Contacts of the strand formed by residues 1041 - 1050 (chain B) in PDB entry 5FLM


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 ILE1041 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684A  GLY*     5.7     0.4    -      -       -      -
    685A  HIS      4.8     4.7    -      -       -      +
    686A  THR*     4.0     9.0    -      -       -      -
    781B  ALA*     3.6    29.2    -      -       +      -
    782B  ILE      3.3    18.4    -      -       -      +
    783B  ALA*     3.6    20.4    -      -       +      -
   1025B  ASN*     4.5     0.2    -      -       -      -
   1026B  GLU*     3.0    31.2    +      -       -      +
   1028B  LEU*     3.5    33.7    -      -       +      -
   1037B  ILE*     3.5    37.0    -      -       +      -
   1039B  SER*     3.5     7.6    -      -       -      +
   1040B  GLN*     1.3    73.9    -      -       -      +
   1042B  PHE*     1.3    64.9    +      -       -      +
   1043B  ILE*     3.5     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1042 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686A  THR*     3.4     8.4    +      -       -      +
    687A  ILE      3.6    20.6    -      -       -      +
    688A  GLY*     4.0     4.9    -      -       -      -
    689A  ILE*     4.3    14.1    -      -       +      -
    780B  VAL      3.5     1.2    -      -       -      +
    781B  ALA*     3.2     1.2    -      -       -      -
    782B  ILE*     2.9    46.8    +      -       +      -
    981B  LEU*     3.6    32.8    -      -       +      -
    984B  CYS*     3.4    33.7    -      -       +      -
    985B  LEU*     4.3     7.4    -      -       +      -
   1023B  ARG      3.4    20.9    -      -       -      -
   1024B  GLY*     3.7    26.2    -      -       -      -
   1025B  ASN*     3.8    12.6    -      -       -      +
   1040B  GLN      3.8     0.6    +      -       -      -
   1041B  ILE*     1.3    74.0    -      -       -      +
   1043B  ILE*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1043 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    779B  ILE*     3.8    20.6    -      -       +      -
    780B  VAL      3.1     4.7    -      -       -      +
    781B  ALA*     3.5    21.8    -      -       +      -
    957B  THR*     3.7    15.9    -      -       +      -
    961B  ILE*     5.5     3.6    -      -       +      +
    963B  PRO*     5.4     5.2    -      -       +      -
    984B  CYS*     4.1     5.5    -      -       -      +
    988B  LYS*     3.5    19.4    +      -       -      +
   1024B  GLY*     3.6    12.7    +      -       -      +
   1026B  GLU*     3.7    15.0    -      -       +      +
   1028B  LEU*     3.5    39.3    -      -       +      -
   1041B  ILE      3.5     8.3    +      -       -      +
   1042B  PHE*     1.3    77.8    -      -       -      +
   1044B  GLY*     1.3    62.5    +      -       -      +
     43J  TYR*     3.5    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1044 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    779B  ILE*     4.5     1.8    -      -       -      -
    780B  VAL*     2.9    30.6    +      -       -      +
    984B  CYS*     3.4    24.0    -      -       -      -
    988B  LYS*     4.4     3.8    -      -       -      -
   1043B  ILE*     1.3    79.6    -      -       -      +
   1045B  PRO*     1.3    75.9    -      -       -      +
   1046B  THR      3.5     1.2    +      -       -      -
     43J  TYR*     4.7     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO1045 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    758B  LEU*     4.0    22.2    -      -       +      +
    759B  VAL*     5.8     0.3    -      -       -      +
    777B  ASN*     5.2     2.2    -      -       +      +
    778B  SER      2.9    17.3    -      -       -      +
    779B  ILE*     3.9    12.1    -      -       +      -
    983B  GLU*     4.3     1.9    -      -       -      +
    984B  CYS*     3.9    10.9    -      -       -      +
    987B  GLY*     3.5    30.2    -      -       -      +
    988B  LYS*     3.8    17.0    -      -       -      +
    991B  ALA*     4.7     0.4    -      -       +      -
   1044B  GLY*     1.3    84.5    -      -       -      +
   1046B  THR*     1.3    62.2    +      -       -      +
     43J  TYR*     3.9    23.3    -      -       +      -
     47J  ARG*     4.5     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR1046 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777B  ASN*     4.3     3.6    -      -       -      -
    778B  SER*     2.9    27.0    +      -       -      -
