Contacts of the strand formed by residues 41 - 45 (chain A) in PDB entry 1CG4


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 HIS 41 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  LYS*     4.3     5.4    -      -       +      -
     17A  GLY*     3.5    18.0    +      -       -      -
     32A  ARG*     4.0     8.7    +      -       -      -
     39A  ALA*     3.4    24.8    -      -       +      +
     40A  GLY*     1.3    74.4    -      -       -      -
     42A  THR*     1.3    61.3    +      -       -      +
     43A  LEU*     3.9     3.2    +      -       +      +
     50A  THR      3.4     1.9    -      -       -      +
     51A  VAL*     3.2     4.8    -      -       -      +
     52A  LEU*     2.7    53.3    +      -       +      +
     53A  HIS      4.0     6.5    -      -       -      -
     55A  ILE      5.4     1.1    -      -       -      -
     57A  SER*     3.7     8.5    -      -       -      +
    221A  GLU*     3.4    25.0    +      -       -      -
    222A  GLY      3.8    20.4    -      -       -      -
    223A  ALA*     4.7     0.2    -      -       -      -
    432A  GDP      2.8    25.4    +      -       -      +
    440A  IMO      3.9    13.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  GLY*     4.9     0.6    -      -       -      -
     18A  LYS*     3.9    16.5    +      -       -      +
     41A  HIS*     1.3    70.6    -      -       -      +
     43A  LEU*     1.3    63.5    +      -       -      +
     44A  VAL*     3.9     7.2    +      -       +      -
     49A  LYS*     3.5    36.2    +      -       +      -
     50A  THR      3.5     2.9    -      -       -      -
     51A  VAL*     3.6    14.1    -      -       -      +
    299A  ALA*     3.9    12.5    -      -       -      +
    417A  PRO      5.1     0.5    -      -       -      +
    432A  GDP      2.9    57.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  GLY*     3.8    25.1    -      -       -      +
     18A  LYS*     4.9     3.8    -      -       -      +
     21A  ASP*     3.3    36.1    -      -       +      +
     41A  HIS      4.0     9.9    -      -       -      +
     42A  THR*     1.3    78.5    -      -       -      +
     44A  VAL*     1.3    61.1    +      -       -      +
     45A  ILE*     4.1    11.7    -      -       +      -
     48A  GLU      3.5     1.5    -      -       -      +
     49A  LYS*     3.3     3.3    -      -       -      +
     50A  THR*     2.7    42.6    +      -       -      +
     52A  LEU*     4.1    14.8    -      -       +      -
     57A  SER*     3.5    27.8    -      -       -      +
     60A  LEU*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LYS*     5.6     0.8    -      -       -      +
     42A  THR*     3.9    18.2    -      -       +      -
     43A  LEU*     1.3    79.1    -      -       -      +
     45A  ILE*     1.3    58.9    +      -       -      +
     47A  GLY*     4.0    19.7    -      -       -      +
     48A  GLU      3.7     2.7    -      -       -      -
     49A  LYS*     4.1    13.9    -      -       +      -
    417A  PRO*     3.4    35.6    +      -       +      +
    418A  ASP*     3.2    26.6    -      -       +      +
    419A  ARG*     2.7    34.7    +      -       -      +
    432A  GDP      4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ASP*     4.1    12.1    -      -       -      +
     43A  LEU*     4.1     6.5    -      -       +      -
     44A  VAL*     1.3    85.1    -      -       -      +
     46A  ASN*     1.3    86.9    +      -       +      +
     47A  GLY      3.1     0.4    -      -       -      -
     48A  GLU*     2.9    33.5    +      -       +      +
     50A  THR*     5.2     0.2    -      -       -      +
     60A  LEU*     3.7    29.8    -      -       +      -
    418A  ASP*     3.9     2.0    -      -       -      -
    419A  ARG*     3.6    42.2    -      -       +      +
----------------------------------------------------------
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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