Contacts of the strand formed by residues 35 - 44 (chain A) in PDB entry 1U3T


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 35 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PRO*     3.8     2.7    -      -       -      -
     32A  LYS*     3.1    33.9    +      -       -      +
     33A  ALA      3.3     9.6    -      -       -      +
     34A  HIS*     1.3    83.5    -      -       -      +
     36A  VAL*     1.3    68.6    +      -       -      +
     77A  GLY      3.0    24.9    +      -       -      -
     80A  VAL*     3.3     1.6    -      -       -      +
    123A  LEU*     3.6    12.1    -      -       -      +
    125A  ASP*     4.3     7.1    -      -       -      +
    129A  ARG*     2.7    46.8    +      -       -      -
    151A  VAL*     3.6    11.8    -      -       +      +
    152A  VAL      3.3    10.5    -      -       -      +
    153A  ASP*     4.0    15.0    -      -       -      +
    154A  GLU      4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PRO*     4.3     0.7    -      -       -      -
     35A  GLU*     1.3    82.9    -      -       -      +
     37A  ARG*     1.3    65.6    +      -       -      +
     38A  ILE*     3.9    13.5    +      -       +      -
     73A  VAL*     3.7    29.2    -      -       +      -
     75A  SER      3.7     3.6    -      -       -      +
     76A  VAL*     4.4     2.7    -      -       +      -
     80A  VAL*     4.0    16.2    -      -       +      -
     83A  VAL*     3.7    26.5    -      -       +      -
    150A  THR      3.6     0.9    -      -       -      +
    151A  VAL*     3.2     5.1    -      -       -      -
    152A  VAL*     2.8    39.8    +      -       +      +
    154A  GLU*     4.5     5.8    -      -       -      -
    157A  VAL*     4.2    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  THR      3.2    17.0    +      -       -      -
      4A  GLY      4.1     8.3    -      -       -      +
      5A  LYS      2.8    27.1    +      -       -      -
      7A  ILE*     3.3    22.9    -      -       -      +
     28A  VAL*     2.9    32.4    +      -       -      -
     29A  ALA      3.6     6.1    +      -       -      -
     30A  PRO*     3.7     9.1    -      -       -      +
     31A  PRO*     3.8     8.3    -      -       +      +
     36A  VAL*     1.3    71.9    -      -       -      +
     38A  ILE*     1.3    61.9    +      -       -      +
     73A  VAL*     3.8     4.2    -      -       -      +
     74A  GLU*     2.7    54.1    +      -       +      +
     75A  SER*     2.9    27.1    +      -       -      +
    149A  TYR*     4.5    10.1    -      -       +      -
    150A  THR      3.2    10.8    -      -       -      +
    151A  VAL*     3.6    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     4.0    14.8    -      -       +      +
     37A  ARG*     1.3    78.6    -      -       -      +
     39A  LYS*     1.3    72.4    +      -       -      +
     40A  MET*     3.6    10.8    +      -       +      +
     71A  GLY*     3.8     9.4    -      -       -      -
     72A  ILE      3.5    18.6    -      -       -      +
     73A  VAL*     5.0     0.4    -      -       -      -
     74A  GLU*     4.8     0.2    -      -       -      -
     89A  VAL*     3.7    15.9    -      -       +      -
     91A  PRO*     4.1    22.0    -      -       +      -
    149A  TYR*     3.3     9.8    -      -       -      -
    150A  THR*     2.7    43.7    +      -       +      +
    152A  VAL*     4.1    11.9    -      -       +      -
    157A  VAL*     3.6    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ARG      4.3     0.4    +      -       -      -
     38A  ILE*     1.3    72.1    -      -       -      +
     40A  MET*     1.3    68.0    +      -       -      +
     41A  VAL*     3.6     6.4    +      -       +      +
     71A  GLY*     3.1     2.9    -      -       -      -
     72A  ILE*     2.8    45.5    +      -       +      +
     74A  GLU*     4.5     5.3    -      -       +      +
    148A  GLN*     3.4     8.1    -      -       +      +
    149A  TYR*     3.4    40.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ILE*     3.6    15.2    +      -       +      +
     39A  LYS*     1.3    79.5    -      -       -      +
     41A  VAL*     1.3    61.9    +      -       -      +
     42A  ALA      4.3     0.4    -      -       -      +
     69A  ALA*     3.6    12.3    -      -       +      -
     70A  ALA*     3.2    41.5    -      -       -      +
     71A  GLY*     3.4     7.2    -      -       -      +
     91A  PRO*     4.2     9.6    -      -       +      -
    145A  THR*     3.6    33.0    -      -       -      +
    147A  SER      3.2    19.3    -      -       -      +
    148A  GLN*     2.9    10.5    +      -       -      +
    150A  THR*     4.5    14.6    -      -       -      -
    374A  PHE*     3.3    41.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LYS*     4.0     8.7    -      -       +      +
     40A  MET*     1.3    77.5    -      -       -      +
     42A  ALA*     1.3    64.2    +      -       +      +
     70A  ALA      2.9    12.0    +      -       -      +
     71A  GLY*     3.9     9.6    -      -       -      -
     72A  ILE*     4.4    12.1    -      -       +      +
    166A  LEU*     3.7    37.5    -      -       +      -
    167A  GLU*     5.4     1.3    -      -       +      +
    373A  MET*     3.7    10.7    -      -       -      +
    374A  PHE*     3.1    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  MET*     4.3     1.2    -      -       -      +
     41A  VAL*     1.3    81.2    -      -       +      +
     43A  VAL*     1.3    60.5    +      -       -      +
     69A  ALA*     3.1     6.6    -      -       -      +
     70A  ALA      3.0    29.0    +      -       -      +
    166A  LEU      3.5    26.2    -      -       -      +
    167A  GLU*     3.8    15.3    -      -       -      -
    170A  CYS*     4.2     3.6    -      -       -      -
    371A  ILE*     3.9    13.2    -      -       +      -
    372A  LEU      3.4     7.0    -      -       -      +
    373A  MET*     4.2     4.9    -      -       -      -
    374A  PHE*     4.3     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA*     1.3    77.7    -      -       -      +
     44A  GLY*     1.3    69.2    +      -       -      +
     67A  HIS      4.6     0.7    -      -       -      +
     68A  GLU      3.2    17.3    -      -       -      +
     69A  ALA*     3.8     3.8    -      -       +      -
    145A  THR*     3.2    27.8    -      -       -      +
    146A  PHE*     3.8    23.6    -      -       +      -
    170A  CYS*     4.8     0.9    -      -       -      -
    371A  ILE*     4.2     3.5    -      -       -      +
    372A  LEU*     2.8    51.3    +      -       +      +
    374A  PHE*     3.5    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  VAL*     1.3    87.1    -      -       -      +
     45A  ILE*     1.3    63.6    +      -       -      +
     46A  CYS      3.8     2.1    +      -       -      -
     49A  ASP*     4.1     6.4    -      -       -      +
     68A  GLU*     2.7    37.3    +      -       -      +
    146A  PHE*     4.1     1.7    -      -       -      -
    170A  CYS*     4.5     1.8    -      -       -      -
    369A  ARG*     5.1     0.4    -      -       -      -
    370A  THR      3.6     7.6    -      -       -      -
    371A  ILE*     3.8    15.2    -      -       -      +
----------------------------------------------------------
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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