Contacts of the strand formed by residues 310 - 319 (chain B) in PDB entry 5YL4


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 TYR 310 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267B  MET*     5.0     2.5    -      -       -      -
    294B  PHE*     4.5    11.2    +      +       -      -
    299B  MET*     3.7     9.0    -      -       -      +
    305B  PRO*     3.2    37.2    -      -       +      +
    309B  ARG*     1.3    70.5    -      -       -      +
    311B  LEU*     1.3    62.7    +      -       -      +
    312B  THR      4.2     5.6    -      -       -      +
    313B  VAL*     3.8    18.6    -      -       +      -
    340B  TYR*     2.7    27.1    +      -       +      +
    341B  PHE*     3.9    28.0    -      +       +      -
    342B  VAL*     3.1    26.7    +      -       -      +
    348B  ASN*     3.4     3.1    +      -       -      -
    367B  PHE*     3.4    33.4    -      +       -      -
    369B  GLY*     4.2     6.5    -      -       -      -
    370B  ASN      3.9     1.3    -      -       -      -
    371B  SER*     3.8    24.9    -      -       -      -
    505B  MES      4.1    17.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259B  PRO*     4.0    28.7    -      -       +      -
    260B  PHE*     4.7     1.6    -      -       +      -
    263B  LEU*     4.4    25.1    -      -       +      -
    310B  TYR*     1.3    73.2    -      -       -      +
    312B  THR*     1.3    69.5    +      -       -      +
    342B  VAL*     4.0    14.5    -      -       +      +
    344B  TRP*     4.0    27.1    -      -       +      -
    345B  ILE*     3.5    10.9    -      -       +      +
    348B  ASN*     3.1    19.3    +      -       -      +
    370B  ASN*     2.8    35.6    +      -       -      +
    372B  THR*     3.9    27.8    -      -       +      +
    422B  TYR*     5.2     1.6    -      -       +      -
    425B  TYR*     4.5     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  VAL*     5.1     2.0    -      -       +      -
    404A  PHE*     4.1    17.5    -      -       +      -
    256B  ASN      3.6    18.8    -      -       -      +
    257B  MET*     3.0    47.0    +      -       -      +
    259B  PRO*     4.6     2.7    -      -       +      -
    310B  TYR*     4.2     1.2    -      -       -      -
    311B  LEU*     1.3    82.9    -      -       -      +
    313B  VAL*     1.3    68.9    +      -       -      +
    345B  ILE*     4.7     2.2    -      -       +      -
    348B  ASN*     3.5    17.7    -      -       +      +
    370B  ASN*     3.1    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257B  MET*     4.3     6.4    -      -       -      +
    294B  PHE*     4.1    10.3    -      -       +      -
    310B  TYR*     3.8    22.0    -      -       +      -
    312B  THR*     1.3    79.7    -      -       -      +
    314B  ALA*     1.3    73.8    +      -       -      +
    315B  ALA*     5.2     1.3    -      -       +      -
    341B  PHE*     3.7    28.5    -      -       +      -
    348B  ASN*     3.0     9.8    +      -       -      +
    349B  VAL*     4.0    15.9    -      -       +      -
    350B  LYS*     3.1    24.8    +      -       -      +
    367B  PHE*     3.4    30.3    -      -       +      -
    368B  ILE      3.5     6.7    -      -       -      +
    506B  8WR      5.2     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257B  MET*     3.9     7.4    -      -       +      +
    313B  VAL*     1.3    78.1    -      -       -      +
    315B  ALA*     1.3    62.9    +      -       -      +
    350B  LYS      3.3     6.7    -      -       -      -
    367B  PHE*     3.8     0.5    -      -       -      -
    368B  ILE*     2.9    43.4    +      -       +      +
    506B  8WR      3.2    50.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293B  MET*     3.7    21.5    -      -       +      -
    313B  VAL*     5.2     3.1    -      -       +      -
    314B  ALA*     1.3    76.8    -      -       -      +
    316B  ILE*     1.3    62.6    +      -       -      +
