Contacts of the strand formed by residues 311 - 320 (chain I) in PDB entry 5LK5


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 PHE 311 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81I  PHE*     3.4    10.7    -      -       +      -
     83I  PRO*     3.0    24.3    -      -       -      +
     84I  PHE*     2.7    52.1    +      +       +      +
     85I  SER*     4.7     0.2    -      -       -      -
     86I  ASN*     3.4    30.3    -      -       +      -
     91I  LEU*     3.9    20.2    -      -       +      -
    112I  LEU*     3.8    29.8    -      -       +      -
    113I  PHE      3.6     4.7    -      -       -      +
    129I  ASN*     3.4    30.5    -      -       +      -
    130I  ILE*     3.9     5.4    -      -       +      -
    308I  TYR*     3.6    27.1    -      +       +      -
    310I  ASN*     1.3    76.5    -      -       -      +
    312I  GLY*     1.3    57.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 312 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80I  SER*     3.2     6.2    -      -       -      -
     81I  PHE*     2.9    42.5    +      -       -      +
     83I  PRO*     4.4     0.9    -      -       -      -
    113I  PHE      2.9     7.4    +      -       -      -
    115I  ASN*     3.6    24.8    +      -       -      +
    310I  ASN*     3.5     2.2    +      -       -      -
    311I  PHE*     1.3    74.3    -      -       -      +
    313I  VAL*     1.3    66.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 313 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78I  SER*     3.6    31.6    -      -       -      +
     79I  ALA      3.3    11.7    -      -       -      +
     80I  SER*     4.1     6.3    -      -       -      -
     81I  PHE*     3.6     7.1    -      -       -      -
    111I  LYS      3.7     0.5    -      -       -      +
    112I  LEU*     3.5     3.5    -      -       -      +
    113I  PHE*     2.7    46.1    +      -       +      +
    114I  PRO      4.6     6.3    -      -       -      +
    115I  ASN*     4.6     7.4    -      -       -      +
    117I  LEU*     4.1    20.6    -      -       +      +
    119I  GLN*     4.0    22.9    -      -       +      +
    312I  GLY*     1.3    85.5    -      -       -      +
    314I  LEU*     1.3    63.8    +      -       -      +
    315I  GLY      4.3     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 314 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23I  PHE*     3.8    24.7    -      -       +      -
     37I  TRP*     4.1    13.8    -      -       +      -
     78I  SER*     3.4     1.6    -      -       -      -
     79I  ALA      2.9    38.2    +      -       -      +
     81I  PHE*     3.5    11.9    -      -       +      -
     93I  VAL*     4.9     3.4    -      -       +      -
    110I  VAL*     4.0    26.0    -      -       +      -
    111I  LYS      3.4     3.4    -      -       -      +
    112I  LEU*     3.3    26.9    -      -       +      -
    313I  VAL*     1.3    73.0    -      -       -      +
    315I  GLY*     1.3    59.4    +      -       -      +
    316I  LEU*     5.7     0.4    -      -       +      -
    330I  PHE*     3.2    40.6    -      -       +      -
    332I  ILE*     3.9    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 315 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77I  LEU      3.6     7.2    -      -       -      -
     78I  SER*     3.7    10.3    -      -       -      -
    110I  VAL*     3.6     6.4    -      -       -      +
    111I  LYS*     2.8    41.1    +      -       -      +
    113I  PHE*     4.1     6.0    -      -       -      -
    122I  MET*     4.1    10.1    -      -       -      -
    313I  VAL      4.1     1.4    -      -       -      -
    314I  LEU*     1.3    75.9    -      -       -      +
    316I  LEU*     1.3    64.4    +      -       -      -
    317I  ASP*     3.7     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 316 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37I  TRP*     4.1    12.1    -      -       +      -
     49I  PHE*     3.9    31.9    -      -       +      -
     66I  LEU*     3.8    29.2    -      -       +      -
     75I  TYR      3.6     0.9    -      -       -      +
     76I  ALA*     3.3     6.4    +      -       -      -
     77I  LEU*     2.8    35.2    +      -       +      +
    109I  TYR      4.2     8.7    -      -       -      +
    110I  VAL*     3.7    28.3    -      -       +      -
    122I  MET*     3.6     0.6    -      -       -      +
    314I  LEU*     5.7     0.7    -      -       +      -
    315I  GLY*     1.3    71.0    -      -       -      +
    317I  ASP*     1.3    58.9    +      -       -      +
    318I  LEU*     4.1     7.4    -      -       +      -
    327I  PHE*     4.1    22.7    -      -       +      -
    330I  PHE*     4.1    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 317 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46I  PHE*     5.4     1.6    -      -       -      -
     75I  TYR      3.3    12.3    -      -       -      +
     76I  ALA*     3.9     6.4    -      -       -      +
    109I  TYR*     3.5    18.7    +      -       -      -
    111I  LYS*     3.5    32.2    +      -       +      +
    113I  PHE*     5.1     0.6    -      -       +      -
    122I  MET*     4.0    18.4    -      -       +      -
    123I  HIS*     3.2    27.8    +      -       -      +
    124I  GLY*     3.2    27.2    +      -       -      -
    315I  GLY      3.7     2.9    +      -       -      -
    316I  LEU*     1.3    75.6    -      -       -      +
    318I  LEU*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 318 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49I  PHE*     5.2     0.7    -      -       +      -
     68I  THR*     4.8     5.4    -      -       +      -
     73I  ARG      4.0     0.3    -      -       -      +
     74I  PHE*     3.3     8.6    -      -       -      +
     75I  TYR*     2.7    57.3    +      -       +      +
    107I  GLY*     3.8    21.1    -      -       -      +
    109I  TYR*     3.6    44.2    -      -       +      +
    316I  LEU*     4.5     9.0    -      -       +      -
    317I  ASP*     1.3    82.7    +      -       -      +
    319I  TRP*     1.3    69.3    +      -       -      +
    320I  GLN*     4.3     9.9    -      -       -      +
    327I  PHE*     3.9    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 319 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72I  ALA*     3.4    33.0    -      -       +      -
     73I  ARG*     3.3    37.5    -      -       -      -
     74I  PHE*     3.6    44.0    -      +       +      -
    105I  CYS*     4.8    13.7    -      -       -      -
    106I  GLY*     3.3     4.8    -      -       -      -
    107I  GLY*     3.0    26.2    +      -       -      +
    109I  TYR*     4.8     3.8    +      -       -      +
    318I  LEU*     1.3    77.8    -      -       -      +
    320I  GLN*     1.3    69.6    +      -       -      +
    321I  VAL*     3.7    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 320 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68I  THR*     2.6    35.8    +      -       -      +
     70I  GLN      4.7     0.6    -      -       -      +
     71I  LYS      4.1     0.2    -      -       -      -
     72I  ALA*     3.0    24.9    +      -       -      -
     73I  ARG      3.0    11.6    +      -       -      -
     75I  TYR*     4.1    15.3    -      -       +      -
    103I  ILE*     3.6    23.3    -      -       +      +
    105I  CYS      3.9     2.7    -      -       -      -
    106I  GLY*     3.9     0.9    -      -       -      -
    107I  GLY      3.1    24.0    +      -       -      -
    318I  LEU*     4.3     5.7    -      -       +      +
    319I  TRP*     1.3    83.4    -      -       -      +
    321I  VAL*     1.3    62.6    +      -       -      +
    322I  LYS      3.7     6.7    -      -       -      +
    323I  SER*     3.6     9.6    -      -       -      -
    325I  THR*     2.9    30.8    +      -       -      +
    327I  PHE*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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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