Contacts of the strand formed by residues 303 - 314 (chain B) in PDB entry 4LEY


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 GLU 303 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  ASN*     3.3    21.7    +      -       -      +
    297B  LEU*     3.9    19.3    -      -       +      +
    298B  ILE      3.4     4.9    -      -       -      -
    299B  ARG*     3.3    39.6    +      -       -      -
    301B  PRO      4.6     1.8    -      -       -      +
    302B  GLU*     1.3    75.7    -      -       -      +
    304B  ILE*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 304 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ALA*     3.7    32.3    -      -       +      +
    170B  THR*     5.4     1.1    -      -       -      -
    171B  VAL*     4.1     9.6    -      -       +      -
    209B  PRO      4.2     7.4    -      -       -      +
    210B  ASN*     3.5    10.1    -      -       -      +
    212B  PHE*     3.5    33.9    -      -       +      -
    296B  LEU      3.4     2.8    -      -       -      +
    297B  LEU*     3.6     5.4    -      -       -      +
    298B  ILE*     2.9    43.4    +      -       +      +
    300B  ASN*     3.8    27.1    -      -       +      -
    302B  GLU*     4.1    15.3    -      -       +      +
    303B  GLU*     1.3    78.9    -      -       -      +
    305B  SER*     1.3    64.2    +      -       -      +
    306B  VAL*     4.1     1.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 305 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  ASN      2.7    10.7    +      -       -      +
    211B  GLU*     3.2    27.4    +      -       -      +
    212B  PHE*     2.9    25.1    +      -       -      +
    285B  GLU*     5.9     0.7    -      -       -      -
    295B  THR*     4.3    13.9    -      -       -      -
    296B  LEU      3.3     7.6    -      -       -      -
    297B  LEU*     4.9     4.9    -      -       -      +
    304B  ILE*     1.3    74.3    -      -       -      +
    306B  VAL*     1.3    62.9    +      -       -      +
    307B  ASP*     4.2     5.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 306 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  VAL*     4.0    28.3    -      -       +      -
    175B  VAL*     4.6     8.5    -      -       +      -
    212B  PHE*     3.4    18.2    -      -       +      +
    214B  VAL*     4.4     9.4    -      -       +      -
    294B  VAL      3.4     2.3    -      -       -      +
    295B  THR*     3.4     1.9    -      -       -      -
    296B  LEU*     2.9    48.0    +      -       +      +
    298B  ILE*     4.3    16.4    -      -       +      -
    304B  ILE*     4.5     3.6    -      -       +      +
    305B  SER*     1.3    78.3    -      -       -      +
    307B  ASP*     1.3    66.7    +      -       -      +
    308B  ILE*     3.4    24.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 307 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  PHE      2.9     9.8    +      -       -      -
    213B  ASP*     3.5    21.5    -      -       -      +
    214B  VAL*     3.0    31.7    +      -       -      +
    291B  SER*     5.6     1.2    +      -       -      -
    293B  ALA*     3.8    16.9    -      -       +      +
    294B  VAL      4.0     3.4    -      -       -      -
    295B  THR*     3.0    29.7    +      -       -      +
    305B  SER*     4.9     3.9    +      -       -      -
    306B  VAL*     1.3    71.9    +      -       -      +
    308B  ILE*     1.3    60.7    +      -       -      +
    309B  ILE*     3.5     8.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 308 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  VAL*     4.7     5.8    -      -       +      -
    178B  LEU*     4.3    19.3    -      -       +      -
    214B  VAL*     3.5    14.6    -      -       +      -
    216B  PHE*     4.0    27.4    -      -       +      -
    266B  PHE*     3.7    31.3    -      -       +      -
    270B  ILE*     3.8    14.4    -      -       +      -
    293B  ALA*     3.3     2.3    -      -       -      -
    294B  VAL      2.9    41.3    +      -       -      +
    296B  LEU*     4.1    17.0    -      -       +      -
    306B  VAL*     3.8    21.1    -      -       +      -
    307B  ASP*     1.3    71.0    -      -       -      +
    309B  ILE*     1.3    60.3    +      -       -      +
    310B  LEU      3.6     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  THR*     4.5     2.2    -      -       -      +
