Contacts of the helix formed by residues 1177 - 1192 (chain A) in PDB entry 5XA0
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 LYS1177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090A ARG 4.4 0.2 + - - -
1133A VAL* 3.2 13.0 - - - +
1134A TYR* 2.7 59.3 + - + +
1176A VAL* 1.3 79.6 - - - +
1178A GLU* 1.3 67.5 + - - +
1179A ILE 2.9 4.5 + - - -
1180A LEU 3.1 2.4 + - - -
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Residues in contact with GLU1178 (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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1090A ARG* 3.8 18.8 + - + +
1095A GLN* 5.3 3.6 - - + -
1096A ALA* 4.3 29.4 - - + +
1099A GLN* 5.9 2.7 - - + -
1176A VAL 3.7 1.6 - - - -
1177A LYS* 1.3 76.3 - - - +
1179A ILE* 1.3 54.1 + - - +
1180A LEU 2.9 1.2 + - - -
1181A ILE* 3.2 7.1 + - - +
1182A ARG* 2.7 40.5 + - + +
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Residues in contact with ILE1179 (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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1090A ARG* 4.1 21.8 - - + +
1125A ILE* 4.7 2.7 - - + +
1126A VAL* 5.7 0.8 - - - -
1129A SER* 3.3 32.8 - - - -
1130A GLU 5.1 1.5 + - - -
1133A VAL* 4.5 2.7 - - + -
1176A VAL 6.1 0.2 - - - +
1177A LYS 2.9 1.6 + - - -
1178A GLU* 1.3 77.6 - - - +
1180A LEU* 1.3 56.4 + - - +
1182A ARG* 4.3 5.2 - - - -
1183A LEU* 2.9 30.5 + - - +
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Residues in contact with LEU1180 (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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1130A GLU* 4.6 15.3 - - - +
1132A TRP 4.7 0.9 - - - +
1133A VAL* 3.9 6.9 - - + +
1134A TYR* 2.7 51.1 - - + +
1177A LYS 3.1 2.0 + - - -
1179A ILE* 1.3 77.2 - - - +
1181A ILE* 1.3 64.5 + - - +
1183A LEU* 3.3 5.1 + - - +
1184A SER* 2.9 22.3 + - - -
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Residues in contact with ILE1181 (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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1134A TYR* 3.5 13.0 - - + +
1177A LYS 4.7 0.9 - - - +
1178A GLU* 3.2 8.6 + - - +
1180A LEU* 1.3 76.8 - - - +
1182A ARG* 1.3 55.2 + - - +
1184A SER* 2.8 28.7 + - - -
1185A LYS* 2.9 13.0 + - - +
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Residues in contact with ARG1182 (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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1178A GLU* 2.7 28.5 + - + +
1179A ILE* 4.2 3.8 - - - +
1181A ILE* 1.3 70.6 - - - +
1183A LEU* 1.3 66.0 + - - +
1185A LYS* 3.1 10.5 + - - +
1186A LEU* 2.9 23.7 + - - +
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Residues in contact with LEU1183 (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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1126A VAL* 4.9 8.7 - - + -
1130A GLU* 4.8 14.4 - - + -
1179A ILE 2.9 24.2 + - - +
1180A LEU* 3.7 6.3 - - - +
1182A ARG* 1.3 75.8 - - - +
1184A SER* 1.3 55.9 + - - +
1186A LEU* 3.2 8.7 + - - +
1187A CYS* 2.8 29.3 + - - +
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Residues in contact with SER1184 (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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1180A LEU 2.9 11.4 + - - -
1181A ILE* 2.8 17.2 + - - -
1183A LEU* 1.3 73.9 - - - +
1185A LYS* 1.3 64.8 + - - -
1187A CYS* 3.1 6.1 + - - +
1188A VAL* 3.0 24.5 + - - +
1229A LYS 5.8 4.3 - - - -
1232A GLU* 4.6 20.0 - - - +
