Contacts of the strand formed by residues 341 - 344 (chain G) in PDB entry 1F1H


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 ALA 341 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329G  PRO*     4.4     1.1    -      -       -      +
    331G  MET*     3.9     5.6    -      -       -      -
    333G  ALA*     3.5    22.9    -      -       +      +
    335G  SER*     4.0    16.8    -      -       -      +
    338G  ASN*     3.5    23.6    +      -       -      +
    339G  ARG      3.1     7.6    -      -       -      +
    340G  SER*     1.3    78.9    -      -       -      +
    342G  SER*     1.3    59.3    +      -       -      +
    343G  ILE      3.0    17.4    +      -       -      +
    344G  ARG*     4.5     0.7    +      -       -      +
    359G  ARG*     3.9    14.0    -      -       -      -
    392G  MET*     5.1     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 342 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329G  PRO*     3.3    34.5    -      -       -      -
    330G  VAL      4.6     0.9    -      -       -      -
    331G  MET      2.5    31.1    +      -       -      -
    332G  LEU*     3.7    15.0    -      -       -      +
    333G  ALA      3.7     1.3    +      -       -      -
    340G  SER      3.5     1.2    +      -       -      -
    341G  ALA*     1.3    71.8    -      -       -      +
    343G  ILE*     1.3    66.1    +      -       -      +
    344G  ARG      4.1     0.7    -      -       -      -
    358G  VAL*     3.6     2.8    -      -       -      +
    359G  ARG*     2.8    28.5    +      -       -      -
    360G  PHE*     4.0    16.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 343 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298G  ILE*     4.0    25.8    -      -       +      -
    301G  VAL*     4.3    22.0    -      -       +      -
    302G  ILE*     4.2    15.3    -      -       +      -
    332G  LEU*     6.3     0.2    -      -       -      -
    333G  ALA      3.4    13.4    +      -       -      +
    334G  TYR*     3.3    13.0    -      -       +      +
    335G  SER      3.1    24.8    +      -       -      +
    341G  ALA*     3.0     5.6    -      -       -      +
    342G  SER*     1.3    92.0    -      -       -      +
    344G  ARG*     1.3    61.5    +      -       -      +
    345G  ILE*     4.5     3.1    -      -       +      -
    356G  ILE*     4.2    27.1    -      -       +      -
    357G  GLU      3.2    11.2    -      -       -      +
    358G  VAL*     4.5     8.7    -      -       +      -
    360G  PHE*     5.7     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 344 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271G  HIS*     4.8     2.8    -      -       -      -
    335G  SER      3.2     6.7    -      -       -      +
    336G  ALA      3.4    26.1    +      -       -      -
    338G  ASN      4.5     7.4    -      -       -      +
    339G  ARG*     3.4    40.9    -      -       -      +
    341G  ALA      5.2     0.4    -      -       -      +
    342G  SER      4.1     0.8    -      -       -      -
    343G  ILE*     1.3    74.2    -      -       -      +
    345G  ILE*     1.3    71.0    +      -       -      +
    346G  PRO*     3.4    22.7    -      -       -      +
    357G  GLU*     2.9    70.5    +      -       -      +
    359G  ARG*     4.0    14.3    -      -       -      +
     49L  PHE      4.8     0.4    +      -       -      -
     50L  ASP*     4.2    19.6    -      -       -      +
     64L  ASP*     3.5    25.6    +      -       -      -
----------------------------------------------------------
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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