Contacts of the helix formed by residues 963 - 976 (chain A) in PDB entry 1FO4
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 SER 963 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961A GLY 3.1 7.9 + - - -
962A PHE* 1.3 71.7 - - - +
964A VAL* 1.3 65.1 + - - +
965A PRO* 3.2 3.4 - - - -
966A ARG* 3.2 14.5 + - - +
967A CYS* 3.1 19.9 + - - -
1155A TYR* 3.4 10.7 - - - +
1181A ASP* 2.6 37.0 + - - +
1244A LEU* 3.8 16.6 - - - -
1247A CYS* 5.6 2.7 - - - -
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Residues in contact with VAL 964 (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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888A CYS* 3.9 10.5 - - - -
946A MET* 3.6 21.3 - - + -
962A PHE* 3.4 22.7 - - + -
963A SER* 1.3 75.8 + - - +
965A PRO* 1.3 61.5 - - + +
967A CYS* 2.9 10.0 + - - +
968A TRP* 2.6 36.1 + - + +
1002A PRO* 3.9 25.4 - - + -
1003A THR 4.3 1.3 - - - +
1155A TYR* 3.3 34.5 - - + -
1156A GLY 5.0 1.1 - - - +
1157A VAL* 4.1 8.5 - - + -
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Residues in contact with PRO 965 (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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943A TRP* 4.2 28.5 - - + -
946A MET* 4.6 3.8 - - - -
947A TYR 4.7 4.5 - - - +
948A LYS* 5.7 2.2 - - - -
949A GLU 5.9 0.9 - - - +
962A PHE* 3.6 30.1 - - + +
963A SER 3.4 3.8 - - - -
964A VAL* 1.3 94.2 - - + +
966A ARG* 1.3 57.8 + - + +
968A TRP* 3.2 6.3 + - + +
969A ASP* 2.8 39.0 + - - +
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Residues in contact with ARG 966 (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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963A SER* 3.2 14.8 + - - +
965A PRO* 1.3 77.2 - - + +
967A CYS* 1.3 61.7 - - - +
969A ASP* 4.2 4.4 - - - +
970A GLU* 2.8 55.1 + - - +
1244A LEU* 3.7 27.6 - - + +
1245A ARG* 3.1 34.4 + - - +
1246A ASP* 3.3 17.0 + - - +
1247A CYS* 4.3 2.6 - - - +
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Residues in contact with CYS 967 (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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963A SER* 3.1 17.2 + - - -
964A VAL* 2.9 8.9 + - - +
966A ARG* 1.3 78.6 - - - +
968A TRP* 1.3 58.2 + - - +
971A CYS* 2.8 33.4 + - - +
1155A TYR 4.7 0.2 - - - -
1156A GLY* 4.4 7.4 - - - -
1157A VAL* 3.6 18.4 - - + +
1179A VAL* 3.8 34.5 - - - +
1181A ASP* 4.0 29.8 - - - -
1244A LEU* 4.1 8.7 - - - -
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Residues in contact with TRP 968 (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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939A GLU* 3.5 34.4 + - + +
942A ARG* 4.0 19.7 - - + -
943A TRP* 3.8 29.2 - + + +
946A MET* 3.8 19.1 - - + -
964A VAL* 2.6 23.6 + - + +
965A PRO* 3.4 6.1 - - + +
967A CYS* 1.3 71.2 - - - +
969A ASP* 1.3 74.4 + - - +
971A CYS* 3.3 1.7 + - - +
972A LEU* 2.9 52.2 + - + +
1000A ILE* 3.8 34.7 - - + +
1002A PRO* 3.8 31.4 - - + -
1157A VAL* 3.9 25.1 - - + -
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Residues in contact with ASP 969 (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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943A TRP* 4.6 14.0 - - - -
965A PRO* 2.8 27.0 + - - +
966A ARG* 4.2 3.9 - - - +
968A TRP* 1.3 82.5 - - - +
970A GLU* 1.3 62.5 + - - +
972A LEU* 3.5 10.9 + - - +
