Contacts of the strand formed by residues 113 - 122 (chain B) in PDB entry 3F5O


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 LEU 113 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  VAL*     4.5     4.0    -      -       +      -
    108B  LYS*     4.3     0.5    +      -       -      +
    109B  GLN*     3.7     0.9    -      -       -      -
    110B  GLY*     2.9    29.0    +      -       -      -
    111B  LYS      3.8     0.4    -      -       -      -
    112B  THR*     1.3    91.7    -      -       -      +
    114B  ALA*     1.3    60.8    +      -       -      +
    115B  PHE*     4.1    17.3    -      -       +      -
    135B  THR*     3.9    15.5    -      -       +      -
    136B  LYS      3.4    13.7    -      -       -      +
    137B  HIS*     4.1    11.7    -      -       +      +
    138B  LEU*     4.3     2.7    -      -       -      -
     84D  VAL*     3.9    24.2    -      -       +      -
    113D  LEU*     4.4    17.3    -      -       +      -
    137D  HIS*     4.1    11.2    -      -       +      +
    150D  COA      3.1    40.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  LEU*     3.7    33.7    -      -       +      -
    108B  LYS      3.4     9.2    -      -       -      +
    109B  GLN*     4.2     4.9    -      -       +      -
    113B  LEU*     1.3    74.5    -      -       -      +
    115B  PHE*     1.3    63.7    +      -       -      +
    116B  THR*     5.0     1.1    -      -       -      -
    134B  HIS      3.8     0.7    -      -       -      +
    135B  THR*     3.3     5.2    -      -       -      +
    136B  LYS*     2.9    35.9    +      -       +      +
    138B  LEU*     4.1    20.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  VAL*     3.7     1.4    -      -       -      +
    107B  LEU*     2.8    26.9    +      -       +      -
    108B  LYS*     2.9    29.8    +      -       +      +
    113B  LEU*     4.1    24.2    -      -       +      -
    114B  ALA*     1.3    74.9    -      -       -      +
    116B  THR*     1.3    67.1    +      -       -      +
    133B  ARG*     5.9     1.1    -      -       +      -
    134B  HIS      3.7     3.4    -      -       -      -
    135B  THR*     3.4    15.9    -      -       +      -
     89C  THR*     3.2    29.4    -      -       +      -
     90C  TYR      3.9     7.2    -      -       -      -
     91C  MET*     3.4    34.5    -      -       +      -
     84D  VAL*     3.5    32.3    -      -       +      -
    150D  COA      3.5    27.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  SER*     3.1    33.9    +      -       -      +
     71B  ALA*     5.3     0.2    -      -       +      -
     72B  LEU*     3.9    37.7    -      -       +      -
    105B  HIS      3.2    13.5    -      -       -      +
    106B  VAL*     4.2     8.1    -      -       +      -
    107B  LEU*     4.1     4.9    -      -       -      +
    114B  ALA      5.0     0.2    -      -       -      -
    115B  PHE*     1.3    81.7    -      -       -      +
    117B  SER*     1.3    60.8    +      -       -      +
    118B  VAL*     5.2     0.2    -      -       -      -
    133B  ARG*     3.1    10.8    -      -       -      +
    134B  HIS*     2.9    47.6    +      -       -      +
    136B  LYS*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  THR      3.8     0.2    -      -       -      +
    104B  ALA*     3.3     0.3    -      -       -      +
    105B  HIS*     2.6    71.6    +      -       -      -
    107B  LEU*     4.0    14.8    -      -       -      +
    116B  THR*     1.3    75.4    -      -       -      +
    118B  VAL*     1.3    66.9    +      -       -      +
    119B  ASP*     5.6     1.3    +      -       -      -
    131B  GLN*     5.7     4.9    -      -       -      -
    132B  GLY      3.3    10.3    -      -       -      -
    133B  ARG*     4.3     0.7    -      -       -      +
    131C  GLN*     4.2    13.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  LEU      4.9     0.4    -      -       -      +
     64B  VAL*     3.7    33.2    -      -       +      +
     67B  ILE*     5.1     0.4    -      -       +      -
     68B  SER*     3.7    29.6    -      -       -      +
    102B  ILE*     3.4    32.5    -      -       +      -
    103B  THR      3.2     9.2    -      -       -      +
    104B  ALA*     3.8     7.9    -      -       +      -
    116B  THR*     4.9     0.4    -      -       -      +
    117B  SER*     1.3    82.4    -      -       -      +
    119B  ASP*     1.3    67.9    +      -       -      +
    120B  LEU*     4.1    10.1    -      -       +      +
    130B  ALA      4.1     0.2    -      -       -      +
    131B  GLN*     3.2     6.1    -      -       -      +
    132B  GLY      2.8    35.4    +      -       -      +
    134B  HIS*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  VAL      3.5     1.7    -      -       -      +
    102B  ILE*     3.3     3.5    -      -       -      -
    103B  THR*     2.8    42.9    +      -       -      +
    105B  HIS*     6.5     0.4    -      -       -      -
    117B  SER*     5.6     1.9    +      -       -      -
    118B  VAL*     1.3    74.2    -      -       -      +
    120B  LEU*     1.3    61.3    +      -       -      +
    121B  THR*     4.1     7.4    -      -       +      +
    128B  LEU*     3.8    21.7    -      -       +      +
    130B  ALA      3.7     3.8    -      -       -      -
    131B  GLN*     3.0    32.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  LEU*     4.5     4.9    -      -       +      -
     60B  THR*     3.8    28.0    -      -       +      +
     63B  LEU*     3.9    27.4    -      -       +      -
     64B  VAL*     3.9    28.3    -      -       +      -
    100B  ILE*     4.2    12.8    -      -       +      -
    101B  VAL      3.3     4.5    -      -       -      +
    102B  ILE*     3.9    13.9    -      -       +      -
    118B  VAL*     4.1    10.1    -      -       +      +
    119B  ASP*     1.3    76.0    -      -       -      +
    121B  THR*     1.3    59.6    +      -       -      +
    128B  LEU*     3.6     1.0    -      -       -      +
    129B  ILE*     2.7    39.0    +      -       +      -
    130B  ALA*     2.9    26.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  ILE*     3.3     5.9    -      -       -      +
    101B  VAL*     2.8    51.2    +      -       -      +
    119B  ASP*     4.6     8.1    -      -       +      +
    120B  LEU*     1.3    80.1    -      -       -      +
    122B  ASN*     1.3    65.6    +      -       -      +
    123B  LYS*     5.4     0.2    -      -       -      -
    126B  GLY*     4.1    15.3    -      -       -      +
    127B  LYS      3.4     6.5    -      -       -      +
    128B  LEU*     3.7    26.9    -      -       +      +
    129B  ILE*     3.7     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  SER*     5.9     0.7    -      -       -      +
     93B  PRO      5.6     1.4    +      -       -      -
     98B  GLU*     3.6    36.6    +      -       -      +
     99B  ASP      3.8     9.5    +      -       -      +
    100B  ILE*     6.1     0.2    -      -       -      -
    121B  THR*     1.3    71.0    -      -       -      +
    123B  LYS*     1.3    56.9    +      -       -      +
    124B  ALA*     2.8    24.5    +      -       -      +
    125B  THR*     3.3    31.0    +      -       -      +
    126B  GLY*     2.7    34.0    +      -       -      -
    127B  LYS*     2.9    15.2    +      -       +      +
    129B  ILE*     3.7    16.1    -      -       +      +
----------------------------------------------------------
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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