Contacts of the strand formed by residues 92 - 101 (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 ALA 92 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ARG*     4.5     9.6    -      -       -      +
     39H  GLN      3.3    29.2    -      -       -      +
     40H  ALA*     3.6     6.3    -      -       +      +
     41H  PRO*     4.5     2.7    -      -       -      -
     89H  GLU      5.8     0.2    -      -       -      +
     90H  ASP      3.2     9.6    +      -       -      +
     91H  THR*     1.3    81.0    -      -       -      +
     93H  VAL*     1.3    62.2    +      -       -      +
     94H  TYR*     3.5    13.8    -      -       +      -
    122H  LEU*     3.5     7.1    -      -       -      +
    123H  VAL      2.8    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ARG*     3.4     2.1    -      -       -      -
     39H  GLN*     2.9    37.0    +      -       +      +
     92H  ALA*     1.3    73.7    -      -       -      +
     94H  TYR*     1.3    62.5    +      -       -      +
     95H  TYR*     3.5    36.0    -      -       +      +
    119H  GLN      5.2     0.4    -      -       -      +
    120H  GLY*     3.8     4.9    -      -       -      -
    121H  THR      3.4    18.8    -      -       -      +
    122H  LEU*     3.8    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 94 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLN*     2.8    27.0    +      -       -      -
     18H  VAL*     5.8     4.7    -      -       +      -
     20H  VAL*     4.9     6.3    -      -       +      -
     36H  TRP*     4.7     5.8    -      +       +      -
     37H  VAL      4.1     2.0    -      -       -      -
     38H  ARG*     2.9    45.1    +      -       +      -
     48H  MET*     3.6    24.2    -      -       +      -
     81H  LEU*     3.8    20.9    -      -       +      -
     83H  LEU*     3.6    17.0    -      -       +      +
     86H  LEU*     5.1     1.1    -      -       +      +
     90H  ASP*     2.7    29.9    +      -       -      +
     92H  ALA*     3.5    19.5    -      -       +      -
     93H  VAL*     1.3    74.1    -      -       -      +
     95H  TYR*     1.3    57.0    +      -       -      +
    120H  GLY*     3.3     0.9    -      -       -      -
    121H  THR*     2.8    31.6    +      -       -      +
    123H  VAL*     3.7    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 95 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLN*     3.3     3.6    -      -       -      -
     36H  TRP*     3.2    10.7    -      -       -      -
     37H  VAL*     2.8    51.3    +      -       -      +
     39H  GLN*     3.9    19.7    +      -       +      -
     45H  LEU*     4.6     7.2    -      -       +      -
     93H  VAL*     3.5    28.2    -      -       +      +
     94H  TYR*     1.3    76.3    -      -       -      +
     96H  CYS*     1.3    60.0    +      -       -      +
    117H  TRP*     3.7    31.6    -      +       +      -
    118H  GLY      3.7    15.9    -      -       -      -
    119H  GLN      3.9     5.6    +      -       -      -
    120H  GLY*     3.7    16.4    -      -       -      -
     39L  GLN*     3.5    18.5    +      -       -      -
     42L  GLY      5.1     2.9    +      -       -      -
     43L  GLN      3.6     8.3    +      -       -      -
     44L  ALA*     3.6    24.0    -      -       +      -
     45L  PRO*     4.3     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 96 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     3.9     6.7    -      -       -      -
      6H  GLN*     2.9    25.7    +      -       -      -
     22H  CYS*     2.0    54.3    -      -       +      -
     34H  LEU*     4.2     7.0    -      -       +      -
     35H  SER      3.4     5.2    -      -       -      +
     36H  TRP*     3.7    14.3    -      -       +      -
     95H  TYR*     1.3    77.8    -      -       -      +
     97H  ALA*     1.3    62.5    +      -       -      +
    117H  TRP*     3.6     3.5    -      -       -      -
    118H  GLY*     3.1    32.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 97 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  ALA      3.9     0.5    -      -       -      +
     34H  LEU*     3.2     4.3    -      -       -      +
     35H  SER*     2.6    44.7    +      -       -      +
     37H  VAL*     4.6     3.1    -      -       +      -
     96H  CYS*     1.3    76.7    -      -       -      +
     98H  ARG*     1.3    61.6    +      -       -      +
    114H  PHE*     3.7    37.2    -      -       +      -
    116H  HIS      3.4     5.6    -      -       -      -
    117H  TRP*     4.2    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2H  VAL*     3.6    37.3    -      -       +      +
      4H  LEU*     4.1    17.3    -      -       +      -
     24H  ALA*     6.1     1.4    -      -       -      +
     26H  GLY      5.2     0.8    +      -       -      -
     27H  GLY*     6.0     0.4    -      -       -      -
     28H  SER      3.5    22.4    +      -       -      +
     29H  PHE*     5.3     1.8    -      -       -      +
     32H  TYR*     3.4    40.6    -      -       -      +
     33H  ALA      3.4     8.1    -      -       -      +
     34H  LEU*     4.1    12.8    -      -       +      +
     97H  ALA*     1.3    76.4    -      -       -      +
     99H  GLU*     1.3    87.0    +      -       -      +
    101H  THR*     3.7    21.6    +      -       -      +
    106H  TRP*     4.2     7.1    +      -       -      +
    114H  PHE*     3.6     5.7    -      -       -      -
    115H  ALA      3.3    17.0    +      -       -      -
    116H  HIS*     3.0    29.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 99 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  TYR*     3.7     5.8    -      -       +      -
     33H  ALA*     2.9    46.9    +      -       +      +
     98H  ARG*     1.3   105.9    +      -       -      +
    100H  GLY*     1.3    65.9    +      -       -      +
    110H  PRO*     3.4    14.4    -      -       +      +
    112H  GLY*     3.2    45.2    +      -       -      +
    113H  ALA      3.8     5.6    -      -       -      -
    114H  PHE*     4.8     0.8    -      -       -      -
    116H  HIS*     3.4     4.9    -      -       -      -
     48S  PHE*     4.0    10.0    -      -       -      +
     51S  THR*     2.8    30.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 100 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98H  ARG      3.6     0.2    +      -       -      -
     99H  GLU*     1.3    77.0    -      -       -      +
    101H  THR*     1.3    66.9    +      -       -      +
    110H  PRO*     3.2     6.9    -      -       -      +
    111H  ILE*     2.9    32.2    +      -       -      +
    113H  ALA      3.1    13.3    +      -       -      -
    115H  ALA*     3.4    25.3    -      -       -      +
    116H  HIS*     4.4     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 101 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1H  GLN*     4.2    11.8    +      -       -      +
     32H  TYR*     3.4    20.2    -      -       +      -
     98H  ARG*     3.7    16.6    +      -       -      +
    100H  GLY*     1.3    79.8    -      -       -      +
    102H  THR*     1.3    65.2    +      -       -      +
    103H  GLY      4.0     5.5    +      -       -      +
    106H  TRP*     3.7    23.8    +      -       -      +
    108H  GLY*     3.2    29.7    +      -       -      +
    109H  LYS      3.2     5.6    -      -       -      +
    111H  ILE*     3.9     6.9    -      -       -      +
    115H  ALA*     5.1     0.2    -      -       -      +
    116H  HIS*     5.1     4.1    +      -       -      -
----------------------------------------------------------
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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