973A LYS* 3.1 24.3 + - - +
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Residues in contact with GLU 970 (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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966A ARG* 2.8 32.7 + - - +
967A CYS 3.9 2.9 - - - +
969A ASP* 1.3 78.0 - - - +
971A CYS* 1.3 57.2 + - - +
973A LYS* 3.4 7.3 + - + +
974A SER* 2.9 32.3 + - - -
1179A VAL* 4.1 16.5 - - + +
1242A SER* 5.4 4.5 - - - -
1244A LEU* 3.4 31.7 - - - +
1245A ARG* 5.1 5.1 + - - +
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Residues in contact with CYS 971 (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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967A CYS 2.8 23.5 + - - +
968A TRP 3.8 2.2 - - - +
970A GLU* 1.3 70.6 - - - +
972A LEU* 1.3 60.9 + - - +
974A SER* 3.8 2.0 - - - -
975A SER* 2.6 38.2 + - - -
1000A ILE* 4.0 2.0 - - + -
1157A VAL* 3.8 23.6 - - + -
1159A CYS* 3.9 22.4 - - - -
1177A ASP* 3.5 32.8 - - - -
1179A VAL* 3.6 15.7 - - + +
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Residues in contact with LEU 972 (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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939A GLU* 5.1 2.7 - - + -
968A TRP* 2.9 50.4 + - + +
969A ASP* 3.6 12.8 - - - +
970A GLU 3.4 0.2 - - - -
971A CYS* 1.3 75.5 - - - +
973A LYS* 1.3 58.0 + - - +
975A SER* 3.7 4.0 - - - -
976A GLN* 3.1 6.8 + - - -
977A TYR* 3.0 63.6 + - + +
978A TYR* 4.0 30.4 + - + +
1000A ILE* 3.7 22.2 - - + +
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Residues in contact with LYS 973 (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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969A ASP 3.1 15.0 + - - +
970A GLU* 3.7 7.0 - - + +
972A LEU* 1.3 75.5 - - - +
974A SER* 1.3 66.8 + - - +
975A SER 3.1 1.8 - - - -
976A GLN* 3.1 19.3 + - - +
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Residues in contact with SER 974 (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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559A LEU* 6.0 4.9 - - - -
970A GLU 2.9 22.9 + - - -
971A CYS* 3.5 8.5 + - - -
973A LYS* 1.3 75.2 - - - +
975A SER* 1.3 59.3 + - - +
976A GLN* 3.3 4.6 + - - +
1175A ARG* 3.2 16.1 + - - -
1177A ASP* 4.1 10.6 + - - +
1179A VAL* 4.5 7.1 - - - +
1240A ARG* 3.7 9.5 + - - -
1242A SER* 5.3 5.5 + - - -
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Residues in contact with SER 975 (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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971A CYS 2.6 25.2 + - - -
972A LEU* 3.2 9.5 + - - -
974A SER* 1.3 77.6 + - - +
976A GLN* 1.3 63.4 + - - +
977A TYR* 3.4 10.4 + - - +
980A ARG* 2.5 40.6 + - - +
1159A CYS* 4.0 12.8 - - - +
1175A ARG* 3.7 3.9 + - - +
1177A ASP* 3.2 31.4 - - - -
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Residues in contact with GLN 976 (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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972A LEU 3.1 7.5 + - - -
973A LYS* 3.1 14.1 + - - +
974A SER 4.5 4.9 - - - +
975A SER* 1.3 80.4 - - - +
977A TYR* 1.3 65.8 + - - +
978A TYR* 3.3 2.7 - - - -
979A ALA* 3.1 18.4 + - + +
980A ARG* 3.0 26.1 + - + +
1175A ARG* 3.8 18.5 + - - -
1240A ARG* 5.4 1.6 + - - -
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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