Contacts of the strand formed by residues 297 - 300 (chain 3) in PDB entry 1O1F


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 ASN 297 (chain 3).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1513  ILE*     3.4    20.0    +      -       -      +
    1533  LEU*     4.5    14.6    -      -       -      +
    2783  THR*     3.2    34.2    +      -       -      +
    2823  ILE*     4.6     1.9    -      -       -      +
    2933  LEU      4.5     3.0    -      -       -      +
    2943  TYR*     5.0     1.6    -      -       -      +
    2963  ASN*     1.3    71.3    -      -       -      +
    2983  VAL*     1.3    62.5    +      -       -      +
    2993  MET*     4.8     2.4    -      -       -      -
    3133  MET*     4.4    12.3    -      -       -      +
    3173  ILE*     3.9     9.7    -      -       -      +
    3283  LYS      2.9    15.2    +      -       -      +
    3293  ILE*     3.5    27.2    -      -       +      +
    3303  ILE      2.7    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 298 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1413  SER*     4.5     9.9    -      -       -      +
    1423  LEU*     3.7    33.0    -      -       +      -
    1453  SER*     3.5    28.3    -      -       -      +
    1473  ARG*     4.3     8.3    -      -       -      -
    1513  ILE      2.9     7.1    +      -       -      +
    1523  VAL*     3.1    20.2    -      -       +      +
    1533  LEU*     2.9    25.5    +      -       -      +
    2963  ASN      3.4     3.3    +      -       -      +
    2973  ASN*     1.3    76.0    -      -       -      +
    2993  MET*     1.3    72.5    -      -       -      +
    3003  SER*     5.3     0.2    -      -       -      -
    3303  ILE*     3.3    18.6    -      -       +      +
    3323  PRO*     5.3     4.0    -      -       +      -
    3383  SER*     5.9     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 299 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1533  LEU*     3.6    35.9    -      -       +      +
    2973  ASN*     4.8     5.6    -      -       -      -
    2983  VAL*     1.3    78.3    -      -       -      +
    3003  SER*     1.3    62.2    +      -       -      +
    3043  THR*     3.8    18.2    -      -       -      +
    3093  ILE*     4.3    13.7    -      -       +      -
    3103  ALA*     4.0    14.8    -      -       +      +
    3133  MET*     4.8    11.0    -      -       -      -
    3293  ILE*     3.6    32.8    -      -       +      -
    3303  ILE      2.8    10.6    +      -       -      +
    3313  ALA*     3.4    28.9    -      -       +      -
    3323  PRO*     3.9    11.3    -      -       -      +
    3353  ARG*     3.8    13.4    -      -       -      +
    3383  SER*     4.4     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 300 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1413  SER*     3.0    34.3    +      -       -      -
    1523  VAL*     3.6     5.2    -      -       -      +
    1533  LEU      3.1     9.7    +      -       -      +
    1543  ASP*     3.0    23.7    +      -       -      +
    1553  SER      3.1    20.8    +      -       -      -
    2983  VAL*     4.2     0.6    +      -       -      -
    2993  MET*     1.3    77.8    -      -       -      +
    3013  GLY*     1.3    60.4    +      -       -      +
    3043  THR*     3.3    11.5    -      -       -      +
    3353  ARG*     4.0     5.2    -      -       -      -
    3383  SER*     3.7    15.5    -      -       -      -
    3393  VAL*     4.5     1.7    -      -       -      +
----------------------------------------------------------
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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