Contacts of the strand formed by residues 34 - 39 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     4.5     7.4    -      -       +      -
     22H  CYS*     4.1    23.1    -      -       -      -
     24H  ALA*     6.0     1.3    -      -       +      -
     29H  PHE*     5.5     7.9    -      -       +      -
     32H  TYR      3.6     4.0    +      -       -      +
     33H  ALA*     1.3    74.7    -      -       -      +
     35H  SER*     1.3    69.7    +      -       -      +
     36H  TRP*     3.8    23.8    -      -       +      +
     50H  GLY*     3.1     1.2    -      -       -      -
     51H  VAL*     2.9    48.0    +      -       +      +
     53H  PRO*     5.6     4.3    -      -       +      -
     79H  ALA*     3.6    29.6    -      -       +      -
     96H  CYS*     4.2     5.4    -      -       +      -
     97H  ALA      3.2     7.2    -      -       -      +
     98H  ARG*     4.1    19.7    -      -       +      +
     47S  TRP*     5.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 35 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  ALA*     4.3     1.1    -      -       -      +
     34H  LEU*     1.3    77.2    +      -       -      +
     36H  TRP*     1.3    64.7    +      -       -      +
     37H  VAL      4.1     0.2    -      -       -      -
     47H  TRP*     3.1    33.4    +      -       -      -
     49H  GLY      3.3     6.7    +      -       -      -
     50H  GLY*     3.9     4.9    -      -       -      -
     95H  TYR      3.7     0.3    -      -       -      +
     96H  CYS*     3.4     3.8    -      -       -      -
     97H  ALA*     2.6    41.9    +      -       -      +
    114H  PHE*     3.5    27.6    -      -       -      -
     47S  TRP*     4.4     9.0    -      -       -      -
     48S  PHE*     4.4     0.3    -      -       -      -
----------------------------------------------------------
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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  GLN*     3.8    14.4    -      -       -      -
     20H  VAL*     3.7    31.4    -      -       +      -
     21H  SER      4.2     0.2    -      -       -      -
     22H  CYS*     3.6    30.7    -      -       +      -
     34H  LEU*     3.8    16.0    -      -       +      +
     35H  SER*     1.3    74.6    -      -       -      +
     37H  VAL*     1.3    63.8    +      -       -      +
     47H  TRP*     4.0     0.7    -      -       -      -
     48H  MET*     3.0    37.3    +      -       +      +
     49H  GLY      2.9    10.9    +      -       -      +
     70H  ILE*     3.8    28.3    -      -       +      +
     79H  ALA      3.9     7.9    -      -       -      -
     80H  TYR      4.0     4.8    -      -       -      +
     81H  LEU*     3.4    56.9    -      -       +      +
     94H  TYR*     4.7     2.9    -      -       +      -
     95H  TYR*     3.2    23.8    -      -       -      -
     96H  CYS*     3.7    15.3    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     36H  TRP*     1.3    81.2    -      -       -      +
     38H  ARG*     1.3    63.5    +      -       -      +
     45H  LEU*     3.9    26.5    -      -       +      -
     46H  GLU      3.3    10.1    -      -       -      +
     47H  TRP*     4.0    20.9    -      -       +      -
     48H  MET*     4.8     0.7    -      -       -      -
     94H  TYR*     4.8     0.4    -      -       -      -
     95H  TYR*     2.8    38.8    +      -       -      +
     97H  ALA*     4.6     4.7    -      -       +      -
    114H  PHE*     4.0    18.2    -      -       +      -
    117H  TRP*     4.0    21.5    -      -       +      -
     99L  PHE*     3.9    21.3    -      -       +      -
----------------------------------------------------------
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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    75.6    -      -       -      +
     39H  GLN*     1.3    65.1    +      -       -      +
     40H  ALA*     5.1     1.5    -      -       -      +
     45H  LEU*     3.5     2.3    -      -       -      -
     46H  GLU*     2.8    48.6    +      -       +      +
     48H  MET*     3.8    12.2    -      -       +      +
     63H  ARG*     6.0     0.2    -      -       -      +
     64H  PHE*     3.6    33.4    -      -       -      -
     67H  ARG*     5.4     0.4    -      -       -      +
     83H  LEU*     4.3     2.4    -      -       -      +
     89H  GLU*     4.4    17.2    +      -       -      +
     90H  ASP*     3.0    33.1    +      -       -      +
     92H  ALA*     4.5     8.5    -      -       +      -
     93H  VAL      3.4     7.2    -      -       -      +
     94H  TYR*     2.9    54.7    +      -       +      +
----------------------------------------------------------
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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    78.6    -      -       -      +
     40H  ALA*     1.3    66.6    +      -       -      +
     41H  PRO*     4.7     0.2    -      -       -      +
     43H  ARG      3.2    26.8    +      -       -      +
     44H  GLY*     3.9     6.9    -      -       -      +
     45H  LEU*     3.8    19.4    -      -       +      +
     92H  ALA*     3.5     3.5    -      -       -      -
     93H  VAL*     2.9    37.5    +      -       +      +
     95H  TYR*     3.9    12.3    +      -       +      -
     39L  GLN*     3.0    39.3    +      -       -      -
     88L  TYR*     3.3    13.5    +      -       -      -
----------------------------------------------------------
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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