Contacts of the helix formed by residues 918 - 923 (chain B) in PDB entry 1FVR
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 ARG 918 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914B LEU 4.0 7.6 - - - +
915B ARG* 3.2 20.5 + - - +
916B LYS 3.3 0.4 - - - -
917B SER* 1.3 71.9 + - - +
919B VAL* 1.3 58.4 + - - +
920B LEU 3.1 3.4 - - - -
921B GLU* 3.0 37.6 + - + +
922B THR* 3.2 14.4 + - + +
933B ALA 3.6 3.4 - - - -
934B SER* 5.2 0.4 - - - -
1033B SER 3.0 25.3 + - - -
1034B LEU* 3.0 25.6 + - + +
1035B GLY 3.8 0.2 - - - -
1036B GLY* 3.5 13.1 - - - +
1113B TYR* 3.2 45.6 - - + +
1114B ALA 3.0 31.4 + - - +
1116B ILE* 3.6 23.9 - - - +
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Residues in contact with VAL 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917B SER 2.6 11.1 + - - +
918B ARG* 1.3 67.0 - - - +
920B LEU* 1.3 60.9 + - - +
921B GLU 2.9 5.8 - - - -
922B THR* 3.3 10.5 - - - +
923B ASP* 2.8 58.8 + - + +
926B PHE* 3.3 26.9 - - + -
927B ALA* 3.8 5.2 - - + +
932B THR* 3.6 24.0 - - + +
934B SER* 3.6 28.0 - - - +
935B THR* 4.3 10.5 - - + +
1113B TYR* 3.5 0.2 + - - -
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Residues in contact with LEU 920 (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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919B VAL* 1.3 80.2 - - - +
921B GLU* 1.3 59.2 + - - +
924B PRO* 3.6 23.4 - - + +
927B ALA* 3.6 22.7 - - + -
928B ILE* 4.5 17.7 - - + -
933B ALA* 4.7 4.9 - - + -
1107B LEU* 3.9 27.8 - - + -
1111B PHE* 5.0 13.7 - - + +
1113B TYR* 3.0 32.9 + - + +
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Residues in contact with GLU 921 (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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918B ARG* 3.0 31.4 + - + +
919B VAL 2.9 0.4 - - - -
920B LEU* 1.3 81.6 - - - +
922B THR* 1.3 66.3 + - + +
923B ASP 3.4 0.9 - - - -
924B PRO* 4.2 5.9 - - - +
1113B TYR* 3.5 26.6 - - + +
1116B ILE* 5.8 1.0 - - - +
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Residues in contact with THR 922 (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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915B ARG 5.0 2.5 - - - +
916B LYS* 4.0 26.7 + - + +
918B ARG* 3.2 9.5 + - + +
919B VAL* 3.3 18.9 + - - +
921B GLU* 1.3 81.5 - - + +
923B ASP* 1.3 66.2 + - - +
924B PRO* 3.9 1.9 - - - +
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Residues in contact with ASP 923 (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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919B VAL* 2.8 24.0 + - + +
922B THR* 1.3 80.5 + - - +
924B PRO* 1.3 61.1 - - - +
925B ALA* 3.6 11.1 + - - +
926B PHE* 2.9 43.5 + - - +
927B ALA 3.1 8.5 + - - -
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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
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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