Contacts of the strand formed by residues 34 - 39 (chain L) in PDB entry 3H3P


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 34 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  LEU*     4.4    11.4    -      -       +      -
     23L  CYS*     4.0    18.8    -      -       -      -
     29L  VAL*     4.4     6.5    -      -       +      -
     32L  ASN      2.9     7.3    +      -       -      +
     33L  LYS*     1.3    74.4    -      -       -      +
     35L  ALA*     1.3    64.9    +      -       -      +
     36L  TRP*     3.8    21.8    -      -       +      +
     49L  ILE*     4.3     0.9    -      -       -      +
     50L  TYR*     3.9     0.5    -      -       -      -
     51L  GLY      3.5     3.5    +      -       -      -
     52L  ALA*     2.8    34.6    +      -       -      +
     72L  PHE*     3.1    68.0    -      -       +      -
     89L  CYS*     4.9     0.2    -      -       +      -
     90L  GLN      3.1    23.1    -      -       -      +
     91L  GLN      4.4     0.9    -      -       -      +
     92L  TYR*     3.7     2.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 35 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113H  ALA*     3.8    27.1    -      -       +      -
     34L  LEU*     1.3    75.7    -      -       -      +
     36L  TRP*     1.3    65.8    +      -       -      +
     37L  TYR*     3.9    12.8    -      -       +      -
     47L  LEU*     3.9     8.1    -      -       +      -
     49L  ILE      3.1    14.6    -      -       -      +
     50L  TYR*     4.2     0.7    -      -       -      -
     88L  TYR      4.0     0.2    -      -       -      +
     89L  CYS*     3.2     6.6    -      -       -      +
     90L  GLN*     2.6    41.2    +      -       -      +
     92L  TYR*     3.7     6.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 36 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  GLN*     4.1    16.6    -      -       -      -
     21L  LEU*     3.8    25.4    -      -       +      -
     22L  SER      4.1     6.3    -      -       -      -
     23L  CYS*     3.6    31.6    -      -       +      -
     34L  LEU*     3.8    17.6    -      -       +      +
     35L  ALA*     1.3    76.7    -      -       -      +
     37L  TYR*     1.3    67.3    +      -       -      +
     47L  LEU*     3.6     3.6    -      -       -      +
     48L  LEU*     3.1    26.1    +      -       +      -
     49L  ILE*     2.9    38.8    +      -       +      +
     52L  ALA      4.8     3.7    +      -       -      -
     65L  GLY*     5.2     0.4    -      -       -      -
     66L  SER      5.5     0.2    +      -       -      -
     72L  PHE*     4.2     4.5    -      -       +      +
     73L  THR*     4.0    11.5    +      -       -      -
     74L  LEU*     3.4    57.8    -      -       +      +
     87L  TYR*     4.7     4.9    -      -       +      -
     88L  TYR      3.3    18.4    -      -       -      -
     89L  CYS*     4.0    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 37 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45H  LEU*     5.4     0.7    -      -       +      -
    113H  ALA*     3.8     1.6    -      -       -      +
    114H  PHE*     2.8    52.4    +      +       +      +
    117H  TRP*     4.0    20.4    -      +       -      -
     35L  ALA*     3.9     7.6    -      -       +      -
     36L  TRP*     1.3    76.5    -      -       -      +
     38L  GLN*     1.3    60.0    +      -       -      +
     45L  PRO*     4.2    13.0    -      -       +      -
     46L  ARG      3.3    19.5    -      -       -      +
     47L  LEU*     3.5    18.3    -      -       +      +
     48L  LEU*     4.1     5.6    -      -       -      -
     86L  VAL      3.9     0.2    -      -       -      +
     87L  TYR*     3.2     8.7    -      -       -      +
     88L  TYR*     2.7    47.5    +      -       +      +
     90L  GLN*     2.7    39.3    +      -       +      -
     99L  PHE*     4.0    16.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 38 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37L  TYR*     1.3    73.6    -      -       -      +
     39L  GLN*     1.3    63.5    +      -       -      +
     40L  ARG*     3.1    37.6    +      -       -      +
     44L  ALA      4.4     0.5    -      -       -      +
     45L  PRO*     3.2     2.1    -      -       -      +
     46L  ARG*     2.7    66.3    +      -       +      +
     48L  LEU*     3.8    16.5    -      -       +      +
     63L  PHE*     3.8    18.2    -      -       -      -
     82L  GLU      4.3     3.4    +      -       -      -
     83L  ASP*     4.1     7.7    +      -       -      -
     85L  ALA*     3.9    10.3    -      -       +      -
     86L  VAL      3.7     2.9    -      -       -      -
     87L  TYR*     3.2    34.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 39 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     3.0    40.6    +      -       -      -
     45H  LEU*     4.6     0.7    -      -       -      +
     95H  TYR*     3.5    10.1    +      -       -      -
     38L  GLN*     1.3    75.3    -      -       -      +
     40L  ARG*     1.3    64.4    +      -       -      +
     41L  PRO*     4.6     1.0    -      -       -      +
     42L  GLY      5.9     0.8    -      -       -      +
     43L  GLN      2.9    29.0    +      -       -      +
     44L  ALA      4.1     1.1    -      -       -      -
     45L  PRO*     3.9    27.8    -      -       +      +
     85L  ALA*     3.2     4.6    -      -       -      +
     86L  VAL*     2.8    44.9    +      -       +      +
     88L  TYR*     3.4    19.8    +      -       +      -
----------------------------------------------------------
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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