Contacts of the strand formed by residues 307 - 312 (chain B) in PDB entry 1U0O


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 307 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ASN*     4.2     9.6    -      -       -      +
     96A  VAL*     3.5    33.9    -      -       +      +
    300B  ALA      3.6     0.2    -      -       -      +
    302B  LYS*     3.2    21.7    +      -       +      +
    305B  ASN*     3.1    47.2    +      -       +      +
    306B  ASN*     1.3    76.3    -      -       -      +
    308B  TRP*     1.3    62.8    +      -       -      +
    309B  TRP*     3.3    21.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 308 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  GLN*     6.4     0.7    -      -       +      -
     84A  TRP*     3.1    40.6    -      +       -      -
     90A  VAL*     5.6     1.1    -      -       +      -
     92A  TYR*     3.2    21.3    -      +       -      -
     93A  GLU*     3.3    24.9    -      -       +      -
     94A  ASN*     3.3    32.4    +      -       +      +
     95A  VAL*     3.4    19.7    -      -       +      +
     96A  VAL*     2.6    34.5    +      -       -      +
    242B  PHE*     3.9    24.3    -      +       +      -
    266B  ILE*     5.4     1.8    -      -       +      -
    268B  LEU*     3.7    11.2    -      -       +      -
    299B  VAL*     3.6    26.7    -      -       +      -
    300B  ALA      3.3     3.8    -      -       -      -
    301B  SER*     4.0    14.3    -      -       -      -
    306B  ASN*     3.7    21.0    +      -       -      +
    307B  LYS*     1.3    76.3    -      -       -      +
    309B  TRP*     1.3    61.3    +      -       -      +
    310B  ILE*     4.1     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  VAL*     3.8    25.0    -      -       +      +
     98A  ARG*     4.8    14.6    -      -       +      -
     99A  THR*     3.3    29.2    -      -       +      -
    263B  VAL*     3.8    23.3    -      -       +      +
    299B  VAL*     3.3     2.8    -      -       -      -
    300B  ALA*     2.5    43.5    +      -       +      +
    302B  LYS*     4.2    25.4    -      -       +      +
    307B  LYS*     3.3    25.4    +      -       +      +
    308B  TRP*     1.3    73.2    -      -       -      +
    310B  ILE*     1.3    58.8    +      -       -      +
    311B  ILE*     2.7    30.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LYS      4.0     3.4    -      -       -      +
     79A  GLN*     3.9    17.0    -      -       +      -
     95A  VAL*     3.3    42.0    -      -       +      -
     99A  THR*     3.3    26.3    +      -       -      +
    100A  VAL*     4.6     1.1    -      -       +      -
    101A  LYS*     3.3    20.3    +      -       -      -
    271B  VAL*     3.6    24.5    -      -       +      -
    272B  TRP*     3.8    19.3    -      -       +      +
    297B  GLU*     3.5    21.1    -      -       +      +
    298B  CYS      3.4     6.7    -      -       -      +
    299B  VAL*     4.6    11.2    -      -       +      -
    308B  TRP      5.1     0.2    -      -       -      +
    309B  TRP*     1.3    72.4    -      -       -      +
    311B  ILE*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  THR*     5.5     0.4    -      -       +      -
    263B  VAL*     5.1     0.7    -      -       +      -
    265B  TRP*     3.7    18.2    -      -       +      -
    297B  GLU*     2.9     7.8    -      -       -      +
    298B  CYS      2.6    40.3    +      -       -      +
    300B  ALA*     3.2    26.9    -      -       +      +
    309B  TRP*     2.7    52.0    -      -       +      +
    310B  ILE*     1.3    79.0    -      -       -      +
    312B  PRO*     1.3    74.0    -      -       +      +
    315B  ARG*     4.1    23.8    -      -       -      +
    317B  LYS*     5.2     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  LYS*     5.7     0.2    -      -       -      +
    265B  TRP*     3.5     7.3    -      -       -      -
    295B  GLU*     4.0    15.9    -      -       -      +
    296B  TYR      3.7     8.1    -      -       -      +
    297B  GLU*     3.2    19.1    -      -       +      +
    311B  ILE*     1.3    93.2    -      -       +      +
    313B  CYS*     1.3    58.3    +      -       -      +
    314B  THR*     3.1    21.3    +      -       +      +
    315B  ARG*     3.2    46.1    +      -       +      +
----------------------------------------------------------
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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