    213B  ASP*     4.1    24.0    -      -       +      -
    214B  VAL      2.9    14.1    +      -       -      +
    215B  MET*     3.6    24.1    -      -       +      +
    216B  PHE*     2.9    28.2    +      -       -      -
    266B  PHE*     4.7     1.3    -      -       -      -
    292B  PRO*     3.7    23.3    -      -       +      +
    293B  ALA*     3.8    12.6    -      -       +      -
    307B  ASP*     3.8    17.9    -      -       +      +
    308B  ILE*     1.3    72.3    -      -       -      +
    310B  LEU*     1.3    62.8    +      -       -      +
    311B  ALA*     3.4     1.3    +      -       +      -
    348B  VAL*     4.0    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  PHE*     3.7    25.4    -      -       +      -
    192B  VAL*     5.5     0.9    -      -       +      -
    216B  PHE      3.8     6.7    -      -       -      +
    218B  LEU*     5.5     2.9    -      -       +      -
    262B  MET*     4.0    31.2    -      -       +      +
    263B  LEU*     3.9    42.8    -      -       +      +
    266B  PHE*     3.9    28.6    -      -       +      -
    292B  PRO      3.2     7.2    +      -       -      +
    308B  ILE      3.6     3.6    +      -       -      -
    309B  ILE*     1.3    70.0    -      -       -      +
    311B  ALA*     1.3    70.1    +      -       -      +
    348B  VAL*     3.8     5.4    -      -       -      +
    349B  PRO*     3.2    33.5    -      -       +      +
    363B  TRP*     4.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  MET*     3.6    32.3    -      -       +      -
    216B  PHE      2.9     9.8    +      -       -      +
    217B  LYS*     3.3    11.6    -      -       +      -
    218B  LEU*     2.9    27.1    +      -       -      +
    309B  ILE      4.4     2.7    -      -       -      +
    310B  LEU*     1.3    79.4    -      -       -      +
    312B  LEU*     1.3    66.5    +      -       -      +
    346B  TYR*     4.5     5.8    -      -       +      -
    347B  LEU      3.5     8.1    -      -       -      +
    348B  VAL*     4.1     8.5    -      -       +      -
    363B  TRP*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  LEU*     3.4     4.0    -      -       +      +
    220B  VAL*     3.8    24.7    -      -       +      -
    223B  ILE*     5.8     3.1    -      -       +      -
    237B  VAL*     4.1    16.2    -      -       +      -
    257B  LEU*     4.0    11.0    -      -       +      -
    262B  MET*     3.6    31.0    -      -       +      -
    310B  LEU*     5.4     0.9    -      -       +      -
    311B  ALA*     1.3    77.2    -      -       -      +
    313B  GLU*     1.3    60.8    +      -       -      +
    314B  SER*     5.4     0.6    -      -       -      -
    345B  PHE      3.6     0.9    -      -       -      +
    346B  TYR*     3.1     9.3    -      -       -      -
    347B  LEU*     2.9    45.6    +      -       +      +
    363B  TRP*     3.6    48.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  GLU*     4.7     2.3    -      -       -      +
    217B  LYS*     2.5    36.8    +      -       +      -
    218B  LEU      2.9    11.4    +      -       -      +
    219B  GLU*     3.3    35.6    +      -       +      +
    220B  VAL*     3.1    24.0    +      -       -      +
    223B  ILE*     6.1     0.2    -      -       -      -
    312B  LEU*     1.3    73.2    -      -       -      +
    314B  SER*     1.3    63.9    +      -       -      +
    315B  LYS*     4.3    12.1    -      -       +      -
    344B  PRO*     3.7    21.3    -      -       +      +
    345B  PHE      3.6     3.4    -      -       -      -
    346B  TYR*     3.0    33.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  GLU*     5.3     0.7    -      -       -      -
    220B  VAL      5.1     2.7    +      -       -      -
    223B  ILE*     4.2    23.7    -      -       -      +
    312B  LEU      4.0     1.1    +      -       -      -
    313B  GLU*     1.3    74.1    -      -       -      +
    315B  LYS*     1.3    60.5    +      -       -      +
    316B  GLY*     3.3     8.7    +      -       -      -
    344B  PRO*     3.1     5.2    -      -       -      +
    345B  PHE*     2.9    75.0    +      -       -      -
    347B  LEU*     6.0     1.1    -      -       -      -
----------------------------------------------------------
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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