Contacts of the strand formed by residues 10 - 15 (chain X) in PDB entry 2OTT


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 GLU 10 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8X  ALA*     3.7     5.7    +      -       +      +
      9X  VAL*     1.3    77.2    -      -       -      +
     11X  SER*     1.3    62.2    +      -       -      +
     26X  VAL*     3.1    27.0    -      -       -      +
     27X  ARG*     2.8    57.6    +      -       -      +
     28X  GLN      4.9     2.8    -      -       -      +
     32X  TRP*     3.6    14.5    -      -       +      -
     53X  GLU*     3.4    10.1    -      -       -      +
     89Y  TRP*     3.8    15.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 11 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9X  VAL*     5.6     0.2    -      -       -      -
     10X  GLU*     1.3    76.7    -      -       -      +
     12X  ARG*     1.3    69.2    +      -       -      +
     24X  VAL*     4.5     1.6    -      -       -      -
     25X  GLU      3.2    10.8    -      -       -      -
     26X  VAL*     4.0    11.7    -      -       -      -
     32X  TRP*     4.0     3.8    -      -       -      -
     50X  VAL*     3.8    27.3    -      -       -      +
     53X  GLU*     2.5    33.9    +      -       -      +
     54X  GLN*     3.0    20.7    +      -       -      +
     82X  LEU*     4.2     4.7    -      -       -      -
     89Y  TRP*     5.3     2.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 12 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11X  SER*     1.3    81.0    +      -       -      +
     13X  LEU*     1.3    69.0    +      -       -      +
     14X  VAL*     3.8    25.0    -      -       -      +
     23X  THR      3.5     0.7    -      -       -      +
     24X  VAL*     3.5     4.3    -      -       -      +
     25X  GLU*     2.8    32.1    +      -       +      +
     32X  TRP*     3.2    56.2    -      -       +      +
     50X  VAL*     4.9     0.4    -      -       -      +
     54X  GLN*     3.6    15.4    -      -       -      +
     76Y  PHE*     5.6     1.2    -      -       -      -
     89Y  TRP*     3.5    48.4    -      -       +      +
     90Y  GLU      3.7    21.0    +      -       -      +
     91Y  ARG*     5.8     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 13 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12X  ARG*     1.3    82.8    -      -       -      +
     14X  VAL*     1.3    62.3    -      -       -      +
     15X  GLY      4.1     0.7    +      -       -      -
     19X  ILE*     3.6    29.7    +      -       -      +
     20X  CYS      3.7    18.2    -      -       -      +
     21X  GLU*     3.7    21.0    -      -       -      +
     22X  GLY      3.6    11.9    -      -       -      +
     23X  THR      3.5     1.3    -      -       -      -
     24X  VAL*     3.5    32.5    -      -       +      -
     50X  VAL*     3.9    15.3    -      -       +      -
     54X  GLN*     4.2    12.6    +      -       +      -
    100X  VAL*     4.0     8.5    -      -       +      +
    102X  CYS*     3.7    21.3    -      -       -      -
     91Y  ARG*     4.2    11.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 14 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12X  ARG*     3.8    28.7    -      -       -      +
     13X  LEU*     1.3    74.8    -      -       -      +
     15X  GLY*     1.3    68.9    +      -       -      +
     16X  GLY      3.3     2.9    -      -       -      -
     22X  GLY*     3.4     0.5    -      -       -      -
     23X  THR*     2.9    40.0    +      -       -      +
     25X  GLU*     3.4    43.7    -      -       +      +
     99X  PHE*     5.5     0.2    -      -       -      -
     91Y  ARG*     5.4     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 15 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13X  LEU      4.1     0.6    +      -       -      -
     14X  VAL*     1.3    82.9    -      -       -      +
     16X  GLY*     1.4    61.4    -      -       -      +
     22X  GLY*     4.8     0.9    -      -       -      -
     99X  PHE*     5.5     3.5    -      -       -      -
     91Y  ARG*     4.6     5.7    -      -       -      +
     93Y  SER*     4.1    20.3    +      -       -      -
     94Y  TYR*     4.4     7.8    -      -       -      -
----------------------------------------------------------
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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