Contacts of the helix formed by residues 1073 - 1088 (chain A) in PDB entry 1FP7
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 GLY1073 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SO4 5.3 4.9 - - - -
1072A GLU* 1.3 91.2 + - - +
1074A LYS* 1.3 65.1 + - - +
1075A THR 3.9 0.2 - - - -
1076A THR* 4.5 11.8 - - - -
1077A THR* 3.9 10.4 + - - -
1331A VAL* 3.8 12.4 - - - +
1382A ASN* 4.2 3.5 + - - -
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Residues in contact with LYS1074 (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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271A SO4 2.9 34.7 + - - +
1062A VAL* 4.0 30.2 - - + +
1063A THR* 4.2 6.3 - - - -
1064A ALA* 4.3 19.3 - - + +
1072A GLU* 4.6 9.7 + - - +
1073A GLY* 1.3 71.2 - - - +
1075A THR* 1.3 68.1 + - - +
1077A THR* 3.0 17.0 + - - -
1078A SER* 3.1 10.0 + - - -
1301A GLU* 4.1 15.7 - - + +
1302A ALA 2.9 29.9 + - - +
1303A GLY 3.3 4.2 - - - -
1304A PHE* 3.1 25.0 + - - +
1331A VAL* 4.6 6.3 - - + -
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Residues in contact with THR1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074A LYS* 1.3 74.6 - - - +
1076A THR* 1.3 68.9 + - - +
1078A SER* 2.9 11.2 + - - -
1079A VAL* 2.9 24.4 + - + +
1096A LEU* 4.2 10.9 - - + +
1097A ARG* 5.0 0.9 + - - -
1112A ALA* 3.5 14.6 - - + +
1113A GLY* 3.4 25.8 - - - +
1301A GLU* 2.5 36.5 + - - +
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Residues in contact with THR1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SO4 4.1 11.0 + - - +
1073A GLY* 4.5 11.9 - - - -
1074A LYS 3.2 1.6 + - - +
1075A THR* 1.3 78.2 - - - +
1077A THR* 1.3 59.4 + - - +
1080A GLY* 3.0 23.4 + - - -
1113A GLY* 3.2 32.2 + - - -
1117A ALA* 3.1 27.9 - - + +
1382A ASN* 4.5 8.3 - - - +
1409A SER* 3.8 1.6 + - - -
1412A TRP* 3.8 39.7 - - + +
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Residues in contact with THR1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A VAL* 4.7 3.8 - - + -
1073A GLY 3.9 1.6 + - - -
1074A LYS 3.0 10.1 + - - -
1076A THR* 1.3 76.6 - - - +
1078A SER* 1.3 57.1 + - - +
1080A GLY 4.4 0.2 - - - +
1081A LEU* 2.7 36.2 + - + +
1329A VAL* 4.4 8.1 - - + -
1331A VAL* 3.8 26.1 - - + +
1380A ALA* 4.3 6.2 + - + -
1382A ASN* 3.5 21.8 + - - +
1407A ALA* 4.7 8.0 - - + +
1409A SER* 4.6 8.0 - - - -
1422A LEU* 3.8 28.0 - - + -
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Residues in contact with SER1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A VAL* 3.8 23.5 - - - +
1074A LYS 3.1 12.6 + - - -
1075A THR* 2.9 6.9 + - - -
1077A THR* 1.3 76.9 - - - +
1079A VAL* 1.3 54.2 + - - +
1081A LEU* 3.9 1.7 - - - +
1082A THR* 2.8 29.5 + - - -
1094A VAL* 3.7 6.8 - - - +
1096A LEU* 4.4 13.0 - - - -
1299A VAL* 3.9 8.2 - - - +
1301A GLU* 2.6 38.4 + - - +
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Residues in contact with VAL1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075A THR* 2.9 33.0 + - + +
1078A SER* 1.3 75.1 - - - +
1080A GLY* 1.3 66.8 + - - +
1082A THR* 3.0 9.3 + - - -
1083A ASP* 2.9 23.3 + - - +
1094A VAL* 4.6 4.0 - - + -
1096A LEU* 4.1 17.3 - - + -
1112A ALA 4.1 0.9 - - - +
1117A ALA* 3.5 8.3 - - - -
1118A GLN* 3.3 25.8 - - - +
1119A VAL* 4.2 7.0 - - + -
1262A THR* 3.2 38.1 - - + +
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Residues in contact with GLY1080 (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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1076A THR 3.0 11.9 + - - -
1079A VAL* 1.3 72.8 - - - +
1081A LEU* 1.3 65.8 + - - +
1083A ASP* 3.4 8.1 + - - +
1084A ALA* 2.8 26.0 + - - +
1116A TYR 5.4 0.2 - - - -
1117A ALA* 4.0 5.3 - - - +
1409A SER* 2.8 29.4 - - - -
1415A GLY 5.3 0.2 - - - -
1416A GLY* 4.0 7.0 - - - +
1419A GLY* 5.0 1.6 - - - -
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Residues in contact with LEU1081 (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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1060A ILE* 4.2 17.3 - - + -
