Contacts of the helix formed by residues 918 - 923 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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914A LEU 4.1 7.6 - - - +
915A ARG* 3.3 19.5 + - - +
917A SER* 1.3 72.8 + - - +
919A VAL* 1.3 58.4 + - - +
920A LEU 3.1 3.4 - - - -
921A GLU* 2.9 35.4 + - + +
922A THR* 3.2 14.2 + - + +
933A ALA 3.7 2.9 - - - -
934A SER* 5.3 0.2 - - - -
1033A SER 3.0 23.8 + - - -
1034A LEU* 3.0 27.2 + - + +
1035A GLY 3.8 0.8 - - - -
1036A GLY* 3.5 14.3 - - - +
1113A TYR* 3.2 52.8 - - + +
1114A ALA 3.0 29.9 + - - +
1116A ILE* 3.5 23.2 - - - +
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Residues in contact with VAL 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916A LYS 5.4 0.2 - - - -
917A SER 2.6 11.5 + - - +
918A ARG* 1.3 67.0 - - - +
920A LEU* 1.3 59.2 + - - +
921A GLU 2.9 5.8 - - - -
922A THR* 3.3 12.8 - - - +
923A ASP* 2.7 56.2 + - + +
926A PHE* 3.3 28.9 - - + -
927A ALA* 3.8 4.7 - - + +
932A THR* 3.7 22.4 - - + +
934A SER* 3.6 28.3 - - - +
935A THR* 4.2 12.1 - - + -
1113A TYR* 3.6 0.2 + - - -
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Residues in contact with LEU 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ARG 3.1 1.0 + - - -
919A VAL* 1.3 78.3 - - - +
921A GLU* 1.3 59.1 + - + +
924A PRO* 3.7 23.6 - - + +
927A ALA* 3.7 22.0 - - + -
928A ILE* 4.4 18.8 - - + -
933A ALA* 4.6 5.6 - - + -
1107A LEU* 3.8 26.9 - - + -
1111A PHE* 5.0 13.0 - - + +
1113A TYR* 3.1 30.0 + - + +
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Residues in contact with GLU 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ARG* 2.9 24.8 + - - +
920A LEU* 1.3 83.3 - - + +
922A THR* 1.3 66.1 + - + +
923A ASP 3.4 0.4 - - - -
924A PRO* 4.0 5.7 - - - +
1113A TYR* 3.5 33.9 - - + +
1116A ILE* 6.0 0.7 - - - +
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Residues in contact with THR 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915A ARG 4.7 5.4 - - - +
916A LYS* 4.1 25.0 + - - +
918A ARG* 3.5 11.0 - - + +
919A VAL* 3.3 18.2 - - - +
921A GLU* 1.3 81.7 - - + +
923A ASP* 1.3 63.4 + - - +
924A PRO* 3.9 1.5 - - - +
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Residues in contact with ASP 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919A VAL* 2.7 24.5 + - + +
922A THR* 1.3 79.5 + - - +
924A PRO* 1.3 65.7 - - - +
925A ALA* 3.0 10.7 + - - +
926A PHE* 3.0 36.2 + - - +
927A 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