Contacts of the helix formed by residues 913 - 919 (chain B) in PDB entry 6VSB
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.
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 GLN 913 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089A PHE* 3.7 5.3 - - + +
1090A PRO* 2.2 63.0 + - - +
1091A ARG 5.0 1.7 - - - -
1093A GLY 4.8 3.6 - - - +
1107A ARG* 4.9 8.8 + - - -
1121A PHE* 3.3 17.7 - - + -
903B ALA* 4.1 29.8 - - + +
906B PHE* 5.1 1.6 - - - -
907B ASN* 4.9 18.2 + - + +
911B VAL 3.3 3.5 + - - -
912B THR* 1.3 70.5 + - - +
914B ASN* 1.3 67.0 + - - +
915B VAL 2.9 1.9 + - - -
916B LEU* 3.0 21.1 + - - +
917B TYR* 3.8 13.6 + - + -
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Residues in contact with ASN 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A PHE* 3.9 34.5 - - + -
1121A PHE* 3.0 17.5 - - + -
1123A SER* 3.3 20.5 + - - +
912B THR* 3.0 34.1 + - - +
913B GLN* 1.3 80.0 - - - +
915B VAL* 1.3 70.8 + - - +
916B LEU 3.2 0.4 - - - -
917B TYR* 3.2 2.7 + - - +
918B GLU* 3.0 33.7 + - - +
1111B GLU* 3.2 22.6 + - - +
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Residues in contact with VAL 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B PHE* 4.0 27.8 - - + -
906B PHE* 4.8 3.1 - - + -
911B VAL* 3.7 19.1 - - + -
912B THR* 3.0 34.0 + - + +
913B GLN 2.9 0.8 + - - -
914B ASN* 1.3 83.8 - - - +
916B LEU* 1.3 64.5 + - - +
918B GLU* 3.6 4.4 + - - -
919B ASN* 3.1 27.1 + - - +
1067B TYR* 5.7 0.4 - - + +
1106B GLN* 4.0 0.2 - - - +
1109B PHE* 3.7 37.7 - - + -
1111B GLU* 4.7 1.8 - - - +
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Residues in contact with LEU 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B PHE* 4.9 3.1 - - + -
899B ALA* 3.2 19.3 - - + +
902B MET* 3.5 22.2 - - + -
903B ALA* 3.1 36.1 - - + +
906B PHE* 3.6 17.7 - - + -
913B GLN 3.0 11.3 + - - +
915B VAL* 1.3 78.9 - - - +
917B TYR* 1.3 59.4 + - + +
919B ASN 3.1 1.6 + - - -
920B GLN* 2.6 52.9 + - + -
923B ILE* 3.4 34.1 - - + -
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Residues in contact with TYR 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079A PRO* 3.6 40.2 + - + +
1089A PHE* 3.3 34.8 - + + -
1090A PRO* 6.1 0.2 - - + -
1107A ARG* 5.5 1.2 + - - -
1128A VAL 4.5 9.4 - - - +
1129A VAL* 4.3 17.1 - - + -
1130A ILE* 5.2 4.0 + - + +
899B ALA* 4.0 24.0 - - + -
900B MET* 3.3 33.0 - - + +
903B ALA* 3.4 20.9 - - + +
913B GLN* 4.0 18.5 + - + -
914B ASN* 3.2 5.6 + - - +
916B LEU* 1.3 84.8 - - + +
918B GLU* 1.3 63.8 + - - +
919B ASN 3.3 0.2 + - - -
920B GLN* 3.4 25.7 + - - +
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Residues in contact with GLU 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A PHE* 4.7 1.7 - - + -
1123A SER* 3.5 27.4 + - - +
1124A GLY* 3.9 8.0 - - - -
1128A VAL* 4.4 31.9 - - + +
1129A VAL* 4.9 6.7 - - + -
914B ASN* 3.0 37.6 + - + +
915B VAL* 4.1 3.1 - - - +
917B TYR* 1.3 76.6 - - - +
919B ASN* 1.3 70.4 + - - +
920B GLN 3.9 0.3 + - - -
921B LYS 5.3 0.3 + - - -
1111B GLU* 4.2 8.8 - - - +
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Residues in contact with ASN 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B ASN* 5.8 0.2 + - - -
718B PHE* 3.9 22.4 - - + -
915B VAL* 3.1 17.9 + - - +
916B LEU 3.2 2.5 - - - -
918B GLU* 1.3 92.1 - - - +
920B GLN* 1.3 65.1 + - - +
921B LYS 3.2 3.4 - - - -
922B LEU* 3.0 22.7 + - + +
923B ILE* 3.0 29.8 + - + +
1109B PHE* 4.9 10.0 - - - -
1J NAG 4.8 6.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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