Contacts of the helix formed by residues 867 - 877 (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 867 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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859A GLU 5.5 4.9 - - - +
860A TYR 6.6 0.2 - - - -
868A ASP* 1.3 66.1 + - - +
869A PHE* 3.1 10.8 - - + +
870A ALA* 3.8 20.7 - - + +
871A GLY* 3.1 19.6 + - - -
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Residues in contact with ASP 868 (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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867A ARG* 1.3 75.3 - - - +
869A PHE* 1.3 60.5 + - - +
871A GLY* 3.6 1.9 + - - -
872A GLU* 3.4 34.0 + - - +
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Residues in contact with PHE 869 (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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857A MET* 3.9 38.4 - - + -
858A LYS 3.7 20.9 - - - +
859A GLU* 3.6 54.7 - - + +
860A TYR 6.0 0.9 - - - -
867A ARG* 4.0 5.8 - - + +
868A ASP* 1.3 75.8 - - - +
870A ALA* 1.3 71.7 + - + +
871A GLY 3.0 1.9 + - - -
872A GLU* 3.3 14.1 + - - +
873A LEU* 3.1 40.7 + - + +
898A LEU* 3.7 21.8 - - + -
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Residues in contact with ALA 870 (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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813A PRO* 5.5 5.0 - - + +
867A ARG* 3.4 24.3 + - + +
869A PHE* 1.3 88.5 - - + +
871A GLY* 1.3 61.4 + - - +
873A LEU* 3.8 7.3 - - - +
874A GLU* 3.2 23.9 + - - +
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Residues in contact with GLY 871 (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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867A ARG 3.1 14.3 + - - -
868A ASP* 3.6 2.7 + - - -
869A PHE 3.0 1.2 - - - -
870A ALA* 1.3 79.1 - - - +
872A GLU* 1.3 59.4 + - - +
873A LEU 3.1 1.1 + - - -
874A GLU* 3.4 11.8 + - - +
875A VAL* 3.3 21.2 + - - +
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Residues in contact with GLU 872 (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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857A MET* 3.5 24.9 - - + +
868A ASP* 3.4 28.7 + - - +
869A PHE* 3.3 20.6 + - - +
871A GLY* 1.3 74.8 - - - +
873A LEU* 1.3 56.6 + - - +
875A VAL* 3.9 9.5 - - - +
876A LEU* 3.0 32.4 + - - +
983A PHE* 3.5 24.3 - - + -
984A GLY* 5.1 14.9 + - - +
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Residues in contact with LEU 873 (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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813A PRO* 3.4 39.5 - - + +
815A ILE* 3.6 31.6 - - + -
857A MET* 5.0 2.7 - - + -
869A PHE* 3.1 43.3 + - + +
870A ALA* 3.8 7.6 - - - +
871A GLY 3.1 0.4 - - - -
872A GLU* 1.3 77.9 - - - +
874A GLU* 1.3 63.6 + - - +
875A VAL 3.2 0.7 - - - -
876A LEU* 3.4 10.0 + - + +
877A CYS* 3.1 26.5 + - - -
898A LEU* 3.7 22.0 - - + -
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Residues in contact with GLU 874 (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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813A PRO* 5.3 6.3 - - + +
870A ALA 3.2 17.0 + - - +
871A GLY* 3.7 6.4 - - - +
873A LEU* 1.3 73.8 - - - +
875A VAL* 1.3 67.4 + - - +
877A CYS* 3.5 11.8 + - - +
878A LYS* 3.1 40.8 + - - +
987A ARG* 5.9 0.7 + - - -
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Residues in contact with VAL 875 (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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871A GLY 3.3 16.4 + - - +
872A GLU* 4.0 9.4 - - - +
873A LEU 3.2 0.2 - - - -
874A GLU* 1.3 80.1 - - + +
876A LEU* 1.3 66.9 + - + +
878A LYS* 2.9 22.7 + - - +
879A LEU* 3.6 4.7 + - + -
960A PHE* 3.5 28.7 - - + -
982A ASP 5.9 0.7 - - - +
984A GLY* 6.0 0.9 - - - +
985A LEU* 3.5 33.4 - - + +
987A ARG* 4.8 15.5 - - + +
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Residues in contact with LEU 876 (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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815A ILE* 4.3 3.8 - - + -
835A PHE* 5.1 2.2 - - + -
857A MET* 4.3 10.5 - - + -
872A GLU 3.0 23.1 + - - +
873A LEU* 3.7 11.7 - - + +
874A GLU 3.4 0.4 - - - -
875A VAL* 1.3 81.1 - - + +
877A CYS* 1.3 59.6 + - - +
879A LEU* 3.4 41.3 + - + +
880A GLY 4.8 0.5 + - - -
888A LEU* 3.5 27.9 - - + +
900A LEU* 3.6 27.1 - - + -
982A ASP 3.8 15.9 - - - +
983A PHE* 4.0 29.6 - - + -
984A GLY 4.9 2.7 - - - +
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Residues in contact with CYS 877 (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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813A PRO* 4.9 4.0 - - - -
814A THR 4.1 21.1 - - - -
815A ILE* 3.6 29.8 - - - -
873A LEU* 3.1 23.9 + - - +
874A GLU* 3.8 7.9 - - - +
875A VAL 3.1 0.8 - - - -
876A LEU* 1.3 75.6 - - - +
878A LYS* 1.3 65.1 + - + +
879A LEU 3.3 0.7 - - - -
880A GLY* 4.5 4.6 + - - -
888A LEU* 5.3 0.4 - - - -
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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