Contacts of the strand formed by residues 311 - 320 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81F  PHE*     3.4    10.8    -      -       +      -
     83F  PRO*     3.0    23.6    -      -       -      +
     84F  PHE*     2.7    49.5    +      +       +      +
     85F  SER*     4.7     0.2    -      -       -      -
     86F  ASN*     3.4    29.6    -      -       +      -
     91F  LEU*     3.9    11.7    -      -       +      -
    112F  LEU*     3.8    31.4    -      -       +      -
    113F  PHE      3.6     4.0    -      -       -      +
    129F  ASN*     3.4    31.2    -      -       +      -
    130F  ILE*     3.9    13.9    -      -       +      -
    308F  TYR*     3.6    27.6    -      +       +      -
    310F  ASN*     1.3    78.2    -      -       -      +
    312F  GLY*     1.3    58.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 312 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80F  SER*     3.2     7.1    -      -       -      -
     81F  PHE*     2.9    41.9    +      -       -      +
     83F  PRO*     4.4     0.9    -      -       -      -
    113F  PHE      2.9     7.4    +      -       -      -
    115F  ASN*     3.7    24.0    -      -       -      +
    310F  ASN*     3.5     2.8    +      -       -      -
    311F  PHE*     1.3    74.3    -      -       -      +
    313F  VAL*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 313 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78F  SER*     3.4    33.9    -      -       -      +
     79F  ALA      3.3    10.5    -      -       -      +
     80F  SER*     4.1     9.6    -      -       -      -
     81F  PHE*     3.6     8.7    -      -       -      -
    111F  LYS      3.7     0.3    -      -       -      +
    112F  LEU*     3.5     3.1    -      -       -      -
    113F  PHE*     2.7    45.7    +      -       +      +
    114F  PRO      4.6     7.4    -      -       -      +
    115F  ASN*     4.7     6.3    -      -       -      +
    117F  LEU*     4.1    20.6    -      -       +      +
    119F  GLN*     4.1    18.2    -      -       +      +
    312F  GLY*     1.3    85.1    -      -       -      +
    314F  LEU*     1.3    63.1    +      -       -      +
    315F  GLY      4.3     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 314 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23F  PHE*     4.7    12.8    -      -       +      -
     37F  TRP*     4.1    14.9    -      -       +      -
     78F  SER*     3.3     1.4    -      -       -      -
     79F  ALA*     2.9    37.1    +      -       +      +
     81F  PHE*     3.5    12.6    -      -       +      -
     93F  VAL*     4.9     3.8    -      -       +      -
     94F  GLN      6.2     0.2    -      -       -      +
     95F  PHE*     6.1     0.4    -      -       +      -
    110F  VAL*     4.1    20.0    -      -       +      -
    111F  LYS      3.3     8.1    -      -       -      +
    112F  LEU*     4.1    10.5    -      -       +      +
    313F  VAL*     1.3    74.4    -      -       -      +
    315F  GLY*     1.3    67.1    +      -       -      +
    316F  LEU*     4.7     1.1    -      -       +      +
    330F  PHE*     4.0    37.0    -      -       +      -
    332F  ILE*     3.8    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 315 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77F  LEU      3.6     7.2    -      -       -      -
     78F  SER*     3.8     8.3    -      -       -      -
    110F  VAL*     3.6     6.8    -      -       -      +
    111F  LYS*     2.8    40.3    +      -       -      +
    113F  PHE*     4.1     4.6    -      -       -      -
    122F  MET*     4.1    12.8    -      -       -      -
    313F  VAL      4.0     0.8    -      -       -      -
    314F  LEU*     1.3    76.9    -      -       -      +
    316F  LEU*     1.3    64.2    +      -       -      -
    317F  ASP*     3.7     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 316 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37F  TRP*     4.1    11.0    -      -       +      -
     49F  PHE*     3.8    31.3    -      -       +      -
