Contacts of the strand formed by residues 120 - 130 (chain B) in PDB entry 6YB9


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 120 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  GLY      5.7     0.8    +      -       -      -
    319A  ASP*     5.7     5.3    -      -       -      +
    102B  ARG*     3.4    14.8    -      -       +      +
    103B  ILE*     3.9    31.2    -      -       +      -
    118B  GLY      3.3    11.6    +      -       -      +
    119B  TYR*     1.3    90.4    +      -       -      +
    121B  PHE*     1.3    60.0    +      -       -      +
    122B  TYR*     3.7    44.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  ARG*     3.7    37.2    -      -       +      +
    102B  ARG*     2.9    46.2    +      -       -      -
    104B  ALA*     3.6    30.1    -      -       +      -
    108B  PHE*     3.6    45.5    -      +       -      -
    119B  TYR*     4.0    21.8    -      +       -      -
    120B  LYS*     1.3    70.7    -      -       -      +
    122B  TYR*     1.3    59.4    +      -       -      +
    123B  PRO      3.3    16.9    -      -       -      +
    124B  PRO      3.6     0.7    -      -       -      -
    125B  LYS*     3.8    28.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311A  ARG*     4.2    15.8    +      -       -      +
    314A  ALA*     3.8    17.3    -      -       -      +
    315A  GLU*     4.0    41.7    -      -       +      +
    318A  GLY*     3.6    25.8    -      -       -      -
    319A  ASP*     4.1    12.7    -      -       +      +
    102B  ARG*     3.7    16.8    -      -       -      -
    120B  LYS*     3.7    48.0    +      -       +      +
    121B  PHE*     1.3    72.6    -      -       -      +
    123B  PRO*     1.4    62.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310A  LEU      6.0     0.2    -      -       -      +
    311A  ARG*     4.9     9.6    -      -       +      -
    314A  ALA*     3.7    21.5    -      -       +      +
    102B  ARG*     4.6     0.7    -      -       -      +
    121B  PHE*     3.3    12.7    -      -       -      +
    122B  TYR*     1.4    84.2    +      -       -      +
    124B  PRO*     1.4    79.6    -      -       +      +
    125B  LYS*     3.4     2.1    +      -       -      -
    170B  GLN*     3.9    22.0    -      -       -      +
    174B  GLU*     5.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  CYS*     3.4    24.0    -      -       -      -
    101B  ARG      3.2    13.0    -      -       -      +
    102B  ARG*     3.5    33.7    -      -       -      +
    121B  PHE      3.6     5.4    -      -       -      +
    123B  PRO*     1.4    90.9    -      -       +      +
    125B  LYS*     1.3    62.0    +      -       -      +
    126B  VAL*     3.7     1.4    +      -       -      +
    170B  GLN*     2.9    32.9    +      -       +      -
    173B  PHE*     4.1    15.7    -      -       +      -
    174B  GLU*     4.2    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  VAL      3.6     0.9    -      -       -      +
    100B  CYS*     3.1     5.7    -      -       -      -
    101B  ARG*     2.8    40.5    +      -       +      +
    108B  PHE*     4.4    12.3    -      -       +      -
    121B  PHE*     3.8    41.6    -      -       +      +
    123B  PRO      3.4     2.7    +      -       -      -
    124B  PRO*     1.3    70.0    -      -       -      +
    126B  VAL*     1.3    68.1    +      -       -      +
    127B  GLU*     4.0    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  TRP*     4.1    17.3    -      -       +      -
     99B  VAL      3.2     8.1    -      -       -      +
    100B  CYS*     4.2     7.9    -      -       -      -
    124B  PRO      3.7     6.7    +      -       -      +
    125B  LYS*     1.3    82.9    -      -       -      +
    127B  GLU*     1.3    69.4    -      -       -      +
    128B  LEU*     5.1     4.2    -      -       +      +
    166B  SER*     3.7    39.9    -      -       -      +
    169B  THR*     4.1    11.4    -      -       +      -
    170B  GLN*     4.2    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  GLU      3.7     0.7    -      -       -      +
     98B  TRP*     3.5     4.5    -      -       -      -
     99B  VAL*     2.8    36.3    +      -       +      +
    101B  ARG*     2.9    38.2    +      -       +      +
    108B  PHE*     3.5    17.1    -      -       -      -
    111B  ARG*     2.6    33.7    +      -       -      -
    125B  LYS*     4.0    13.9    -      -       +      +
    126B  VAL*     1.3    79.8    -      -       -      +
    128B  LEU*     1.3    66.3    -      -       -      +
    129B  PHE*     3.7    14.2    -      -       +      -
    139B  GLN*     3.8    16.7    +      -       -      +
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Residues in contact with LEU 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ILE*     4.1     8.7    -      -       +      -
     97B  GLU      3.5     4.5    -      -       -      -
     98B  TRP*     3.6    31.0    -      -       +      +
    126B  VAL*     5.1     4.5    -      -       +      +
    127B  GLU*     1.3    79.2    -      -       -      +
    129B  PHE*     1.3    63.8    +      -       -      +
    139B  GLN*     3.4    10.8    -      -       -      +
    140B  TRP*     3.0    40.5    +      -       +      +
    141B  SER      4.3     9.4    -      -       -      +
    142B  GLU*     4.4    24.7    -      -       +      +
    145B  LEU*     3.5    41.1    -      -       +      -
    166B  SER*     5.5     1.1    -      -       -      +
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Residues in contact with PHE 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ILE*     3.3     6.8    -      -       -      +
     97B  GLU*     2.6    59.4    +      -       +      +
     99B  VAL*     3.7    23.6    -      -       +      -
    101B  ARG*     4.1     4.9    -      -       -      -
    107B  SER*     4.3     4.3    -      -       -      -
    111B  ARG*     3.7    32.8    -      -       -      -
    127B  GLU*     3.7    31.2    -      -       +      -
    128B  LEU*     1.3    74.3    -      -       -      +
    130B  PHE*     1.3    62.6    +      -       -      +
    131B  LYS      3.7     0.2    +      -       -      -
    137B  ASP*     3.4    32.5    -      -       +      +
    138B  PRO      3.5     3.1    -      -       -      -
    139B  GLN*     3.7    25.6    -      -       +      -
    703B  OK8      4.5     4.3    -      +       -      -
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Residues in contact with PHE 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  PRO*     3.6    24.5    -      -       +      -
     96B  ILE*     3.9     5.3    -      -       +      +
    128B  LEU      4.4     0.2    -      -       -      -
    129B  PHE*     1.3    70.8    -      -       -      +
    131B  LYS*     1.3    71.2    +      -       -      +
    132B  ASP*     3.5    27.0    +      -       +      -
    137B  ASP*     3.3    26.0    -      -       -      +
    138B  PRO*     3.1    18.9    +      -       +      +
    140B  TRP*     3.4    59.9    -      +       +      +
    150B  PHE*     4.1    19.1    -      +       -      -
----------------------------------------------------------
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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