Contacts of the strand formed by residues 341 - 345 (chain B) in PDB entry 3CFV


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 LEU 341 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333B  ALA*     4.1    10.8    -      -       +      -
    334B  SER      3.4    10.1    -      -       -      +
    335B  SER*     4.2     5.6    -      -       -      -
    340B  ARG*     1.3    73.8    -      -       -      +
    342B  ASN*     1.3    67.0    +      -       -      +
    343B  VAL*     3.9    16.0    +      -       +      +
    367B  PHE      3.8     0.9    -      -       -      +
    368B  ILE*     3.7     0.3    -      -       -      -
    369B  HIS*     2.7    48.3    +      -       +      +
    376B  ILE*     3.9    10.0    -      -       +      +
    379B  PHE*     3.5    41.7    -      -       +      -
    389B  ILE*     4.4     3.1    -      -       +      -
    391B  SER*     4.1    11.4    -      -       -      -
    401B  TRP*     3.8    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 342 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314B  SER*     4.0     5.2    -      -       -      -
    315B  HIS*     3.2    46.0    +      -       +      -
    333B  ALA*     3.1     5.4    -      -       -      +
    334B  SER      2.8    33.6    +      -       -      -
    340B  ARG*     4.0     8.1    -      -       -      +
    341B  LEU*     1.3    77.8    -      -       -      +
    343B  VAL*     1.3    62.0    +      -       -      +
    344B  TRP*     3.7    24.4    +      -       +      -
    365B  LEU*     4.2     7.0    -      -       +      -
    367B  PHE      3.4     2.0    -      -       -      -
    368B  ILE*     3.4    36.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 343 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  ILE*     3.7    23.8    -      -       +      -
    332B  LEU      3.3     8.3    -      -       -      +
    333B  ALA*     4.4     4.9    -      -       +      -
    341B  LEU*     3.9    18.6    -      -       +      -
    342B  ASN*     1.3    77.4    -      -       -      +
    344B  TRP*     1.3    65.6    +      -       -      +
    365B  LEU*     3.9     2.9    -      -       -      +
    366B  LEU*     2.9    39.9    +      -       +      +
    367B  PHE*     2.8    39.4    +      -       +      +
    381B  TRP*     4.4     9.9    -      -       +      -
    387B  TRP*     4.3     7.6    -      -       +      -
    389B  ILE*     5.0     0.2    -      -       +      -
    401B  TRP*     4.5     7.9    -      -       +      -
    403B  MSE      5.5     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 344 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297B  VAL*     4.5     4.3    -      -       +      +
    312B  PHE*     3.4    56.5    -      +       +      -
    313B  GLU      3.6    27.6    -      -       -      -
    314B  SER*     3.7    13.5    -      -       -      -
    315B  HIS*     4.2     6.7    -      -       -      -
    330B  THR      3.5     0.5    -      -       -      +
    331B  ILE*     3.3     9.8    -      -       -      +
    332B  LEU*     2.5    64.2    +      -       +      +
    333B  ALA*     4.4     0.7    -      -       -      -
    334B  SER*     3.0    26.0    +      -       -      -
    342B  ASN*     3.7    27.4    +      -       +      -
    343B  VAL*     1.3    76.1    -      -       -      +
    345B  ASP*     1.3    60.5    +      -       -      +
    346B  LEU      4.0     0.7    -      -       -      +
    362B  PRO*     4.2     6.7    -      -       +      -
    364B  GLU*     3.2    13.9    -      -       +      +
    365B  LEU*     3.8    28.0    -      -       +      -
    366B  LEU*     4.5     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 345 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  THR*     3.0    26.4    +      -       -      +
    331B  ILE*     3.6    14.3    -      -       +      +
    343B  VAL      4.4     0.2    +      -       -      -
    344B  TRP*     1.3    71.7    -      -       -      +
    346B  LEU*     1.3    65.2    +      -       -      +
    347B  SER*     3.1    21.1    +      -       -      -
    348B  LYS*     3.0    36.7    +      -       +      -
    364B  GLU*     2.8    27.8    +      -       -      +
    366B  LEU*     4.1    18.1    -      -       +      +
----------------------------------------------------------
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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