Contacts of the strand formed by residues 30 - 34 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  VAL*     3.1    24.2    +      -       +      +
     28D  PRO      3.9     6.4    -      -       -      +
     29D  TYR*     1.3    81.8    -      -       -      +
     31D  VAL*     1.3    76.4    +      -       -      +
     43D  GLY*     4.3     8.7    -      -       -      -
     44D  GLY      3.9     2.5    -      -       -      -
     69D  GLY*     4.0    13.7    +      -       -      -
     70D  GLU      5.0     2.4    +      -       -      +
    139D  SER*     2.5    45.7    +      -       -      +
    140D  GLY*     4.1     5.4    -      -       -      -
    141D  TRP*     3.8    24.3    -      -       +      -
    155D  LEU*     3.9    17.4    -      -       +      +
    197D  GLY*     4.5     0.3    -      -       -      -
    198D  PRO*     3.4    22.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  TYR      4.2     7.9    -      -       -      +
     30D  GLN*     1.3    85.5    -      -       -      +
     32D  SER*     1.3    59.3    +      -       -      +
     33D  LEU*     4.4     7.0    -      -       +      -
     43D  GLY*     3.1     5.9    -      -       -      -
     44D  GLY*     3.0    43.1    +      -       -      +
     46D  LEU*     4.3    13.9    -      -       +      +
     52D  VAL*     3.7    21.1    -      -       +      -
     65D  VAL*     3.5    21.1    -      -       +      -
     66D  ARG      3.4    11.0    -      -       -      +
     67D  LEU*     3.7    28.0    -      -       +      -
    118D  VAL*     5.7     0.2    -      -       +      -
    141D  TRP*     4.1     6.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31D  VAL*     1.3    74.0    -      -       -      +
     33D  LEU*     1.3    65.2    +      -       -      +
     34D  ASN*     3.6     1.9    +      -       -      +
     40D  HIS*     2.7    32.8    +      -       -      +
     42D  CYS      3.7     4.0    -      -       -      -
     65D  VAL*     3.6     2.4    -      -       -      -
     66D  ARG*     2.8    57.6    +      -       -      +
     70D  GLU*     4.5     0.4    -      -       -      -
     73D  ILE*     4.2     9.9    -      -       -      +
    141D  TRP*     3.6    20.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31D  VAL*     4.4     9.9    -      -       +      -
     32D  SER*     1.3    74.2    -      -       -      +
     34D  ASN*     1.3    59.9    +      -       -      +
     40D  HIS*     3.6     3.5    -      -       -      -
     41D  PHE*     3.1    40.2    +      -       +      -
     42D  CYS*     2.8    24.7    +      -       +      +
     43D  GLY      3.6    23.8    -      -       -      +
     52D  VAL*     5.1     2.0    -      -       +      -
     54D  SER*     4.0     9.2    -      -       -      +
     58D  CYS*     4.4     9.4    -      -       +      -
     63D  ILE*     3.8    17.3    -      -       +      -
     64D  GLN      3.8     1.3    -      -       -      -
     65D  VAL*     3.7    29.2    -      -       +      -
    104D  MET*     4.5     0.4    -      -       +      -
    106D  ILE*     3.7    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 34 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  SER*     3.6     1.1    +      -       -      +
     33D  LEU*     1.3    75.8    -      -       -      +
     37D  SER*     1.3    62.9    +      -       -      +
     38D  GLY*     2.8    25.8    +      -       -      -
     39D  TYR*     3.3    30.1    -      -       -      +
     40D  HIS*     4.0     2.9    -      -       -      +
     41D  PHE*     3.5     3.7    -      -       -      -
     63D  ILE      3.9     1.4    -      -       -      -
     64D  GLN*     2.8    59.3    +      -       +      +
     66D  ARG*     4.4    29.6    -      -       +      +
     82D  PHE*     5.7     4.9    -      -       -      -
----------------------------------------------------------
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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