Contacts of the strand formed by residues 107 - 111 (chain B) in PDB entry 3U1J


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 LYS 107 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  GLU*     2.8    50.3    +      -       -      +
     97B  VAL      3.4     1.4    -      -       -      +
     98B  ILE*     4.6     0.2    -      -       -      -
     99B  ALA*     2.9    31.3    +      -       +      +
    105B  ASN      3.4     6.0    +      -       -      +
    106B  PRO*     1.3    76.7    -      -       -      +
    108B  ASN*     1.3    69.6    +      -       -      +
    109B  PHE*     3.4    29.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  THR      2.9    24.3    +      -       -      +
     62A  GLU*     3.5    22.1    -      -       +      +
     65A  ALA*     3.4    10.6    -      -       +      +
     66A  GLU*     3.1    25.1    +      -       -      +
     96B  GLN*     2.9    31.6    +      -       -      +
     97B  VAL      3.3     3.8    -      -       -      +
     98B  ILE*     3.7    28.6    -      -       -      +
    106B  PRO      5.4     0.3    -      -       -      -
    107B  LYS*     1.3    81.2    -      -       -      +
    109B  PHE*     1.3    62.9    +      -       -      +
    140B  ILE*     4.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  GLU*     3.4    42.8    -      -       +      +
     67A  GLN      6.2     0.2    -      -       -      -
     68A  THR      6.6     0.7    -      -       -      -
     95B  VAL      3.9     0.2    -      -       -      +
     96B  GLN*     3.1     6.4    -      -       -      -
     97B  VAL*     2.8    32.5    +      -       -      +
     99B  ALA*     4.1     7.0    -      -       +      -
    101B  GLU*     6.1     2.0    -      -       -      -
    107B  LYS*     3.4    48.9    -      -       +      -
    108B  ASN*     1.3    74.0    -      -       -      +
    110B  GLN*     1.3    60.6    +      -       -      +
    111B  THR*     5.0     0.2    -      -       -      +
    128B  LEU*     4.0    19.6    -      -       +      +
    130B  PHE*     3.5    44.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLN 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  TRP*     3.3    23.0    +      -       +      -
     62A  GLU      4.6     0.9    -      -       -      +
     63A  GLU      5.3     1.9    -      -       -      +
     65A  ALA*     4.3     1.9    -      -       +      +
     66A  GLU      2.8     8.7    +      -       -      +
     67A  GLN*     3.5    36.8    +      -       -      +
     68A  THR*     3.7     8.0    -      -       -      -
     69A  GLY      2.8    20.4    +      -       -      -
     94B  GLU*     2.5    31.5    +      -       +      +
     95B  VAL      3.3    11.2    -      -       -      +
     96B  GLN*     3.1    27.3    +      -       +      +
    109B  PHE*     1.3    72.2    -      -       -      +
    111B  THR*     1.3    64.0    -      -       -      +
    128B  LEU*     5.2     0.2    -      -       -      +
    142B  ARG*     4.9     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  THR*     5.4     0.2    -      -       -      -
     69A  GLY*     2.8    38.0    -      -       -      -
     94B  GLU*     3.4     9.6    -      -       -      +
     95B  VAL*     3.0    51.3    +      -       +      +
     97B  VAL*     5.0     1.3    -      -       +      -
    109B  PHE      5.0     0.9    -      -       -      +
    110B  GLN*     1.3    75.4    -      -       -      +
    112B  MET*     1.3    66.2    +      -       -      +
    113B  PRO*     3.5     1.0    -      -       -      +
    126B  ILE*     4.0    18.2    -      -       +      -
    127B  ALA*     4.9     6.4    +      -       -      +
    128B  LEU*     3.8    23.9    -      -       +      +
----------------------------------------------------------
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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