Contacts of the strand formed by residues 4236 - 4249 (chain D) in PDB entry 3CMT


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 ASN4236 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  GLY*     5.2     3.9    -      -       -      -
    289A  ALA*     4.0    18.5    +      -       -      +
   4232D  LYS*     3.2     6.1    -      -       -      +
   4233D  GLU*     2.7    50.6    +      -       +      +
   4235D  GLU*     1.3    83.7    -      -       -      +
   4237D  VAL*     1.3    63.6    +      -       -      +
   4238D  VAL*     3.7     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL4237 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4227D  ARG*     4.0     9.9    -      -       -      +
   4230D  ALA*     4.0    18.4    -      -       +      -
   4231D  VAL      3.7     3.1    -      -       -      +
   4232D  LYS*     4.2    16.6    -      -       +      -
   4235D  GLU      3.9     3.8    +      -       -      +
   4236D  ASN*     1.3    74.5    -      -       -      +
   4238D  VAL*     1.3    61.4    +      -       -      +
   4239D  GLY      3.9    17.0    -      -       -      +
   4264D  TYR*     3.7    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL4238 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4231D  VAL*     2.9    31.5    +      -       +      +
   4232D  LYS      4.7     0.2    -      -       -      -
   4233D  GLU*     3.9    31.9    -      -       +      -
   4236D  ASN*     3.6     4.6    +      -       +      -
   4237D  VAL*     1.3    73.2    -      -       -      +
   4239D  GLY*     1.3    57.4    +      -       -      +
   4263D  LEU*     3.8    12.6    -      -       +      +
   4264D  TYR*     3.1    32.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY4239 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4227D  ARG*     4.0     0.2    +      -       -      -
   4230D  ALA*     3.7     4.5    -      -       -      -
   4231D  VAL*     2.7    40.5    +      -       -      +
   4237D  VAL*     3.9     3.3    -      -       -      +
   4238D  VAL*     1.3    81.1    -      -       -      +
   4240D  SER*     1.3    57.8    +      -       -      -
   4262D  ILE      3.1    12.6    -      -       -      -
   4263D  LEU*     4.1     2.7    -      -       -      -
   4264D  TYR*     3.5    19.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER4240 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4069D  SER      4.9     2.4    +      -       -      -
   4070D  SER      5.7     1.6    -      -       -      -
   4227D  ARG*     3.0    29.0    +      -       -      +
   4229D  GLY      3.7     4.3    -      -       -      -
   4231D  VAL*     4.0     2.9    -      -       -      -
   4239D  GLY*     1.3    71.4    -      -       -      -
   4241D  GLU*     1.3    62.3    +      -       -      +
   4242D  THR*     3.3    10.0    +      -       -      -
   4261D  GLN*     3.6     0.9    -      -       -      -
   4262D  ILE*     2.7    45.3    +      -       -      -
   4264D  TYR*     2.7    29.1    +      -       -      -
   4502D  ADP      4.0     8.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU4241 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4227D  ARG*     3.6     4.0    -      -       -      -
   4228D  ILE*     2.8    43.5    +      -       +      -
   4229D  GLY*     2.8    32.2    +      -       -      +
   4230D  ALA      4.4     3.1    -      -       -      +
   4231D  VAL*     3.4    14.0    -      -       +      +
   4240D  SER*     1.3    70.8    -      -       -      +
   4242D  THR*     1.3    60.8    +      -       -      +
   4259D  GLU*     5.6     2.9    -      -       +      +
   4260D  PHE*     3.8    10.8    +      -       -      +
   4261D  GLN*     3.2    38.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR4242 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4070D  SER      4.2     6.2    +      -       -      +
   4225D  ILE*     3.7    28.7    -      -       +      -
   4226D  ARG      3.5     6.2    +      -       -      +
   4227D  ARG*     4.8     1.0    -      -       -      -
   4228D  ILE*     4.4     4.1    -      -       -      +
   4240D  SER*     3.3    18.2    +      -       -      -
   4241D  GLU*     1.3    75.0    +      -       -      +
   4243D  ARG*     1.3    65.0    +      -       -      +
   4258D  ALA      3.9     0.2    -      -       -      +
   4259D  GLU*     3.2     6.4    -      -       -      +
   4260D  PHE*     2.7    73.9    +      -       +      +
   4262D  ILE*     3.6    14.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG4243 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4224D  ASP      3.6     1.9    -      -       -      +
   4225D  ILE*     3.5     0.9    -      -       -      -
   4226D  ARG*     2.9    39.9    +      -       +      +
   4228D  ILE*     3.6    39.8    -      -       +      +
   4242D  THR*     1.3    75.1    -      -       -      +
