Contacts of the strand formed by residues 308 - 313 (chain B) in PDB entry 1YHQ


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 308 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  GLU*     4.7     3.1    -      -       +      +
     23B  THR*     3.4    43.5    -      -       +      +
     24B  PRO*     3.9    19.6    -      -       +      +
     42B  ALA*     3.9    18.8    -      -       +      -
     43B  GLY      3.5    16.8    -      -       -      +
     44B  TYR*     3.9    29.5    -      -       +      -
    146B  THR*     4.0     9.6    -      -       +      -
    156B  LYS*     5.4     2.0    -      -       -      +
    160B  ASP*     3.6    15.3    -      -       +      +
    162B  MET*     3.6    14.4    -      -       +      -
    204B  GLY*     4.5     1.2    -      -       -      -
    306B  LYS      3.7     1.6    +      -       -      -
    307B  ARG*     1.3    86.1    -      -       +      +
    309B  VAL*     1.3    65.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  ALA*     3.3     5.7    -      -       -      +
     43B  GLY      2.9    41.8    +      -       -      +
     45B  LYS*     4.5     9.4    -      -       +      +
     74B  ILE*     3.6    35.0    -      -       +      -
    202B  VAL*     4.1     7.6    -      -       +      -
    203B  ALA      3.5    11.4    -      -       -      +
    204B  GLY*     5.0     0.7    -      -       -      -
    301B  VAL*     3.5    25.8    -      -       +      -
    302B  PRO      3.8    11.2    -      -       -      +
    307B  ARG*     4.1     9.2    -      -       +      +
    308B  LEU*     1.3    79.9    -      -       -      +
    310B  ARG*     1.3    62.4    +      -       -      +
    311B  PHE*     4.3     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PRO*     3.4    23.1    +      -       +      -
     26B  PHE*     3.4    44.7    -      -       +      +
     29B  TRP*     4.1     3.2    -      -       -      -
     40B  GLY*     5.9     0.2    -      -       -      -
     41B  PHE      3.5    11.5    -      -       -      +
     42B  ALA*     4.2     0.7    -      -       +      -
    162B  MET*     3.0    55.6    -      -       +      +
    163B  GLU      3.4    10.3    +      -       -      -
    164B  THR*     3.2    19.8    +      -       -      +
    202B  VAL*     3.2     8.3    -      -       -      +
    203B  ALA*     3.0    38.2    +      -       +      +
    309B  VAL*     1.3    75.1    -      -       -      +
    311B  PHE*     1.3    60.9    +      -       -      +
   8987B   SR      2.4    40.8    -      -       -      -
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Residues in contact with PHE 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  PHE*     3.7     5.3    -      -       -      -
     40B  GLY*     3.2     5.7    -      -       -      -
     41B  PHE      2.8    37.7    +      -       -      +
     42B  ALA*     4.1     5.2    -      -       -      -
     43B  GLY      4.1    11.4    -      -       -      -
     74B  ILE*     3.5    33.2    -      -       +      -
     76B  THR*     3.5    24.9    -      -       +      -
    190B  MET*     4.1    11.9    -      -       +      -
    194B  PHE*     3.8    22.4    -      -       +      -
    200B  ALA*     4.6     3.4    -      -       +      -
    201B  ASP      3.6     2.2    -      -       -      -
    202B  VAL*     4.2    16.8    -      -       +      -
    269B  LEU*     4.3    17.3    -      -       +      -
    295B  THR*     4.5     6.3    -      -       +      -
    297B  VAL*     3.7    25.4    -      -       +      -
    309B  VAL*     4.3     4.9    -      -       +      -
    310B  ARG*     1.3    76.2    -      -       -      +
    312B  ARG*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   28060    C      4.5     0.4    +      -       -      -
   28070    U      2.6    30.3    +      -       -      -
     26B  PHE*     3.3    40.7    -      -       +      +
     27B  ASN      4.4     1.4    -      -       -      +
     28B  SER*     2.9    30.2    +      -       -      +
     29B  TRP*     4.8     2.5    -      -       +      -
     30B  PRO*     4.1    12.1    -      -       +      -
     39B  GLN      3.9     6.5    -      -       -      +
    194B  PHE*     3.7     4.0    -      -       -      -
    200B  ALA*     3.2     3.5    -      -       -      -
    201B  ASP*     2.7    84.2    +      -       -      +
    263B  THR*     4.1     8.6    +      -       -      +
    265B  LEU*     4.7     2.0    -      -       -      +
    311B  PHE*     1.3    78.4    -      -       -      +
    313B  PRO*     1.3    81.7    -      -       +      +
    314B  ALA      3.1     0.3    +      -       -      -
    315B  VAL*     3.5    19.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  PRO*     3.4    23.9    -      -       +      +
     39B  GLN*     3.2    31.0    -      -       +      +
    193B  ILE*     4.8     8.5    -      -       +      +
    194B  PHE*     3.7    23.3    -      -       +      -
    199B  TYR      4.0     2.9    -      -       -      +
    312B  ARG*     1.3    95.8    -      -       +      +
    314B  ALA*     1.3    70.3    +      -       -      +
    315B  VAL      3.1     2.8    +      -       -      -
----------------------------------------------------------
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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