.6    -      -       +      +
     53A  GLU      3.6     6.3    -      -       -      +
     54A  LEU*     4.2     2.7    -      -       +      -
     63A  GLY*     1.3    76.9    -      -       -      +
     65A  ALA*     1.3    61.6    +      -       -      +
     66A  LEU*     3.3    26.5    +      -       +      -
     75A  ILE*     3.8     4.0    -      -       -      -
     76A  VAL*     3.0    46.4    +      -       +      +
     78A  PHE*     3.9    14.0    -      -       +      -
     97A  VAL*     3.2    35.2    -      -       +      -
    243A  PRO*     5.7     1.3    -      -       -      -
    246A  TYR*     5.3     6.3    -      -       +      -
    247A  LEU*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ILE*     3.7    25.4    -      -       +      -
     50A  GLN      4.2     7.6    -      -       -      +
     51A  ALA*     4.1     2.0    -      -       -      -
     52A  GLU*     2.7    32.4    +      -       -      -
     53A  GLU      2.9    18.4    +      -       -      +
     55A  VAL*     5.1     0.6    -      -       +      +
     64A  MET*     1.3    68.2    -      -       -      +
     66A  LEU*     1.3    61.2    +      -       -      +
     67A  ILE      3.7     0.7    -      -       -      -
     68A  LEU*     4.5     4.9    -      -       +      -
     73A  VAL*     3.9    17.9    -      -       +      -
     74A  GLY      3.8     6.1    -      -       -      -
     75A  ILE*     3.8     6.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  ALA*     5.7     4.3    -      -       -      +
     52A  GLU*     4.4    12.1    -      -       +      +
     64A  MET*     3.3    38.7    +      -       +      +
     65A  ALA*     1.3    74.7    -      -       -      +
     67A  ILE*     1.3    65.1    +      -       +      +
     68A  LEU*     4.2     2.0    +      -       -      -
     74A  GLY      3.2     7.3    +      -       -      +
     76A  VAL*     3.8    31.6    -      -       +      -
    246A  TYR*     5.4     8.5    -      -       +      +
    283A  LEU*     3.9    22.2    -      -       +      -
    287A  LEU*     4.2    19.3    -      -       +      -
    289A  ARG*     4.6    20.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     1.3    88.6    -      -       +      +
     68A  LEU*     1.3    66.3    +      -       -      +
     69A  GLU*     3.9    29.6    +      -       +      +
     73A  VAL*     3.3     9.9    -      -       -      +
     74A  GLY*     2.9    39.2    +      -       -      +
    287A  LEU*     3.7    46.0    -      -       +      +
    289A  ARG*     4.6    18.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ILE*     3.8    37.5    -      -       +      +
     50A  GLN*     4.7     0.4    -      -       -      -
     51A  ALA*     3.9    33.9    -      -       +      +
     65A  ALA*     4.5     9.0    -      -       +      +
     66A  LEU      4.2     1.7    +      -       -      -
     67A  ILE*     1.3    80.2    -      -       -      +
     69A  GLU*     1.3    65.0    +      -       -      +
     70A  PRO*     4.9     0.2    -      -       -      +
     72A  GLN      4.5     2.2    -      -       -      -
     73A  VAL*     3.9    13.5    -      -       +      -
----------------------------------------------------------
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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