Contacts of the strand formed by residues 119 - 128 (chain B) in PDB entry 5HAN


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 VAL 119 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332A  GLU*     4.1     3.6    -      -       -      +
     30B  MET*     4.2    10.3    -      -       +      -
     31B  LYS      4.0     4.0    -      -       -      +
     32B  PRO*     4.5     0.7    -      -       -      -
     33B  LYS*     3.6    13.0    -      -       -      +
     42B  THR*     3.8    15.7    -      -       +      -
     46B  PHE*     4.4     8.3    -      -       +      -
    113B  ASN      4.9     4.9    -      -       -      +
    116B  MET*     3.3    55.3    +      -       +      +
    117B  GLY      3.4     0.4    -      -       -      -
    118B  ASP*     1.3    83.3    -      -       -      +
    120B  GLU*     1.4    61.8    +      -       -      +
    121B  TYR*     3.3    33.0    -      -       -      +
    122B  ALA*     4.2     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  SER*     5.3     0.3    +      -       -      -
    299A  GLN*     3.6    28.4    +      -       +      +
    332A  GLU*     4.7     4.2    -      -       -      +
     31B  LYS*     2.8    43.0    +      -       +      +
     32B  PRO      3.9    12.9    -      -       -      +
     33B  LYS*     3.4    24.8    -      -       +      +
     34B  ALA*     4.8     4.3    +      -       -      +
    119B  VAL*     1.4    73.2    -      -       -      +
    121B  TYR*     1.3    79.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  GLN*     3.8    31.4    -      -       -      +
     29B  ILE*     4.2    21.2    -      -       +      +
     30B  MET*     3.4     3.8    -      -       -      -
     31B  LYS*     3.0    77.5    +      -       +      +
     80B  SER*     5.0     4.6    +      -       -      -
    119B  VAL*     3.3    10.9    -      -       -      +
    120B  GLU*     1.3    90.6    -      -       +      +
    122B  ALA*     1.3    65.4    +      -       -      +
    123B  LYS*     6.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  TYR*     5.0     2.2    -      -       +      -
     29B  ILE      3.3     7.9    -      -       -      -
     30B  MET*     4.0    13.2    -      -       +      -
     46B  PHE*     3.5    35.7    -      -       +      -
     82B  MET*     4.9     1.1    -      -       +      -
    110B  ILE*     5.0     0.9    -      -       -      -
    113B  ASN      5.5     0.4    -      -       -      +
    114B  GLN*     2.9    35.7    +      -       -      +
    119B  VAL*     4.2     4.5    -      -       +      +
    121B  TYR*     1.3    79.1    -      -       -      +
    123B  LYS*     1.3    59.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  TYR*     3.1     5.7    -      -       -      -
     29B  ILE*     2.9    34.6    +      -       +      +
    110B  ILE*     4.8     1.8    -      -       -      -
    121B  TYR*     5.4     1.3    -      -       +      -
    122B  ALA*     1.3    75.0    -      -       -      +
    124B  MET*     1.3    71.7    +      -       -      +
    125B  TYR*     3.5    30.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  CYS*     3.8    11.2    -      -       +      -
     27B  ALA      3.5     7.6    -      -       -      +
     28B  TYR*     3.8    17.3    -      -       +      +
    105B  PHE*     4.1     9.2    -      -       +      -
    109B  THR*     3.3    45.8    -      -       -      +
    110B  ILE*     4.2    18.9    -      -       +      +
    123B  LYS*     1.3    83.1    -      -       -      +
    125B  TYR*     1.3    59.8    +      -       -      +
    126B  ASP      3.5    25.1    -      -       -      +
    127B  PHE*     4.1    23.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  ALA*     2.9    13.4    +      -       +      +
     29B  ILE*     3.5    40.2    -      -       +      +
    123B  LYS*     3.5    41.8    +      -       +      +
    124B  MET*     1.3    74.6    -      -       -      +
    126B  ASP*     1.3    65.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  CYS*     3.5     0.3    -      -       -      -
     27B  ALA*     3.0    36.7    +      -       +      +
    124B  MET*     3.5    10.2    -      -       -      +
    125B  TYR*     1.3    80.7    -      -       +      +
    127B  PHE*     1.3    91.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  VAL*     5.0     0.9    -      -       +      -
     25B  LEU      3.1    13.2    -      -       -      +
     26B  CYS*     4.0     7.0    -      -       -      -
    102B  ILE*     5.6     7.4    -      -       +      -
    105B  PHE*     3.7    42.6    -      +       +      -
    124B  MET*     4.1     8.3    -      -       -      -
    126B  ASP*     1.3    93.6    +      -       -      +
    128B  TYR*     1.3    66.9    +      -       -      +
    129B  VAL*     4.4    20.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU      5.6     0.2    -      -       -      -
     18B  ILE*     3.8    43.8    +      -       +      +
     21B  GLY*     5.9     0.2    -      -       -      -
     23B  HIS      4.1    10.5    -      -       -      -
     24B  VAL*     3.4    13.2    -      -       -      +
     25B  LEU*     2.7    54.9    +      -       +      -
    127B  PHE*     1.3    75.2    -      -       -      +
    129B  VAL*     1.3    73.0    +      -       -      +
    130B  PRO*     3.7    28.1    -      -       +      +
    131B  PRO*     4.0     9.5    -      -       -      +
----------------------------------------------------------
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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