Contacts of the strand formed by residues 45 - 54 (chain C) in PDB entry 1Y1V


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 ALA 45 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  LEU*     1.3    81.5    -      -       -      +
     46C  ILE*     1.3    67.8    +      -       -      +
     47C  ASP*     3.2     2.3    +      -       -      +
     68C  GLY      3.6    18.8    -      -       -      +
     70C  ILE      4.8     2.5    -      -       -      +
     71C  PRO*     6.2     0.2    -      -       +      -
     72C  LEU*     3.1    14.1    -      -       +      -
    159C  ALA*     3.8     2.2    -      -       -      -
    160C  LYS      3.0    22.5    +      -       -      +
    169C  LYS*     3.9    14.4    -      -       +      +
    170C  TRP*     3.4    24.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  ALA*     1.3    70.7    -      -       -      +
     47C  ASP*     1.3    58.9    +      -       -      +
     48C  SER      3.5    23.1    -      -       -      +
     49C  VAL*     4.0     6.7    -      -       +      -
     64C  ALA      5.6     0.2    -      -       -      +
     67C  LEU*     3.9    30.7    -      -       +      +
     68C  GLY*     3.5    10.2    +      -       -      +
     70C  ILE*     4.8     1.3    -      -       +      -
     72C  LEU*     3.1    17.7    -      -       +      +
     99C  LEU*     4.8     4.5    -      -       +      -
    118C  LEU*     4.3    22.4    -      -       +      -
    157C  CYS*     3.3    42.0    -      -       +      -
    158C  VAL      4.1     1.6    -      -       -      +
    159C  ALA*     3.7     9.9    -      -       +      +
    169C  LYS*     3.1     7.6    +      -       -      -
     69L  ALA*     2.9    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 47 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  ALA      3.2     5.3    +      -       -      +
     46C  ILE*     1.3    74.1    -      -       -      +
     48C  SER*     1.3    66.6    +      -       -      +
    158C  VAL      3.5     9.1    +      -       -      -
    160C  LYS*     4.2    31.5    +      -       +      +
    169C  LYS*     2.6    23.4    +      -       -      +
    170C  TRP*     3.4    28.4    -      -       +      -
     68L  GLU*     5.4     0.7    -      -       -      -
     69L  ALA*     3.0    12.2    +      -       -      +
     70L  ARG*     3.4    22.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 48 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ILE*     3.5     2.3    -      -       -      +
     47C  ASP*     1.3    80.8    -      -       -      +
     49C  VAL*     1.3    72.8    +      -       -      +
     50C  GLU      4.3     0.2    -      -       -      -
    156C  THR      4.3     1.3    -      -       -      -
    157C  CYS*     3.6     0.5    -      -       -      -
    158C  VAL*     3.3    43.0    +      -       -      +
    160C  LYS*     5.0     6.7    -      -       -      -
     66L  GLN*     3.6    29.5    +      -       -      +
     67L  PHE      3.6    10.6    +      -       -      -
     69L  ALA*     3.4     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 49 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ILE*     4.0     7.2    -      -       +      -
     48C  SER*     1.3    86.4    +      -       -      +
     50C  GLU*     1.3    62.3    +      -       -      +
     51C  VAL*     3.6    10.1    +      -       +      -
     64C  ALA*     4.3    25.4    -      -       +      +
     67C  LEU*     3.9    11.2    -      -       +      -
    155C  LEU*     3.4    38.8    -      -       +      -
    156C  THR      3.5     4.0    -      -       -      +
    157C  CYS*     3.7    21.8    -      -       -      -
     65L  VAL      3.6     0.2    -      -       -      +
     66L  GLN*     3.4     5.2    -      -       -      -
     67L  PHE*     2.9    37.8    +      -       +      +
     69L  ALA*     5.7     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 50 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  SER*     4.3     0.4    +      -       -      -
     49C  VAL*     1.3    71.5    -      -       -      +
     51C  VAL*     1.3    62.9    +      -       -      +
     52C  GLU      3.6     1.6    +      -       -      -
    155C  LEU*     3.8     2.3    -      -       -      +
    156C  THR*     3.0    58.0    +      -       -      +
    158C  VAL*     5.8     1.5    -      -       +      +
     64L  LEU*     3.1    41.6    -      -       +      +
     65L  VAL      3.5     7.4    -      -       -      +
     66L  GLN*     3.6    22.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 51 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  VAL*     3.7    11.7    -      -       +      -
     50C  GLU*     1.3    72.3    -      -       -      +
     52C  GLU*     1.3    61.6    +      -       -      +
     53C  THR      4.1     9.6    -      -       -      +
     54C  ASN*     4.2    17.3    -      -       +      -
     60C  ASP*     3.7    30.3    -      -       +      +
     64C  ALA*     6.1     0.2    -      -       +      -
    155C  LEU*     3.3    26.5    -      -       +      -
     60L  ARG*     4.1     9.0    +      -       -      +
     64L  LEU*     3.9     6.4    -      -       -      -
     65L  VAL*     2.8    36.6    +      -       +      +
     67L  PHE*     4.0    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 52 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  GLU      3.6     3.3    +      -       -      +
     51C  VAL*     1.3    75.9    -      -       -      +
     53C  THR*     1.3    76.1    +      -       -      +
    102C  GLN*     6.1     0.2    -      -       -      -
    154C  LYS*     3.0    54.4    +      -       +      +
    156C  THR*     5.3     3.5    +      -       -      +
     60L  ARG*     3.7    13.0    -      -       -      -
     61L  THR      4.8     4.7    -      -       -      +
     62L  LYS*     5.0     2.9    -      -       -      +
     64L  LEU*     3.5    27.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 53 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  VAL*     3.7     2.0    -      -       -      -
     52C  GLU*     1.3    98.1    +      -       -      +
     54C  ASN*     1.3    61.8    +      -       -      +
     55C  THR*     4.5    10.8    -      -       -      +
    152C  GLU*     4.1    25.2    +      -       +      +
    153C  LEU*     2.9    12.0    -      -       -      +
    154C  LYS*     2.5    41.3    +      -       -      +
     60L  ARG*     4.5    11.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 54 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  VAL*     4.2    14.5    -      -       +      +
     53C  THR*     1.3    78.5    -      -       -      +
     55C  THR*     1.3    60.6    +      -       -      +
     56C  THR*     2.5    39.3    +      -       -      -
     58C  LEU      3.6    11.1    +      -       -      +
     59C  ALA*     4.6     0.8    -      -       -      +
     60C  ASP*     3.2    35.3    +      -       -      +
     63C  ILE*     4.0     8.0    -      -       +      +
    152C  GLU      3.3     4.7    -      -       -      -
    153C  LEU*     3.9    13.0    -      -       +      -
     60L  ARG*     4.6    16.0    +      -       -      +
----------------------------------------------------------
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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