Contacts of the strand formed by residues 3072 - 3078 (chain 2) in PDB entry 1BMV


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 ILE3072 (chain 2).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30252  ILE*     4.6     0.7    -      -       +      -
   30472  LEU*     4.1     5.4    -      -       +      -
   30512  LEU*     3.8    37.0    -      -       +      -
   30712  MET*     1.3    70.2    -      -       -      +
   30732  LYS*     1.3    59.7    +      -       -      +
   31262  SER*     3.3     2.5    -      -       -      -
   31272  PHE*     3.0    66.2    +      -       +      -
   31292  PRO*     4.2    10.3    -      -       +      -
   31362  TRP*     3.1    50.5    -      -       +      +
   31412  LEU*     4.0     7.6    -      -       +      -
   31702  TRP*     4.0     8.5    -      -       +      -
   31712  PHE      3.6     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS3073 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30202  MET*     2.6    41.4    -      -       +      +
   30712  MET      3.3     5.6    +      -       -      +
   30722  ILE*     1.3    72.2    -      -       -      +
   30742  MET*     1.3    61.6    +      -       -      +
   31242  THR*     4.1    19.9    -      -       +      +
   31252  MET      3.5     3.1    -      -       -      -
   31262  SER*     3.7    12.1    -      -       -      +
   31692  ASP      3.5     4.0    -      -       -      +
   31702  TRP*     3.5     4.4    -      -       -      -
   31712  PHE*     2.9    58.4    +      -       +      +
   31732  SER*     4.2    23.6    -      -       -      +
      4M    C      3.8    19.1    +      -       -      -
      5M    A      5.7     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET3074 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30722  ILE      4.2     0.4    -      -       -      -
   30732  LYS*     1.3    74.6    -      -       -      +
   30752  VAL*     1.3    66.3    +      -       -      +
   30762  ALA*     4.5     2.0    -      -       +      +
   30902  CYS*     3.1    44.4    -      -       +      -
   31152  TRP*     5.0     0.7    -      -       +      -
   31232  MET*     2.8    47.1    -      -       +      +
   31242  THR*     3.1    31.9    -      -       -      +
   31252  MET*     2.8    28.0    +      -       +      +
   31272  PHE*     5.1     3.4    -      -       +      -
   31682  ILE*     3.8    23.8    -      -       +      -
   31692  ASP      3.4     4.3    -      -       -      -
   31702  TRP*     3.8    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL3075 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30202  MET*     4.9     6.5    -      -       +      -
   30732  LYS*     4.8     2.7    -      -       +      -
   30742  MET*     1.3    81.0    -      -       -      +
   30762  ALA*     1.3    65.7    +      -       -      +
   30772  THR*     5.1     4.4    -      -       -      +
   31222  ALA*     5.2     7.2    -      -       +      -
   31232  MET      3.3     9.6    -      -       -      +
   31242  THR*     3.9    17.9    -      -       +      +
   31672  THR      3.6     2.1    -      -       -      +
   31682  ILE*     3.3     2.0    -      -       -      -
   31692  ASP*     2.6    46.1    +      -       +      +
   31712  PHE*     3.1    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA3076 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30742  MET*     4.1     2.2    -      -       +      -
   30752  VAL*     1.3    74.6    -      -       -      +
   30772  THR*     1.3    75.1    +      -       -      +
   31152  TRP*     3.7    33.6    +      -       +      -
   31222  ALA*     3.2    23.2    -      -       -      +
   31232  MET*     2.9    22.2    +      -       +      +
   31662  VAL*     4.6     0.7    -      -       +      -
   31672  THR      3.6     4.0    -      -       -      -
   31682  ILE*     4.2    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR3077 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30752  VAL*     5.1     5.2    -      -       -      +
   30762  ALA*     1.3    85.8    +      -       -      +
   30782  VAL*     1.3    66.8    +      -       -      +
   30792  GLY      5.5     0.4    -      -       -      +
   31152  TRP*     5.4     1.1    -      -       -      +
   31212  LYS      3.8     8.0    +      -       -      +
   31222  ALA*     3.8    14.1    -      -       -      +
   31652  GLN      4.0     2.6    -      -       -      +
   31662  VAL*     3.7     3.0    -      -       -      +
   31672  THR*     3.1    39.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL3078 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   30322  LEU*     4.6     3.1    -      -       +      -
   30772  THR*     1.3    78.9    -      -       -      +
   30792  GLY*     1.3    69.3    +      -       -      +
   30802  ILE*     5.8     1.3    -      -       +      -
   30882  LEU*     5.3     0.7    -      -       +      -
   31152  TRP*     4.9     8.2    +      -       -      +
   31172  PRO*     3.2    39.6    -      -       +      +
   31202  THR      4.7     0.3    -      -       -      +
   31212  LYS*     4.0    13.4    +      -       -      -
   31562  TRP*     6.0     1.3    -      -       +      -
   31642  VAL*     3.1    35.9    -      -       +      -
   31652  GLN      3.7     7.6    -      -       -      +
   31662  VAL*     3.4    28.3    -      -       +      -
----------------------------------------------------------
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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