Contacts of the strand formed by residues 34 - 39 (chain H) in PDB entry 6JOD


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 MET 34 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     4.2    21.3    -      -       +      -
     22H  CYS*     4.7     7.6    -      -       -      -
     27H  PHE*     4.8     6.3    -      -       +      -
     29H  PHE*     3.9    30.5    -      -       +      -
     32H  PHE*     4.6     2.2    -      -       -      +
     33H  GLY*     1.3    77.0    -      -       -      +
     35H  HIS*     1.3    63.6    +      -       -      +
     50H  TYR*     3.1     1.9    -      -       -      -
     51H  ILE*     2.9    34.2    +      -       -      +
     70H  ILE*     4.2     1.2    -      -       -      +
     72H  ARG*     3.7    25.1    -      -       -      +
     79H  LEU*     3.6    31.9    -      -       +      -
     96H  CYS*     4.9     0.9    -      -       +      -
     97H  ALA      4.0     5.8    -      -       -      -
     98H  THR*     3.5    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 35 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  GLY      4.3     4.6    +      -       -      -
     34H  MET*     1.3    76.9    -      -       -      +
     36H  TRP*     1.3    63.0    +      -       -      +
     37H  VAL*     4.3     0.9    -      -       +      -
     47H  TRP*     3.2    21.4    +      -       +      +
     49H  ALA      3.3     8.5    -      -       -      +
     50H  TYR*     3.2    34.3    -      +       +      +
     79H  LEU*     4.3     1.0    -      -       -      +
     96H  CYS*     3.3     7.8    -      -       -      +
     97H  ALA      2.9    41.3    +      -       -      +
     98H  THR*     4.5     1.8    -      -       -      -
     99H  SER      5.0     0.2    -      -       -      -
    103H  GLY*     4.7     0.6    -      -       -      -
    104H  THR      3.4    16.6    +      -       -      -
    105H  PRO*     3.9    13.0    -      -       +      -
    106H  TRP      4.2     3.5    +      -       -      -
    107H  PHE*     3.4    30.8    -      +       +      -
     93L  TYR*     3.4    20.9    -      -       -      -
     95L  LEU*     4.2     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 36 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLU*     3.8    11.4    -      -       +      -
     20H  LEU*     4.1    21.8    -      -       +      -
     21H  SER      4.0    11.0    -      -       -      -
     22H  CYS*     3.7    21.3    -      -       +      -
     35H  HIS*     1.3    72.3    -      -       -      +
     37H  VAL*     1.3    55.4    +      -       -      +
     48H  VAL*     2.8    38.3    +      -       +      -
     49H  ALA*     2.9    19.6    +      -       +      +
     70H  ILE*     3.4    30.7    -      -       +      -
     79H  LEU*     3.2    44.3    -      -       +      +
     80H  PHE      3.5     4.8    +      -       -      -
     81H  LEU*     3.3    41.0    -      -       +      +
     94H  TYR*     4.4    13.2    -      -       +      -
     95H  PHE      3.2    29.2    -      -       -      -
     96H  CYS*     3.7    13.2    -      -       +      -
    114H  THR*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  HIS*     4.1     3.3    -      -       +      +
     36H  TRP*     1.3    80.5    -      -       -      +
     38H  ARG*     1.3    63.4    +      -       -      +
     45H  LEU*     4.4     4.7    -      -       +      -
     46H  GLU      3.1    24.9    -      -       -      +
     47H  TRP*     3.6    25.1    -      -       +      -
     48H  VAL*     4.0     0.9    -      -       -      +
     94H  TYR*     4.6     0.9    -      -       -      -
     95H  PHE*     2.8    42.1    +      -       -      +
     97H  ALA*     5.4     0.9    -      -       +      -
    107H  PHE*     3.6    25.4    -      -       +      -
    110H  TRP*     3.8    28.3    -      -       +      -
     97L  PHE*     4.1     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 38 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  VAL*     1.3    75.3    -      -       -      +
     39H  GLN*     1.3    58.6    +      -       -      +
     40H  ALA      5.3     0.7    -      -       -      +
     45H  LEU*     3.6     1.5    -      -       -      -
     46H  GLU*     2.8    75.1    +      -       +      +
     48H  VAL*     3.5    12.6    -      -       +      +
     63H  THR*     3.8    14.5    +      -       -      -
     64H  VAL*     4.2    11.3    -      -       -      +
     68H  PHE*     4.2    10.7    -      -       -      -
     89H  GLU*     4.3    10.3    +      -       -      +
     90H  ASP*     3.1    38.6    +      -       -      +
     92H  ALA*     4.0    14.4    -      -       +      -
     93H  MET      3.3     8.5    -      -       -      +
     94H  TYR*     2.9    52.4    +      -       +      +
     95H  PHE*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 39 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ARG*     1.3    75.5    -      -       -      +
     40H  ALA*     1.3    65.4    +      -       -      +
     43H  LYS      3.2    27.2    +      -       -      +
     44H  GLY      3.3    13.1    -      -       -      +
     45H  LEU*     3.7    14.8    -      -       +      +
     46H  GLU*     5.6     0.2    -      -       -      -
     92H  ALA*     3.6     3.1    -      -       -      -
     93H  MET*     2.9    40.0    +      -       +      +
     95H  PHE*     4.2    11.3    -      -       +      -
     37L  GLN*     2.9    43.3    +      -       -      +
     86L  TYR*     3.6    11.1    +      -       -      -
----------------------------------------------------------
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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