Contacts of the strand formed by residues 30 - 34 (chain C) in PDB entry 1C9T


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 GLN 30 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  VAL*     3.4    22.9    +      -       +      +
     28C  PRO      3.2     8.0    -      -       -      +
     29C  TYR*     1.3    82.6    -      -       -      +
     31C  VAL*     1.3    76.4    +      -       -      +
     43C  GLY*     4.3     9.0    -      -       -      -
     44C  GLY      3.8     2.7    -      -       -      -
     67C  LEU*     4.8     0.2    -      -       -      +
     69C  GLY*     4.1    12.6    +      -       -      -
     70C  GLU      5.1     2.3    +      -       -      +
    139C  SER*     2.3    44.0    +      -       -      +
    140C  GLY*     4.2     5.9    -      -       -      -
    141C  TRP*     3.7    17.4    -      -       +      -
    155C  LEU*     3.7    24.1    -      -       +      +
    197C  GLY*     4.5     0.2    -      -       -      -
    198C  PRO*     3.5    25.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  TYR      3.9     9.0    -      -       -      +
     30C  GLN*     1.3    84.9    -      -       -      +
     32C  SER*     1.3    58.8    +      -       -      +
     33C  LEU*     4.5     5.6    -      -       +      -
     43C  GLY*     3.3     5.0    -      -       -      -
     44C  GLY*     2.9    49.6    +      -       -      +
     46C  LEU*     4.3    12.3    -      -       +      +
     52C  VAL*     3.7    15.5    -      -       +      -
     65C  VAL*     3.6    22.2    -      -       +      -
     66C  ARG      3.3    10.5    -      -       -      +
     67C  LEU*     3.8    28.3    -      -       +      -
    118C  VAL*     5.7     0.2    -      -       +      -
    141C  TRP*     4.1     6.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 32 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31C  VAL*     1.3    72.8    -      -       -      +
     33C  LEU*     1.3    66.5    +      -       -      +
     34C  ASN*     3.7     0.7    +      -       -      +
     40C  HIS*     2.6    34.0    +      -       -      +
     42C  CYS      3.8     3.6    -      -       -      -
     64C  GLN      3.5     0.7    -      -       -      +
     65C  VAL*     3.4     5.2    -      -       -      -
     66C  ARG*     2.7    58.9    +      -       -      +
     73C  ILE*     4.2    11.1    -      -       -      +
    141C  TRP*     3.8    16.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31C  VAL*     4.5     7.2    -      -       +      -
     32C  SER*     1.3    77.9    -      -       -      +
     34C  ASN*     1.3    58.5    +      -       -      +
     40C  HIS*     3.6     3.3    -      -       -      -
     41C  PHE*     3.1    39.7    +      -       +      -
     42C  CYS*     2.8    24.7    +      -       +      +
     43C  GLY      3.6    21.3    -      -       -      +
     52C  VAL*     5.0     1.6    -      -       +      -
     54C  SER*     4.0     8.5    -      -       -      +
     58C  CYS*     4.3     8.3    -      -       +      +
     63C  ILE*     3.8    27.8    -      -       +      -
     64C  GLN      3.7     0.7    -      -       -      -
     65C  VAL*     3.9    18.4    -      -       +      -
    104C  MET*     4.5     0.7    -      -       +      -
    106C  ILE*     3.7    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 34 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  SER*     4.8     0.7    -      -       -      +
     33C  LEU*     1.3    74.7    -      -       -      +
     37C  SER*     1.3    62.0    +      -       -      +
     38C  GLY*     2.8    19.9    +      -       -      -
     39C  TYR*     3.2    30.9    -      -       -      +
     40C  HIS*     4.0     3.2    -      -       -      +
     41C  PHE*     3.6     1.6    -      -       -      -
     62C  GLY      4.7     0.2    -      -       -      +
     63C  ILE*     3.8     3.8    -      -       -      +
     64C  GLN*     2.7    61.0    +      -       +      +
     66C  ARG*     4.4    30.1    -      -       +      +
     82C  PHE*     5.8     4.7    -      -       -      -
----------------------------------------------------------
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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