   4244D  VAL*     1.3    68.2    +      -       -      +
   4245D  LYS*     4.1    22.3    -      -       -      +
   4257D  GLN*     3.3    31.3    +      -       -      +
   4258D  ALA      3.3     4.9    -      -       -      +
   4259D  GLU*     2.4    43.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL4244 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4047D  LEU*     4.3    19.0    -      -       +      +
   4075D  LEU*     4.3     6.3    -      -       +      -
   4223D  LEU*     3.7    36.1    -      -       +      -
   4224D  ASP      3.3     7.6    -      -       -      +
   4225D  ILE*     3.8    22.2    -      -       +      -
   4243D  ARG*     1.3    76.3    -      -       -      +
   4245D  LYS*     1.3    66.6    +      -       -      +
   4246D  VAL*     4.1     1.2    +      -       -      +
   4257D  GLN*     3.3     5.4    -      -       -      +
   4258D  ALA*     2.8    36.7    +      -       +      +
   4260D  PHE*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS4245 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4223D  LEU*     3.4     4.7    -      -       -      -
   4224D  ASP*     2.8    51.8    +      -       +      +
   4226D  ARG*     5.9     5.5    -      -       -      +
   4243D  ARG*     4.1    18.6    -      -       -      +
   4244D  VAL*     1.3    73.0    -      -       -      +
   4246D  VAL*     1.3    62.6    +      -       -      +
   4247D  VAL*     3.3    12.4    +      -       +      -
   4255D  PHE*     6.1     5.4    -      -       +      +
   4256D  LYS      4.0     2.9    -      -       -      +
   4257D  GLN*     3.4    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL4246 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4047D  LEU*     4.3     9.6    -      -       +      -
   4050D  ALA*     4.1    28.5    -      -       +      +
   4051D  LEU*     4.4     7.0    -      -       +      +
   4222D  ARG      3.7     4.3    -      -       -      +
   4223D  LEU*     4.0    18.4    -      -       +      -
   4244D  VAL      5.2     1.1    -      -       -      +
   4245D  LYS*     1.3    70.5    -      -       -      +
   4247D  VAL*     1.3    60.0    +      -       -      +
   4248D  LYS      3.6    20.0    -      -       -      +
   4249D  ASN*     3.9    25.8    -      -       +      +
   4254D  PRO*     4.5     2.9    -      -       +      -
   4255D  PHE*     2.7    37.4    +      -       -      +
   4256D  LYS      3.0    21.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL4247 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3069D  SER*     6.1     0.2    -      -       -      -
   4065D  TYR*     3.5    26.5    -      -       -      +
   4222D  ARG*     2.8    30.7    +      -       +      +
   4224D  ASP*     3.6    24.2    -      -       +      +
   4245D  LYS*     3.9    13.2    -      -       +      +
   4246D  VAL*     1.3    73.4    -      -       -      +
   4248D  LYS*     1.3    60.5    +      -       +      +
   4254D  PRO*     4.5     1.7    -      -       -      +
   4255D  PHE*     3.5    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS4248 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3068D  GLU*     3.9     5.6    -      -       +      +
   3069D  SER*     3.2    27.1    -      -       -      +
   3501D  ALF      2.6    38.9    -      -       -      -
   4216D  LYS      2.7    29.2    +      -       -      +
   4217D  PHE      2.8    15.4    +      -       -      -
   4219D  ALA      3.0    20.5    +      -       -      +
   4220D  SER      4.8     0.9    -      -       -      +
   4221D  VAL*     3.2     5.1    -      -       -      -
   4222D  ARG*     2.9    46.7    +      -       +      +
   4246D  VAL*     3.6     8.8    -      -       -      +
   4247D  VAL*     1.3    81.8    -      -       +      +
   4249D  ASN*     1.3    66.5    +      -       -      +
   4250D  LYS*     4.5     7.0    -      -       -      -
   4254D  PRO*     4.4     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN4249 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3069D  SER*     5.4     0.2    -      -       -      -
   3502D  ADP      3.0    28.8    +      -       -      -
   4051D  LEU*     3.2    28.7    +      -       -      +
   4220D  SER      3.5     2.2    -      -       -      -
   4221D  VAL*     3.7     9.1    -      -       -      +
   4246D  VAL*     3.9    12.5    -      -       +      +
   4248D  LYS*     1.3    80.8    -      -       -      +
   4250D  LYS*     1.3    59.8    +      -       -      +
   4251D  ILE*     3.0    29.0    +      -       -      +
   4252D  ALA      3.1    31.4    +      -       -      +
   4253D  ALA      3.3    13.1    +      -       -      -
   4254D  PRO*     3.8    19.5    -      -       +      +
----------------------------------------------------------
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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