    317B  PHE*     4.0    10.3    -      -       +      -
    330B  MET*     4.1    25.8    -      -       +      -
    350B  LYS      3.1     7.7    +      -       -      +
    351B  THR*     3.3     5.4    -      -       -      +
    352B  ALA      3.1    22.3    +      -       -      -
    366B  THR      3.4     6.5    -      -       -      -
    367B  PHE*     5.0     2.0    -      -       +      -
    506B  8WR      3.3     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235B  GLY      3.4    21.3    -      -       -      +
    238B  THR*     3.4    34.1    -      -       +      -
    239B  CYS*     4.8     7.6    -      -       +      +
    293B  MET*     4.7     0.2    -      -       -      +
    315B  ALA*     1.3    79.3    -      -       -      +
    317B  PHE*     1.3    65.1    +      -       -      +
    318B  ARG*     3.9    15.7    +      -       +      +
    352B  ALA*     3.6    11.4    -      -       +      +
    353B  VAL      5.4     0.2    -      -       -      -
    354B  CYS*     4.4     4.9    -      -       +      +
    365B  ALA*     3.6     1.2    -      -       -      -
    366B  THR*     3.0    34.5    +      -       -      +
    368B  ILE*     4.9     5.8    -      -       +      -
    506B  8WR      3.6    43.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286B  VAL*     4.7     3.8    -      -       +      -
    289B  LEU*     3.9    23.1    -      -       +      -
    290B  THR*     3.7    24.0    -      -       -      -
    293B  MET*     4.0     9.2    -      -       -      -
    315B  ALA*     4.2     9.2    -      -       +      -
    316B  ILE*     1.3    75.2    -      -       -      +
    318B  ARG*     1.3    61.7    +      -       -      +
    321B  MET*     3.8    22.9    -      -       +      -
    326B  VAL*     3.6    29.4    -      -       +      -
    330B  MET*     3.8    19.5    -      -       -      -
    351B  THR*     3.6    25.4    -      -       +      -
    352B  ALA      2.9    10.6    +      -       -      +
    353B  VAL*     3.3     7.3    -      -       +      +
    354B  CYS*     2.8    26.2    +      -       -      +
    364B  SER      3.5     2.9    -      -       -      -
    365B  ALA*     3.8    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  GLU*     3.0    35.9    +      -       -      -
    234B  SER*     3.2    17.2    +      -       -      -
    235B  GLY*     5.0     5.8    -      -       -      +
    238B  THR*     3.1    33.6    +      -       +      +
    242B  PHE*     3.6    16.3    -      -       -      -
    270B  PHE*     6.2     1.6    -      -       -      -
    316B  ILE*     3.9    17.5    -      -       +      +
    317B  PHE*     1.3    76.8    -      -       -      +
    319B  GLY*     1.3    58.1    +      -       -      +
    321B  MET*     3.2    11.7    -      -       -      +
    354B  CYS*     3.3     4.7    -      -       +      -
    356B  ILE*     3.1    27.3    +      -       -      +
    357B  PRO*     3.8    10.1    +      -       -      -
    358B  PRO*     3.9    23.6    -      -       +      +
    363B  MET*     3.2     5.1    -      -       -      -
    364B  SER*     2.8    46.4    +      -       -      +
    366B  THR*     5.6     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318B  ARG*     1.3    74.2    -      -       -      +
    320B  ARG*     1.3    60.7    +      -       -      -
    321B  MET*     3.3    18.3    +      -       -      +
    353B  VAL*     4.1     5.5    -      -       -      +
    354B  CYS      2.8    17.1    +      -       -      +
    355B  ASP*     3.6    21.8    +      -       -      +
    356B  ILE      4.3     1.4    +      -       -      -
    357B  PRO*     4.2     7.6    -      -       -      -
    362B  LYS      3.8    14.4    -      -       -      -
    363B  MET*     4.3     0.9    -      -       -      -
----------------------------------------------------------
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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