1062A VAL* 5.3 3.4 - - + -
1077A THR* 2.7 22.8 + - + +
1078A SER* 3.9 2.2 - - - +
1080A GLY* 1.3 70.7 - - - -
1082A THR* 1.3 54.0 + - - +
1084A ALA* 3.1 7.4 + - - +
1085A LEU* 2.8 51.8 + - + +
1299A VAL* 3.7 28.5 - - + -
1329A VAL* 4.3 17.7 - - + -
1409A SER* 4.2 1.0 + - - -
1419A GLY* 5.1 2.0 - - - -
1422A LEU* 4.2 24.6 - - + +
1423A ALA* 4.2 18.8 - - - +
1426A VAL* 4.4 8.5 - - + -
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Residues in contact with THR1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078A SER 2.8 21.0 + - - -
1079A VAL* 3.0 7.9 + - - -
1081A LEU* 1.3 77.9 - - - +
1083A ASP* 1.3 58.3 + - - +
1085A LEU* 2.6 29.7 + - - +
1086A ALA* 2.8 11.3 + - - +
1092A VAL* 4.0 7.6 - - + -
1093A MET 3.9 10.1 - - - +
1094A VAL* 3.0 39.1 - - + +
1266A THR* 3.4 24.7 - - + -
1299A VAL* 3.7 11.8 - - - +
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Residues in contact with ASP1083 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079A VAL* 2.9 17.2 + - - +
1080A GLY* 3.8 4.2 - - - +
1082A THR* 1.3 77.5 - - - +
1084A ALA* 1.3 56.8 + - - +
1086A ALA* 3.5 3.1 - - - +
1087A ARG* 3.0 32.4 + - - +
1116A TYR 4.3 9.2 - - - +
1262A THR* 2.9 37.9 + - - +
1263A LEU* 5.2 0.2 - - - +
1264A GLU* 3.1 36.1 - - - +
1266A THR* 2.5 33.4 + - - -
1416A GLY* 4.0 6.3 - - - +
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Residues in contact with ALA1084 (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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1080A GLY 2.8 16.4 + - - +
1081A LEU 3.2 5.4 - - - +
1082A THR 2.8 0.2 + - - -
1083A ASP* 1.3 74.7 - - - +
1085A LEU* 1.3 66.4 + - - +
1087A ARG* 3.0 16.3 + - - +
1088A LEU* 3.0 16.1 + - - +
1416A GLY* 3.1 27.8 - - - +
1419A GLY* 3.4 24.5 - - - +
1420A LEU* 3.9 3.8 - - + +
1423A ALA* 4.0 6.7 - - + -
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Residues in contact with LEU1085 (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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1060A ILE* 4.0 26.2 - - + -
1081A LEU* 2.8 29.6 + - + +
1082A THR 2.6 12.8 + - - +
1084A ALA* 1.3 71.4 - - - +
1086A ALA* 1.3 61.3 + - - +
1088A LEU* 3.3 8.1 + - - +
1090A LYS* 3.2 32.3 + - + +
1092A VAL* 3.9 17.9 - - + -
1297A TYR* 4.4 7.6 - - + -
1299A VAL* 4.1 14.4 - - + -
1423A ALA* 3.9 22.4 - - + +
1426A VAL* 5.4 4.7 - - + -
1427A LEU* 4.0 30.5 - - + -
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Residues in contact with ALA1086 (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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1082A THR 2.8 9.8 + - - +
1083A ASP 3.5 9.4 - - - +
1085A LEU* 1.3 79.0 - - - +
1087A ARG* 1.3 62.6 + - + +
1089A GLY* 3.0 15.8 + - - -
1090A LYS 3.9 13.3 + - - +
1092A VAL* 3.8 3.8 - - + +
1266A THR* 3.8 30.3 - - + +
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Residues in contact with ARG1087 (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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1083A ASP 3.0 15.4 + - - +
1084A ALA 3.0 7.2 + - - +
1086A ALA* 1.3 76.7 - - + +
1088A LEU* 1.3 58.0 + - - +
1089A GLY* 3.0 5.6 + - - -
1264A GLU* 2.9 34.4 + - - +
1414A LYS 4.1 2.0 + - - -
1415A GLY 4.0 1.0 - - - -
1416A GLY* 3.2 14.9 - - - +
1417A GLU* 2.9 48.5 + - - +
1420A LEU* 4.3 10.7 - - + +
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Residues in contact with LEU1088 (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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1084A ALA 3.0 6.5 + - - +
1085A LEU* 3.7 9.6 - - - +
1086A ALA 3.2 0.8 - - - -
1087A ARG* 1.3 74.8 - - - +
1089A GLY* 1.3 58.7 + - - +
1090A LYS* 3.4 18.4 + - + -
1420A LEU* 3.5 26.7 - - + -
1423A ALA* 3.3 34.3 - - + -
1424A ARG* 3.7 34.3 - - + +
1427A LEU* 3.7 22.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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