    780B  VAL*     4.6     3.3    -      -       -      +
    937B  SER*     4.8     2.2    -      -       -      -
    938B  ARG      5.6     0.2    -      -       -      +
    980B  HIS*     4.1    21.5    +      -       +      +
    983B  GLU*     3.6    27.8    -      -       -      +
    984B  CYS*     3.4    26.7    -      -       -      +
   1044B  GLY      3.5     1.5    +      -       -      -
   1045B  PRO*     1.3    77.5    +      -       -      +
   1047B  TYR*     1.3    67.2    -      -       -      +
   1048B  TYR*     3.2    36.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1047 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    755B  GLN      3.0    30.0    +      -       -      -
    757B  PRO*     4.0    10.8    -      -       +      -
    769B  PHE*     3.9    18.0    -      +       -      -
    773B  PRO*     3.7     2.4    -      -       -      +
    774B  ALA      2.9    43.2    +      -       -      -
    775B  GLY*     3.0     9.2    +      -       -      -
    776B  ILE*     3.7    20.2    -      -       -      -
    777B  ASN*     3.6    29.3    +      -       -      +
    937B  SER*     4.0     0.7    -      -       -      -
    938B  ARG*     3.5    66.0    +      -       +      +
    983B  GLU*     3.7     1.8    +      -       -      -
   1046B  THR*     1.3    78.4    -      -       -      +
   1048B  TYR*     1.3    61.7    +      -       -      +
   1049B  GLN*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR1048 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    775B  GLY*     3.3     1.4    -      -       -      -
    776B  ILE      2.9    35.9    +      -       -      +
    778B  SER*     3.3    11.2    -      -       -      +
    780B  VAL*     3.3    28.9    -      -       +      +
    794B  VAL*     6.0     2.5    -      -       +      -
    806B  PHE*     3.4    25.4    -      -       +      -
    935B  PHE*     5.3     7.0    -      -       +      -
    936B  ALA*     4.0     7.0    -      -       -      -
    937B  SER*     3.5    28.7    -      -       -      -
    941B  GLN*     5.2     2.5    -      -       +      -
    965B  ILE*     4.3    11.4    -      -       +      -
    967B  ILE*     3.7    24.6    -      -       +      +
    980B  HIS*     2.8    31.9    +      -       -      -
   1046B  THR*     3.2    35.7    -      -       +      -
   1047B  TYR*     1.3    74.8    -      -       -      +
   1049B  GLN*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1049 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710B  ILE*     4.0    24.7    -      -       -      +
    725B  GLN*     3.4    20.9    +      -       -      +
    728B  MET      4.7     1.9    -      -       -      +
    729B  GLY*     4.1     5.8    +      -       -      -
    732B  ALA*     3.7    27.1    -      -       +      +
    769B  PHE*     5.1     4.2    -      -       -      -
    774B  ALA*     3.5    22.2    +      -       -      +
    775B  GLY*     4.2     4.3    -      -       -      -
    806B  PHE*     4.8     1.3    -      -       -      -
    935B  PHE*     3.7     4.6    -      -       -      +
    936B  ALA*     3.0    36.9    +      -       -      +
    937B  SER      4.2     4.6    -      -       -      +
    938B  ARG*     4.2    16.8    -      -       +      +
   1047B  TYR*     4.3    10.5    -      -       +      -
   1048B  TYR*     1.3    75.2    -      -       -      +
   1050B  ARG*     1.3    61.6    +      -       -      +
   1051B  LEU*     4.1     7.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG1050 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732B  ALA*     3.3     7.1    -      -       -      -
    733B  MET*     2.9    47.3    +      -       +      +
    751B  LEU*     5.4     5.6    -      -       +      +
    775B  GLY*     5.0     3.0    -      -       -      -
    806B  PHE*     2.6    54.3    +      -       +      -
    808B  SER*     3.4    21.3    +      -       -      -
    927B  ARG*     3.4    25.9    +      -       -      +
    929B  PRO*     3.7     7.2    -      -       -      +
    933B  ASP*     2.6    31.9    +      -       +      +
    934B  LYS      4.5     0.2    -      -       -      +
    935B  PHE*     3.4    28.6    -      -       +      -
   1048B  TYR      4.1     1.8    +      -       -      -
   1049B  GLN*     1.3    72.5    -      -       -      +
   1051B  LEU*     1.3    67.2    +      -       -      +
   1054B  MET*     3.1    31.2    -      -       -      +
----------------------------------------------------------
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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