Contacts of the strand formed by residues 219 - 227 (chain v) in PDB entry 6FF7


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 HIS 219 (chain v).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681u  PRO*     3.7    34.1    -      -       +      +
    158v  LEU*     5.3     9.0    -      -       -      -
    212v  GLU      3.9     1.4    -      -       -      +
    213v  LEU*     3.8     4.9    -      -       -      +
    214v  ASP*     3.4    25.5    +      -       +      +
    217v  LEU*     3.5     5.5    -      -       +      +
    218v  ASN*     1.3    80.2    -      -       -      +
    220v  VAL*     1.3    65.2    +      -       -      +
    221v  VAL*     5.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 220 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141v  VAL*     5.7     5.2    -      -       +      -
    158v  LEU*     5.1     9.1    -      -       +      +
    159v  GLU      3.6    26.1    +      -       -      +
    160v  ALA*     4.5    14.3    -      -       +      -
    211v  TYR*     5.4     9.6    -      -       +      -
    212v  GLU      3.9     7.4    -      -       -      +
    213v  LEU*     5.0     4.5    -      -       +      +
    219v  HIS*     1.3    77.7    -      -       -      +
    221v  VAL*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 221 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211v  TYR*     3.7     6.5    -      -       -      -
    212v  GLU*     3.5    28.8    +      -       +      +
    219v  HIS*     4.2     2.0    +      -       +      -
    220v  VAL*     1.3    74.4    -      -       -      +
    222v  ARG*     1.3    62.5    +      -       -      +
    223v  LYS*     3.2     8.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 222 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209v  THR*     6.3     2.9    -      -       -      -
    210v  PHE      4.0     5.4    -      -       -      +
    211v  TYR*     5.2     1.6    -      -       -      +
    221v  VAL*     1.3    71.5    -      -       -      +
    223v  LYS*     1.3    64.1    +      -       -      +
    224v  TYR      3.8     4.0    -      -       -      +
    225v  SER*     6.2     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 223 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210v  PHE*     3.1    18.6    +      -       +      +
    212v  GLU*     4.3    22.2    -      -       +      -
    221v  VAL*     3.2     3.8    +      -       +      +
    222v  ARG*     1.3    75.8    -      -       -      +
    224v  TYR*     1.3    62.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 224 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208v  LEU      4.4     1.6    -      -       -      +
    209v  THR*     3.3     3.1    -      -       -      -
    210v  PHE*     2.9    41.3    +      -       +      +
    222v  ARG*     5.1     3.0    -      -       -      +
    223v  LYS*     1.3    80.3    +      -       +      +
    225v  SER*     1.3    63.4    +      -       -      +
    226v  GLU*     5.3     3.1    -      -       +      +
    261v  PHE*     5.3    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 225 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207v  THR*     5.1     9.4    -      -       -      -
    208v  LEU      3.3     7.2    -      -       -      -
    209v  THR*     4.6     9.2    -      -       -      -
    222v  ARG*     6.2     3.8    -      -       -      -
    224v  TYR*     1.3    77.4    -      -       -      +
    226v  GLU*     1.3    60.0    +      -       -      +
    227v  PRO      4.3     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 226 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207v  THR*     4.2     2.2    -      -       -      -
    208v  LEU*     2.9    37.9    +      -       +      +
    224v  TYR*     6.0     3.1    -      -       +      -
    225v  SER*     1.3    74.7    -      -       -      +
    227v  PRO*     1.3    66.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 227 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205v  GLN*     5.8     2.9    -      -       +      +
    206v  GLN      3.4     9.6    -      -       -      +
    207v  THR*     4.1     5.1    -      -       -      -
    225v  SER      4.3     0.4    -      -       -      -
    226v  GLU*     1.3    80.7    -      -       -      +
    228v  LEU*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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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