Contacts of the strand formed by residues 249 - 255 (chain A) in PDB entry 5IYB


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 ILE 249 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  PRO*     5.9     1.0    -      -       -      +
     93A  PRO*     3.8    16.2    -      -       +      -
     94A  VAL*     3.3    32.5    -      -       -      +
     95A  PHE*     4.3    19.1    -      -       +      -
     96A  HIS      4.8     0.2    -      -       -      +
    103A  THR*     5.4     3.8    -      -       +      -
    218A  PRO*     3.3    25.8    -      -       +      +
    221A  VAL*     3.8    17.9    -      -       +      -
    222A  HIS*     3.8    22.8    +      -       +      +
    225A  PHE*     4.4    12.6    -      -       +      -
    246A  GLU      3.3    14.6    +      -       -      +
    247A  TRP*     3.1     8.5    -      -       -      +
    248A  MET*     1.3    80.0    -      -       +      +
    250A  VAL*     1.3    62.3    +      -       -      +
    251A  THR*     3.3     9.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  LEU*     3.8    10.4    -      -       +      +
     93A  PRO*     3.6     1.6    -      -       -      +
     94A  VAL*     3.0    50.9    +      -       +      +
     95A  PHE      4.2     7.2    -      -       -      +
     96A  HIS*     3.9    17.3    -      -       +      -
    247A  TRP      4.9     4.5    -      -       -      +
    248A  MET      3.7     1.7    +      -       -      +
    249A  ILE*     1.3    69.6    -      -       -      +
    251A  THR*     1.3    61.2    +      -       -      +
    252A  VAL      4.4    11.7    -      -       -      +
    253A  LEU*     4.6    17.9    -      -       +      -
    254A  PRO*     5.8     0.7    -      -       +      -
    314A  VAL*     5.1     3.8    -      -       +      -
   1165B  MET*     3.6    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  PRO*     3.3    27.5    -      -       +      +
     89A  GLU*     4.3     2.3    -      -       -      +
     90A  LEU*     3.3    32.0    +      -       -      +
     93A  PRO*     3.6    29.8    -      -       +      -
    222A  HIS*     3.9    25.8    -      -       +      +
    249A  ILE      3.3     7.1    +      -       -      +
    250A  VAL*     1.3    75.6    -      -       -      +
    252A  VAL*     1.3    68.3    +      -       -      +
    228R  MET*     6.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LEU*     5.9     0.3    -      -       -      +
     28A  PRO*     3.9    24.0    -      -       +      +
     31A  LEU*     3.7    33.4    -      -       +      +
     32A  LYS*     4.1    28.3    -      -       +      -
     87A  HIS*     4.1    22.0    -      -       +      +
     88A  ILE      3.4    10.5    -      -       -      +
     89A  GLU*     4.8    11.2    -      -       +      -
    250A  VAL*     4.4     9.3    -      -       -      +
    251A  THR*     1.3    88.8    +      -       -      +
    253A  LEU*     1.3    63.8    +      -       -      +
    254A  PRO*     3.8     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     4.2     2.7    -      -       -      -
     87A  HIS*     3.4     1.1    -      -       -      -
     88A  ILE*     2.8    57.3    +      -       +      +
     90A  LEU*     4.7    12.6    -      -       +      -
     96A  HIS*     5.9     2.5    -      -       +      -
    250A  VAL*     4.6    26.5    -      -       +      -
    252A  VAL*     1.3    74.4    -      -       -      +
    254A  PRO*     1.3    83.4    -      -       +      +
    255A  VAL*     3.4     1.2    +      -       -      +
    280A  LEU*     4.9     2.0    -      -       +      -
    283A  ILE*     4.3    30.3    -      -       +      -
    314A  VAL*     4.3    21.8    -      -       +      +
    317A  MET*     4.9    11.9    -      -       -      -
    318A  VAL*     6.1     4.7    -      -       +      -
   1165B  MET*     5.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LEU*     5.5     3.8    -      -       +      -
     31A  LEU*     3.8    25.6    -      -       +      -
     85A  PHE*     5.7     8.5    -      -       +      -
     86A  GLY      4.1     6.7    -      -       -      +
    250A  VAL*     5.8     0.2    -      -       +      -
    252A  VAL      3.8     7.0    -      -       -      +
    253A  LEU*     1.3    98.8    -      -       +      +
    255A  VAL*     1.3    62.3    +      -       -      +
    256A  PRO*     3.7     7.7    -      -       -      +
    280A  LEU*     5.6     0.3    -      -       -      +
    317A  MET*     5.0     5.7    -      -       -      +
   1163B  MET      4.9     2.9    -      -       -      +
   1164B  SER*     3.4    46.2    +      -       -      +
   1165B  MET*     5.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  LYS*     5.4     4.0    -      -       -      +
     57A  LEU*     5.6     2.5    -      -       +      +
     62A  GLN*     5.2     3.1    -      -       -      +
     85A  PHE*     3.7     7.2    -      -       -      -
     86A  GLY*     3.0    39.2    +      -       -      +
     87A  HIS      4.0    10.1    -      -       -      +
     88A  ILE*     3.6    37.5    -      -       +      -
    253A  LEU      3.4     0.2    +      -       -      -
    254A  PRO*     1.3    75.0    -      -       -      +
    256A  PRO*     1.3    77.8    -      -       -      +
    257A  PRO      3.5     0.9    -      -       -      -
    261A  ARG*     3.9    12.6    -      -       -      +
    280A  LEU*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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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