Contacts of the strand formed by residues 30 - 34 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  VAL*     3.2    23.5    +      -       +      +
     28E  PRO      3.1     7.8    -      -       -      +
     29E  TYR*     1.3    82.7    -      -       -      +
     31E  VAL*     1.3    75.0    +      -       -      +
     43E  GLY*     4.3     7.3    -      -       -      -
     44E  GLY      3.9     2.7    -      -       -      -
     67E  LEU      4.6     0.2    -      -       -      -
     69E  GLY*     4.0    13.3    +      -       -      -
     70E  GLU      5.0     3.5    +      -       -      +
    139E  SER*     2.5    43.1    +      -       -      +
    140E  GLY*     4.0     5.0    -      -       -      -
    141E  TRP*     3.8    26.7    -      -       +      -
    155E  LEU*     3.8    17.5    -      -       +      -
    197E  GLY*     4.8     0.2    -      -       -      -
    198E  PRO*     3.4    23.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28E  PRO      5.7     0.2    -      -       -      +
     29E  TYR      3.9    10.1    -      -       -      +
     30E  GLN*     1.3    84.2    -      -       -      +
     32E  SER*     1.3    60.2    +      -       -      +
     33E  LEU*     4.3     6.7    -      -       +      -
     43E  GLY*     3.1     5.4    -      -       -      -
     44E  GLY*     3.0    48.8    +      -       -      +
     46E  LEU*     4.2    17.0    -      -       +      +
     52E  VAL*     3.8    14.4    -      -       +      -
     65E  VAL*     3.6    22.0    -      -       +      -
     66E  ARG      3.4    11.2    -      -       -      +
     67E  LEU*     3.9    21.8    -      -       +      -
    118E  VAL*     5.8     0.2    -      -       +      -
    141E  TRP*     4.2     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 32 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  VAL*     1.3    73.1    -      -       -      +
     33E  LEU*     1.3    66.3    +      -       -      +
     34E  ASN*     3.5     2.4    +      -       -      +
     40E  HIS*     2.7    32.9    +      -       -      +
     42E  CYS      3.8     4.0    -      -       -      -
     65E  VAL*     3.6     2.3    -      -       -      -
     66E  ARG*     2.8    57.0    +      -       -      +
     70E  GLU*     4.6     0.2    -      -       -      -
     73E  ILE*     4.2    10.6    -      -       -      +
    141E  TRP*     3.7    17.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  VAL*     4.3    12.6    -      -       +      -
     32E  SER*     1.3    74.6    -      -       -      +
     34E  ASN*     1.3    60.4    +      -       -      +
     40E  HIS*     3.6     3.6    -      -       -      -
     41E  PHE*     3.1    39.3    +      -       +      -
     42E  CYS*     2.9    22.9    +      -       +      +
     43E  GLY      3.7    20.9    -      -       -      +
     52E  VAL*     4.9     1.6    -      -       +      -
     54E  SER*     4.1     9.0    -      -       -      +
     58E  CYS*     4.4     8.3    -      -       +      -
     63E  ILE*     3.8    20.0    -      -       +      -
     64E  GLN      3.8     1.1    -      -       -      -
     65E  VAL*     3.8    28.0    -      -       +      -
    104E  MET*     4.6     0.2    -      -       +      -
    106E  ILE*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 34 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32E  SER*     4.7     1.3    -      -       -      +
     33E  LEU*     1.3    74.8    -      -       -      +
     37E  SER*     1.3    65.7    +      -       -      +
     38E  GLY*     2.7    28.3    +      -       -      -
     39E  TYR*     3.2    29.7    -      -       -      +
     40E  HIS*     4.0     3.2    -      -       -      +
     41E  PHE*     3.5     1.6    -      -       -      -
     63E  ILE*     3.7     5.5    -      -       -      +
     64E  GLN*     2.8    60.0    +      -       +      +
     66E  ARG*     4.5    29.4    -      -       +      +
     82E  PHE*     5.7     4.1    -      -       -      -
----------------------------------------------------------
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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