Contacts of the helix formed by residues 1082 - 1093 (chain A) in PDB entry 2C3O
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 LYS1082 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753A ASP* 3.3 29.6 + - - -
1076A LEU* 4.4 1.8 - - + -
1078A LYS* 3.4 59.6 - - + +
1079A GLY 3.4 11.2 - - - +
1080A MET 3.0 0.8 - - - -
1081A GLY* 1.3 79.0 - - - +
1083A SER* 1.3 52.2 + - - +
1084A GLN 3.3 2.7 - - - -
1085A ASP* 3.0 25.3 + - + -
1086A VAL* 2.7 46.2 + - + +
1219B THR* 3.6 7.4 - - + -
1221B GLU* 2.8 21.3 + - - +
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Residues in contact with SER1083 (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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750A ASN* 3.8 8.3 - - - -
814A GLY 3.3 12.1 + - - -
815A CYS 5.7 0.4 - - - -
816A GLY* 5.4 1.3 - - - -
1070A THR* 2.9 32.7 + - - +
1076A LEU* 3.9 4.5 - - - +
1080A MET* 2.4 34.3 + - - +
1081A GLY 3.3 0.6 - - - -
1082A LYS* 1.3 77.1 - - - +
1084A GLN* 1.3 59.9 + - - +
1086A VAL* 2.9 3.5 + - - +
1087A MET* 2.8 38.1 + - - +
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Residues in contact with GLN1084 (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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698A VAL* 3.2 40.0 - - + +
750A ASN* 3.0 23.9 + - + +
753A ASP* 5.1 4.0 - - - +
754A ILE* 4.4 20.4 - - + +
819A PRO* 4.4 6.8 - - - +
1042A MET* 3.6 23.4 - - - +
1043A GLY* 3.1 50.8 - - - +
1046A LYS* 5.4 0.4 - - - +
1082A LYS 3.3 0.4 - - - -
1083A SER* 1.3 76.2 - - - +
1085A ASP* 1.3 62.6 + - - +
1087A MET* 3.5 12.2 - - - +
1088A ASN* 3.2 10.6 + - - +
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Residues in contact with ASP1085 (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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753A ASP* 4.0 16.7 + - - +
1082A LYS* 3.0 30.0 + - + +
1084A GLN* 1.3 79.5 - - - +
1086A VAL* 1.3 58.8 + - + +
1088A ASN* 3.3 15.5 - - - +
1089A THR* 3.2 29.1 + - - -
1092A LYS* 5.3 2.3 + - - -
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Residues in contact with VAL1086 (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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1068A TYR* 4.6 4.7 - - + +
1070A THR* 4.1 16.4 - - + -
1076A LEU* 3.9 25.6 - - + -
1082A LYS* 2.7 28.3 + - + +
1083A SER 2.9 7.4 + - - +
1085A ASP* 1.3 76.7 - - + +
1087A MET* 1.3 59.9 + - - +
1088A ASN 3.1 1.3 - - - -
1089A THR* 3.2 4.8 + - - +
1090A ALA* 2.8 26.9 + - - +
1127A PHE* 3.6 23.9 - - + -
1130A ALA* 6.1 5.2 - - + -
1131A GLN* 4.6 5.8 - - + +
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Residues in contact with MET1087 (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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816A GLY* 4.0 13.5 - - - +
819A PRO* 5.9 1.6 - - + -
820A TYR* 3.3 36.6 - - + +
1041A SER* 2.9 30.3 + - - +
1042A MET* 4.0 3.6 - - + -
1043A GLY 3.2 24.0 - - - +
1044A TYR 4.3 0.2 - - - -
1068A TYR* 3.3 18.6 - - + +
1069A ALA* 4.3 4.9 - - - -
1070A THR* 4.1 13.7 - - + +
1083A SER* 2.8 26.6 + - - +
1084A GLN* 3.5 26.2 - - - +
1086A VAL* 1.3 77.1 - - - +
1088A ASN* 1.3 62.9 + - - +
1090A ALA* 3.1 18.7 + - - +
1091A VAL* 3.3 4.3 + - - +
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Residues in contact with ASN1088 (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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1043A GLY 3.6 17.7 - - - +
1044A TYR* 2.9 44.0 + - - +
1084A GLN 3.2 6.2 + - - +
1085A ASP* 3.3 21.2 - - - +
1087A MET* 1.3 79.1 - - - +
1089A THR* 1.3 62.2 + - - +
1091A VAL 3.1 10.2 + - - -
1092A LYS* 3.1 37.0 + - - +
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Residues in contact with THR1089 (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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1085A ASP* 3.2 14.7 + - - -
1086A VAL* 3.2 10.3 + - - -
1088A ASN* 1.3 78.4 - - - +
1090A ALA* 1.3 63.6 + - - +
1092A LYS* 3.6 17.5 + - - +
1093A SER* 2.8 28.8 + - - -
1123A SER* 4.1 18.4 - - - +
1126A GLU* 5.9 1.3 - - + +
1127A PHE* 3.2 36.3 - - + -
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Residues in contact with ALA1090 (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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1041A SER* 4.7 0.9 - - - +
1068A TYR* 3.9 27.1 - - + -
1086A VAL 2.8 14.5 + - - +
1087A MET* 3.1 15.7 - - - +
1089A THR* 1.3 76.7 - - - +
1091A VAL* 1.3 52.3 + - - +
1093A SER* 4.0 1.6 - - - -
1095A TYR* 3.1 13.1 + - + +
1096A TRP* 2.7 40.0 + - + -
1127A PHE* 3.8 16.6 - - + -
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Residues in contact with VAL1091 (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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1041A SER* 3.4 33.4 - - - +
1044A TYR* 3.5 41.7 - - + -
1087A MET 3.7 0.2 - - - +
1088A ASN 3.1 1.2 + - - -
1089A THR 3.1 0.4 - - - -
1090A ALA* 1.3 77.4 - - - +
1092A LYS* 1.3 66.6 + - - +
1094A GLY* 3.0 15.4 + - - -
1096A TRP* 3.4 23.0 - - + +
1097A PRO* 4.9 0.7 - - - +
1098A LEU* 3.9 7.9 - - + -
1117A SER* 3.5 30.8 + - - -
1118A LYS 4.5 6.8 - - - +
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Residues in contact with LYS1092 (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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1044A TYR* 3.7 18.4 - - + -
1085A ASP* 5.3 2.6 + - - -
1088A ASN* 3.1 48.7 + - - +
1089A THR* 3.2 16.4 + - - +
1091A VAL* 1.3 78.2 - - - +
1093A SER* 1.3 59.0 + - - +
1094A GLY 3.0 1.0 + - - -
1118A LYS* 4.6 8.3 - - - +
1119A ALA 4.1 2.9 - - - +
1120A PRO* 3.5 3.8 - - - +
1121A ASP* 2.6 43.3 + - + +
1123A SER* 4.8 0.9 - - - +
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Residues in contact with SER1093 (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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1089A THR* 2.8 28.7 + - - -
1090A ALA* 4.0 0.5 - - - -
1092A LYS* 1.3 72.9 - - - +
1094A GLY* 1.3 59.3 + - - +
1095A TYR* 3.3 21.1 - - - +
1120A PRO* 3.0 16.6 - - - +
1121A ASP* 2.9 12.3 + - - -
1123A SER* 3.8 7.6 + - - -
1124A VAL* 3.0 52.4 - - - +
1127A PHE* 4.2 3.4 - - - -
1156A LEU* 4.1 0.7 - - - +
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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