     66F  LEU*     3.7    29.2    -      -       +      -
     75F  TYR      3.6     1.2    -      -       -      +
     76F  ALA*     3.3     6.8    +      -       -      -
     77F  LEU*     2.8    34.2    +      -       +      +
    109F  TYR      4.2     9.2    -      -       -      +
    110F  VAL*     3.8    28.0    -      -       +      -
    122F  MET*     4.1     0.2    -      -       -      -
    314F  LEU*     4.3     0.4    +      -       +      -
    315F  GLY*     1.3    70.8    -      -       -      +
    317F  ASP*     1.3    58.4    +      -       -      +
    318F  LEU*     4.1     7.2    -      -       +      -
    327F  PHE*     4.1    21.8    -      -       +      -
    330F  PHE*     4.0    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 317 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46F  PHE*     5.4     1.6    -      -       -      -
     75F  TYR      3.3    12.3    -      -       -      +
     76F  ALA*     3.9     6.1    -      -       -      +
    109F  TYR*     3.5    10.2    +      -       -      -
    111F  LYS*     3.5    42.4    +      -       +      +
    113F  PHE*     5.4     0.2    -      -       -      -
    122F  MET*     4.0    17.7    -      -       +      -
    123F  HIS*     3.2    27.2    -      -       -      +
    124F  GLY*     3.2    26.8    +      -       -      -
    315F  GLY      3.7     3.3    +      -       -      -
    316F  LEU*     1.3    74.7    -      -       -      +
    318F  LEU*     1.3    65.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 318 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49F  PHE*     5.2     0.9    -      -       +      -
     68F  THR*     4.7     5.6    -      -       +      -
     73F  ARG      4.0     0.2    -      -       -      +
     74F  PHE*     3.3     9.7    -      -       -      -
     75F  TYR*     2.8    53.5    +      -       +      +
    107F  GLY*     3.8    21.3    -      -       -      +
    109F  TYR*     3.6    44.9    -      -       +      +
    316F  LEU*     4.5     8.1    -      -       +      -
    317F  ASP*     1.3    82.4    -      -       -      +
    319F  TRP*     1.3    62.7    +      -       -      +
    320F  GLN*     3.9    20.6    -      -       +      +
    327F  PHE*     3.9    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 319 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72F  ALA*     3.5    32.3    -      -       +      -
     73F  ARG*     3.3    38.6    -      -       -      -
     74F  PHE*     3.6    42.0    -      +       +      -
    105F  CYS*     4.8    14.2    -      -       -      -
    106F  GLY*     3.3     5.3    -      -       -      -
    107F  GLY*     3.0    26.2    +      -       -      +
    109F  TYR*     4.8     3.4    +      -       -      +
    318F  LEU*     1.3    76.1    -      -       -      +
    320F  GLN*     1.3    71.0    +      -       -      +
    321F  VAL*     3.7    24.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 320 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68F  THR*     2.5    34.8    +      -       +      +
     70F  GLN      4.7     0.8    -      -       -      +
     72F  ALA*     3.0     6.6    +      -       -      -
     73F  ARG      3.0    31.3    +      -       -      -
     75F  TYR*     4.2    11.9    -      -       +      -
    103F  ILE*     3.7    12.2    -      -       +      +
    105F  CYS      3.9     4.3    -      -       -      -
    106F  GLY*     4.1     5.8    -      -       -      -
    107F  GLY      3.1    20.6    +      -       -      -
    318F  LEU*     3.9    10.8    -      -       +      +
    319F  TRP*     1.3    85.8    -      -       -      +
    321F  VAL*     1.3    66.2    +      -       -      +
    322F  LYS      4.3     3.1    -      -       -      +
    323F  SER*     3.6    11.2    -      -       -      -
    325F  THR*     2.9    29.8    +      -       -      +
    327F  PHE*     5.0     0.8    -      -       -      -
----------------------------------------------------------
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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