Contacts of the strand formed by residues 36 - 46 (chain B) in PDB entry 4Y1L


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 MET 36 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     5.8     0.9    -      -       -      +
     28B  PRO*     3.7    30.5    -      -       +      +
     29B  THR      3.1    25.6    -      -       -      +
     30B  LYS*     3.9    17.0    -      -       +      -
     31B  ASN*     3.9     5.7    -      -       -      +
     35B  THR*     1.3    76.2    -      -       -      +
     37B  ASN*     1.3    62.2    +      -       -      +
     38B  LEU*     3.5     8.8    +      -       +      -
     14C  GLU*     4.6    19.1    -      -       +      +
     17C  SER*     3.2    59.1    +      -       -      +
     18C  VAL*     4.0    14.4    -      -       +      +
     21C  ALA*     3.0    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  PRO*     3.5     6.8    -      -       -      +
     29B  THR*     2.9    32.2    +      -       -      +
     30B  LYS      5.3     0.2    -      -       -      -
     31B  ASN*     3.8    27.0    +      -       -      +
     35B  THR      4.3     0.2    +      -       -      -
     36B  MET*     1.3    72.0    -      -       -      +
     38B  LEU*     1.3    56.9    +      -       -      +
     39B  MET*     3.2    23.7    +      -       -      +
     40B  ASN*     2.9    42.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     3.3    45.7    -      -       +      +
      9B  LEU*     3.0    40.3    -      -       +      +
     10B  ALA*     4.2    13.0    -      -       +      +
     13B  ARG*     5.0     3.4    -      -       +      -
     28B  PRO*     4.0    22.9    -      -       +      -
     36B  MET*     3.5    17.1    +      -       +      +
     37B  ASN*     1.3    70.0    +      -       -      +
     39B  MET*     1.3    60.8    +      -       -      +
     40B  ASN      3.2     2.7    -      -       -      -
     41B  TRP*     2.4    28.8    +      -       +      +
     18C  VAL*     4.3    18.8    -      -       +      -
     21C  ALA*     4.6     6.5    -      -       +      -
     22C  ILE*     4.4     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  SER*     4.3     7.6    -      -       -      +
      5B  ALA*     4.0    14.6    -      -       +      -
      6B  LEU*     4.1    22.7    -      -       +      -
      9B  LEU*     3.5    23.3    -      -       -      -
     37B  ASN*     3.2    10.9    +      -       -      +
     38B  LEU*     1.3    77.5    -      -       -      +
     40B  ASN*     1.3    57.4    +      -       +      +
     63B  LEU*     3.4     3.8    -      -       -      +
     64B  PHE*     2.8    44.8    +      -       -      +
     65B  LYS      3.4    26.0    -      -       -      +
     66B  ASP*     3.3    30.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  THR*     3.0    21.3    +      -       -      +
     37B  ASN*     2.9    44.2    +      -       -      +
     39B  MET*     1.3    80.8    -      -       -      +
     41B  TRP*     1.3    67.8    +      -       -      +
     61B  ARG*     3.2    43.3    +      -       -      +
     62B  MET      3.4     3.3    -      -       -      +
     63B  LEU*     3.8    19.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  LEU*     3.8    22.4    -      -       +      +
     12B  GLU*     4.1     2.2    -      -       +      -
     13B  ARG*     4.0    27.8    -      -       +      -
     16B  TRP*     5.3     3.8    -      +       +      -
     26B  ALA*     3.8    44.4    -      -       +      -
     27B  VAL      3.4     3.6    -      -       -      +
     28B  PRO*     3.6    24.9    -      -       +      +
     29B  THR*     4.3     0.4    -      -       -      -
     38B  LEU*     2.4    37.5    +      -       +      +
     40B  ASN*     1.3    84.8    +      -       -      +
     42B  GLU*     1.3    60.9    +      -       -      +
     43B  CYS*     3.8    13.7    -      -       -      -
     61B  ARG*     3.3     9.9    -      -       -      +
     62B  MET*     2.9    36.0    +      -       +      -
     64B  PHE*     3.5    14.5    -      +       -      -
    109B  ILE*     3.6    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  VAL*     4.4     3.6    -      -       -      +
     26B  ALA*     4.0     0.2    -      -       -      -
     27B  VAL*     2.7    39.7    +      -       +      +
     29B  THR*     3.6    15.9    -      -       +      +
     41B  TRP*     1.3    71.4    -      -       -      +
     43B  CYS*     1.3    59.8    +      -       -      +
     60B  LEU      4.1     3.1    -      -       -      -
     61B  ARG*     3.0    44.7    +      -       +      +
     78B  GLU*     5.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  VAL*     3.1    13.0    -      -       -      +
     26B  ALA*     4.0    16.4    -      -       -      -
     41B  TRP*     3.8    24.5    -      -       -      -
     42B  GLU*     1.3    80.2    -      -       -      +
     44B  ALA*     1.3    61.7    +      -       -      +
     59B  LYS*     3.5     6.4    -      -       -      +
     60B  LEU*     2.9    48.1    +      -       +      +
     62B  MET*     4.1    24.5    -      -       -      -
    109B  ILE*     5.4     0.2    -      -       -      -
    113B  LEU*     4.3     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     3.6     8.0    -      -       -      -
     25B  VAL*     2.9    52.0    +      -       +      +
     43B  CYS*     1.3    75.1    -      -       -      +
     45B  ILE*     1.3    65.7    +      -       -      +
     57B  LEU*     3.8    24.0    -      -       +      -
     58B  PHE      3.5     8.3    -      -       -      +
     59B  LYS*     4.3    10.5    -      -       +      -
     60B  LEU*     4.2     0.4    -      -       -      -
    113B  LEU*     5.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     4.0     6.3    -      -       +      -
     44B  ALA*     1.3    78.7    -      -       -      +
     46B  PRO*     1.3    79.5    -      -       +      +
     57B  LEU*     3.9     2.0    -      -       -      -
     58B  PHE*     2.9    45.5    +      -       +      +
     60B  LEU*     3.8    18.8    -      -       +      -
     77B  PHE*     4.6     5.2    -      -       +      -
    113B  LEU*     3.8    35.2    -      -       +      +
    116B  ILE*     3.7    29.6    -      -       +      -
    117B  GLN*     3.6    26.0    -      -       +      -
    120B  LEU*     4.1    10.1    -      -       +      -
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Residues in contact with PRO 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  PHE      3.9     4.7    -      -       -      +
     23B  GLY*     3.2    33.4    -      -       -      +
     24B  PHE*     3.6    36.6    -      -       +      -
     45B  ILE*     1.3    85.8    -      -       -      +
     47B  GLY*     1.3    63.5    +      -       -      +
     56B  GLY      3.4     8.5    -      -       -      +
     57B  LEU*     3.9     7.6    -      -       +      -
     58B  PHE*     4.8     0.4    -      -       -      -
    117B  GLN*     2.8    34.7    +      -       -      +
----------------------------------------------------------
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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