Contacts of the strand formed by residues 309 - 315 (chain P) in PDB entry 5IY8


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 LYS 309 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262P  CYS      3.8     7.0    -      -       -      +
    263P  ASP*     3.8    33.2    -      -       +      +
    303P  LEU      3.6     2.0    -      -       -      +
    304P  ILE*     3.8     0.5    -      -       -      +
    305P  PHE*     3.3    28.6    +      -       +      -
    307P  SER*     3.2    19.0    +      -       -      +
    308P  GLY*     1.3    81.4    -      -       -      +
    310P  VAL*     1.3    62.9    +      -       -      +
     82Y    T      3.0    56.2    +      -       -      +
     83Y    A      3.6    18.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 310 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261P  SER*     3.4     3.3    -      -       -      -
    262P  CYS*     3.0    42.2    +      -       -      +
    264P  VAL*     4.5    14.4    -      -       +      -
    302P  LEU*     4.5     7.2    -      -       +      -
    303P  LEU      3.3     4.0    -      -       -      -
    304P  ILE*     3.8    29.4    -      -       +      -
    308P  GLY      3.7     9.9    -      -       -      +
    309P  LYS*     1.3    81.9    -      -       -      +
    311P  VAL*     1.3    72.8    +      -       -      +
    312P  LEU*     3.9    22.7    -      -       +      -
    325P  PHE*     4.7     9.2    -      -       +      -
    328P  ILE*     6.1     0.4    -      -       +      -
    332P  LEU*     4.5    11.7    -      -       +      -
     82Y    T      5.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 311 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259P  VAL*     4.2    12.1    -      -       +      -
    260P  GLY      3.4    13.0    -      -       -      +
    261P  SER*     4.3     8.3    -      -       -      +
    301P  VAL      3.7     0.5    -      -       -      +
    302P  LEU*     3.2     6.1    -      -       -      +
    303P  LEU*     2.8    46.7    +      -       +      +
    305P  PHE*     5.1     1.1    -      -       +      -
    310P  VAL*     1.3    80.3    -      -       -      +
    312P  LEU*     1.3    67.9    +      -       -      +
    313P  THR*     5.6     2.0    -      -       +      -
     13X    T      5.8     0.9    -      -       -      +
     81Y    A      3.5    39.0    -      -       +      +
     82Y    T      4.1    32.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 312 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163P  PRO*     4.9     5.8    -      -       +      -
    258P  MET      4.2     0.3    -      -       -      +
    259P  VAL*     3.5     5.7    -      -       -      +
    260P  GLY      2.9    43.0    +      -       -      +
    261P  SER*     4.8     2.2    -      -       -      +
    262P  CYS*     4.9     1.1    -      -       -      -
    300P  ILE*     4.0    11.2    -      -       +      -
    301P  VAL      3.3     4.3    -      -       -      -
    302P  LEU*     3.6    30.3    -      -       +      -
    310P  VAL*     3.9    16.6    -      -       +      +
    311P  VAL*     1.3    81.6    -      -       -      +
    313P  THR*     1.3    63.4    +      -       -      +
    315P  ALA*     6.0     0.2    -      -       -      -
    321P  ILE*     4.2    35.1    -      -       +      +
    324P  ALA*     4.1    21.1    -      -       +      -
    325P  PHE*     4.5    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 313 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257P  ASN*     3.1    14.4    +      -       -      -
    258P  MET      3.9     7.4    -      -       -      -
    259P  VAL*     4.2    11.5    -      -       -      +
    300P  ILE*     3.2     5.9    -      -       -      +
    301P  VAL*     2.8    43.0    +      -       +      +
    303P  LEU*     5.1     3.8    -      -       +      -
    311P  VAL*     5.6     2.9    -      -       +      -
    312P  LEU*     1.3    76.6    -      -       -      +
    314P  GLY*     1.3    68.0    +      -       -      +
    315P  ALA*     3.3     2.7    -      -       -      +
     13X    T      4.1    18.8    -      -       -      +
     14X    A      2.9    39.2    +      -       -      +
     81Y    A      6.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 314 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257P  ASN*     3.1    11.8    +      -       -      -
    299P  ARG      3.5    16.7    -      -       -      +
    300P  ILE*     3.9     5.4    -      -       -      +
    301P  VAL*     5.6     0.9    -      -       -      -
    313P  THR*     1.3    82.3    +      -       -      +
    315P  ALA*     1.3    62.6    +      -       -      +
    316P  LYS*     3.8    11.5    +      -       -      +
     14X    A      4.1     4.5    -      -       -      -
     15X    A      3.5    27.2    +      -       -      -
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Residues in contact with ALA 315 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257P  ASN*     3.0    13.1    +      -       -      +
    258P  MET*     3.1    41.0    +      -       +      +
    300P  ILE*     3.6    16.4    -      -       +      +
    313P  THR*     3.3     3.0    -      -       -      +
    314P  GLY*     1.3    80.7    -      -       -      +
    316P  LYS*     1.3    63.0    +      -       -      +
    317P  VAL      4.4     5.4    -      -       -      +
    321P  ILE*     3.7    32.1    -      -       +      -
----------------------------------------------------------
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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