1233A ILE* 5.5 4.9 - - - +
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Residues in contact with LYS1185 (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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1181A ILE 2.9 11.4 + - - +
1182A ARG* 3.5 11.7 - - - +
1184A SER* 1.3 75.1 - - - +
1186A LEU* 1.3 57.0 + - - +
1188A VAL* 3.2 6.4 + - - +
1189A GLN* 3.0 30.5 + - - +
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Residues in contact with LEU1186 (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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1182A ARG 2.9 13.1 + - - +
1183A LEU* 3.4 13.0 - - - +
1185A LYS* 1.3 75.4 - - - +
1187A CYS* 1.3 61.2 + - - +
1188A VAL 3.3 0.2 - - - -
1189A GLN* 4.4 4.0 - - - +
1190A GLU* 2.9 32.4 + - - +
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Residues in contact with CYS1187 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1183A LEU 2.8 16.3 + - - +
1184A SER* 3.1 4.7 + - - +
1186A LEU* 1.3 76.4 - - - +
1188A VAL* 1.3 59.2 + - - +
1190A GLU* 4.2 3.8 - - - +
1191A SER* 2.8 32.1 + - - -
1232A GLU 4.1 17.3 - - - +
1233A ILE* 5.1 4.7 - - - +
1236A LEU* 4.7 2.0 - - - -
1237A ALA* 4.2 14.2 + - + +
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Residues in contact with VAL1188 (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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1184A SER 3.0 16.6 + - - +
1185A LYS* 3.6 6.5 - - - +
1187A CYS* 1.3 80.6 - - - +
1189A GLN* 1.3 60.7 + - - +
1191A SER* 3.5 7.2 + - - -
1192A ALA* 3.5 14.0 + - - +
1232A GLU* 4.7 4.5 - - + -
1236A LEU* 3.9 23.8 - - + +
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Residues in contact with GLN1189 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105A THR* 4.6 20.2 - - - -
1108A ASP* 4.5 9.4 - - + +
1185A LYS 3.0 16.1 + - - +
1186A LEU* 4.4 3.8 - - - +
1188A VAL* 1.3 74.0 - - - +
1190A GLU* 1.3 64.7 + - - +
1191A SER 3.3 0.5 + - - -
1192A ALA* 3.5 11.9 + - - +
1193A SER* 3.1 15.1 - - - -
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Residues in contact with GLU1190 (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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1186A LEU 2.9 22.4 + - - +
1187A CYS* 4.2 4.0 - - - +
1189A GLN* 1.3 76.5 - - - +
1191A SER* 1.3 61.3 + - - +
1193A SER* 2.9 30.8 + - - +
1194A VAL 4.8 0.3 - - - +
1197A SER* 5.2 3.5 - - - -
1198A ARG* 5.3 3.8 + - - +
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Residues in contact with SER1191 (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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1187A CYS 2.8 20.7 + - - -
1188A VAL 3.6 6.5 - - - -
1189A GLN 3.2 0.2 - - - -
1190A GLU* 1.3 77.5 - - - +
1192A ALA* 1.3 57.1 + - - +
1193A SER 3.2 4.3 + - - -
1194A VAL 3.9 10.4 - - - +
1198A ARG* 4.7 12.5 - - - +
1236A LEU 3.0 28.3 - - - -
1237A ALA* 3.6 15.0 - - - +
1239A GLU* 5.5 4.6 - - - +
1241A LEU* 5.8 3.6 - - - -
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Residues in contact with ALA1192 (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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1108A ASP* 5.0 3.5 - - - +
1188A VAL 3.5 9.3 + - - +
1189A GLN* 3.5 8.2 + - - +
1190A GLU 3.4 0.2 - - - -
1191A SER* 1.3 75.7 - - - +
1193A SER* 1.3 56.2 + - - +
1194A VAL 3.8 2.8 + - - -
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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