Contacts of the strand formed by residues 199 - 204 (chain B) in PDB entry 1S5H


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 THR 199 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  TRP*     3.4     8.5    -      -       -      -
    160B  ASN*     2.8    39.8    +      -       -      -
    197B  THR*     3.7    14.2    +      -       -      +
    198B  VAL*     1.3    77.9    +      -       -      +
    200B  CYS*     1.3    62.9    +      -       -      +
    201B  ASN*     4.2     7.5    -      -       -      +
    212B  ASP*     4.0    12.8    -      -       +      -
    213B  LYS      3.2    35.2    -      -       -      +
    214B  LYS*     3.6    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  VAL*     3.7    19.3    -      -       -      -
    145B  CYS*     3.1    42.4    -      -       -      -
    157B  VAL*     4.5     2.5    -      -       +      -
    158B  THR      3.3     6.3    -      -       -      +
    159B  TRP*     3.4    26.1    -      -       +      -
    199B  THR*     1.3    74.4    -      -       -      +
    201B  ASN*     1.3    60.5    +      -       -      +
    202B  VAL*     4.3     3.6    -      -       -      -
    211B  VAL      3.9     0.7    -      -       -      +
    212B  ASP*     3.4     3.3    -      -       -      -
    213B  LYS*     3.0    38.0    +      -       -      -
    215B  ILE*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  THR      3.3     5.7    -      -       -      +
    157B  VAL*     3.3     2.4    -      -       -      -
    158B  THR*     2.6    57.4    +      -       -      +
    160B  ASN*     3.7     1.1    +      -       -      +
    161B  SER*     2.7    40.1    +      -       -      +
    199B  THR*     4.3    10.5    +      -       -      +
    200B  CYS*     1.3    75.7    -      -       -      +
    202B  VAL*     1.3    60.9    +      -       -      +
    203B  ALA      4.1     0.2    -      -       -      -
    210B  LYS*     4.5    17.7    -      -       +      -
    211B  VAL      3.6     4.9    -      -       -      +
    212B  ASP*     2.6    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  PRO*     4.1    17.3    -      -       +      +
    126B  VAL*     3.9    31.6    -      -       +      -
    147B  VAL*     3.9    37.9    -      -       +      -
    155B  VAL*     4.4     8.1    -      -       +      -
    156B  THR      3.6     2.9    -      -       -      +
    157B  VAL*     4.3    10.8    -      -       +      -
    200B  CYS*     4.3     9.0    -      -       -      -
    201B  ASN*     1.3    77.6    -      -       -      +
    203B  ALA*     1.3    66.8    +      -       -      +
    204B  HIS*     5.5     0.2    -      -       -      +
    209B  THR*     3.8     1.4    +      -       -      +
    210B  LYS*     3.1     4.9    -      -       -      +
    211B  VAL*     2.9    39.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  VAL*     3.1     8.7    -      -       -      +
    156B  THR*     3.0    46.1    +      -       -      +
    201B  ASN      4.1     0.4    +      -       -      -
    202B  VAL*     1.3    74.7    -      -       -      +
    204B  HIS*     1.3    59.5    -      -       -      +
    205B  PRO*     3.5     8.2    -      -       +      +
    209B  THR      3.4     5.8    -      -       -      +
    210B  LYS*     4.0    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  THR*     4.3     0.4    -      -       +      -
    122B  THR      3.4    12.6    -      -       -      -
    123B  PRO*     3.8     4.8    -      -       -      +
    124B  PRO*     3.6    18.8    -      -       +      -
    150B  TYR*     3.9     5.7    -      +       -      -
    151B  PHE      3.3    22.8    +      -       -      -
    152B  PRO      2.9    22.4    +      -       -      -
    154B  PRO      3.3    19.5    -      -       -      -
    155B  VAL*     3.6    13.0    -      -       +      -
    202B  VAL      4.1     0.4    +      -       -      -
    203B  ALA*     1.3    73.1    -      -       -      +
    205B  PRO*     1.3    67.3    -      -       -      +
    206B  ALA*     3.2    15.7    -      -       +      +
    207B  SER*     2.7    39.6    +      -       -      -
    208B  SER      3.2     7.1    +      -       -      -
    209B  THR*     2.7    25.2    +      -       -      +
----------------------------------------------------------
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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