Contacts of the helix formed by residues 1179 - 1193 (chain A) in PDB entry 6LXT
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 ILE1179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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945A LEU* 3.7 42.0 - - + +
949A GLN* 3.1 22.4 - - + +
1177A VAL* 3.9 9.0 - - + -
1178A ASN* 1.3 77.1 - - - +
1180A GLN* 1.3 56.3 + - - +
1181A LYS 3.1 3.4 - - - -
1182A GLU* 2.8 32.3 + - - +
1183A ILE* 2.9 14.9 + - + +
944B ALA* 3.8 22.7 - - + +
947B LYS* 3.7 31.2 - - + -
948B LEU* 4.1 20.0 - - + -
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Residues in contact with GLN1180 (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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946A GLY* 5.7 0.2 - - - -
949A GLN* 3.5 13.6 + - - +
1178A ASN* 3.5 12.7 + - - +
1179A ILE* 1.3 76.6 - - - +
1181A LYS* 1.3 56.1 + - - +
1183A ILE* 3.8 26.2 - - - +
1184A ASP* 3.0 33.5 + - + +
1302A ZN 3.4 24.9 - - - -
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Residues in contact with LYS1181 (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 ASN* 4.6 5.1 + - - +
1179A ILE 4.7 0.2 - - - -
1180A GLN* 1.3 76.0 - - - +
1182A GLU* 1.3 73.3 + - + +
1184A ASP* 3.3 12.7 - - - +
1185A ARG* 3.1 26.0 + - + +
1303A PG4 5.5 4.2 - - - +
947B LYS* 5.4 5.6 - - - +
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Residues in contact with GLU1182 (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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945A LEU* 5.8 0.2 - - - -
1178A ASN 4.4 0.2 - - - +
1179A ILE* 2.8 29.7 + - - +
1181A LYS* 1.3 84.0 - - + +
1183A ILE* 1.3 62.9 + - - +
1185A ARG* 3.3 8.5 + - - +
1186A LEU* 3.0 29.7 + - + +
940B SER* 3.4 35.4 - - - +
943B SER* 2.6 27.8 + - - +
944B ALA* 3.9 14.1 - - + +
947B LYS* 3.0 27.6 + - - +
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Residues in contact with ILE1183 (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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942A ALA* 3.6 19.3 - - + +
945A LEU* 3.8 22.0 - - + -
946A GLY* 3.5 29.2 - - - +
949A GLN* 3.4 25.1 - - - +
1179A ILE* 2.9 20.5 + - + +
1180A GLN* 3.8 24.5 - - - +
1182A GLU* 1.3 71.6 - - - +
1184A ASP* 1.3 70.9 - - - +
1186A LEU* 3.4 9.5 + - - +
1187A ASN* 3.2 32.2 + - - +
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Residues in contact with ASP1184 (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 GLN* 3.0 23.0 + - + +
1181A LYS* 3.3 10.5 - - - +
1182A GLU 3.2 0.2 - - - -
1183A ILE* 1.3 75.9 - - - +
1185A ARG* 1.3 50.2 + - - +
1187A ASN* 2.8 15.8 + - - +
1188A GLU* 2.8 32.1 + - - +
1303A PG4 2.3 68.0 - - - +
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Residues in contact with ARG1185 (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 LYS* 3.1 15.0 + - + +
1182A GLU* 3.3 9.8 + - - +
1184A ASP* 1.3 76.6 - - - +
1186A LEU* 1.3 56.6 + - - +
1188A GLU* 3.6 8.3 - - - +
1189A VAL* 3.1 60.6 + - + +
1192A ASN* 5.3 5.7 - - - +
1301A PG4 3.3 46.2 + - - -
1303A PG4 3.9 24.6 - - - -
933B LYS* 5.6 4.4 - - - +
936B ASP* 2.7 41.6 + - - +
937B SER* 5.5 0.7 - - - -
940B SER* 3.3 26.0 - - - +
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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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938A LEU* 4.1 19.6 - - + +
941A THR* 3.7 18.4 - - + -
942A ALA* 3.8 20.9 - - + +
945A LEU* 3.7 30.1 - - + -
1182A GLU 3.0 17.2 + - - +
1183A ILE* 3.6 8.7 - - - +
1184A ASP 3.1 0.2 + - - -
1185A ARG* 1.3 75.7 - - - +
1187A ASN* 1.3 56.5 + - - +
1189A VAL* 3.2 6.1 + - - +
1190A ALA* 2.9 29.4 + - - +
937B SER* 3.4 40.2 - - - +
940B SER* 4.6 3.8 - - - -
941B THR* 3.5 11.9 - - - +
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Residues in contact with ASN1187 (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 SER* 4.2 15.9 + - - +
942A ALA* 3.6 17.5 - - - +
1183A ILE* 3.2 26.7 + - - +
1184A ASP* 2.8 14.2 + - - +
1186A LEU* 1.3 71.8 - - - +
1188A GLU* 1.3 65.6 + - - +
1190A ALA* 3.6 6.3 + - - +
1191A LYS* 3.2 36.2 + - - +
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Residues in contact with GLU1188 (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 ASP* 2.8 11.5 + - - +
1185A ARG* 3.6 10.1 - - - +
1187A ASN* 1.3 75.8 - - - +
1189A VAL* 1.3 52.9 + - + +
1191A LYS* 3.2 10.0 + - - +
1192A ASN* 2.8 63.2 + - - +
1303A PG4 2.5 62.1 - - - +
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Residues in contact with VAL1189 (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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938A LEU* 3.9 16.8 - - + -
1185A ARG* 3.1 50.4 + - + +
1186A LEU 3.2 4.0 + - - +
1188A GLU* 1.3 72.4 - - + +
1190A ALA* 1.3 59.0 + - - +
1192A ASN* 3.8 7.8 - - - +
1193A LEU* 3.0 34.5 + - + +
933B LYS* 3.4 44.4 - - + +
934B ILE 4.5 0.2 - - - +
937B SER* 4.1 11.9 - - - +
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Residues in contact with ALA1190 (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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935A GLN* 3.0 59.0 + - + +
938A LEU* 3.9 17.0 - - + +
939A SER* 4.6 7.4 - - - +
1186A LEU 2.9 17.2 + - - +
1187A ASN* 3.7 10.5 - - - +
1189A VAL* 1.3 77.2 - - - +
1191A LYS* 1.3 62.6 + - + +
1193A LEU 3.8 0.2 + - - -
1194A ASN* 4.9 0.2 + - - -
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Residues in contact with LYS1191 (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 SER* 5.8 1.6 + - - -
1187A ASN* 3.2 22.4 + - - +
1188A GLU* 3.2 11.5 + - - +
1190A ALA* 1.3 76.4 - - + +
1192A ASN* 1.3 68.4 + - - +
1193A LEU 3.2 0.2 - - - -
1194A ASN* 3.1 35.0 + - - +
1195A GLU* 5.7 0.5 - - - +
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Residues in contact with ASN1192 (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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1185A ARG* 5.3 6.1 - - - +
1188A GLU* 2.8 48.5 + - - +
1189A VAL* 3.3 9.6 + - - +
1191A LYS* 1.3 74.3 - - - +
1193A LEU* 1.3 55.8 + - - +
1194A ASN 3.1 0.4 - - - -
1195A GLU* 3.2 30.8 + - - +
1301A PG4 4.9 11.1 + - - -
933B LYS* 2.9 39.0 + - + +
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Residues in contact with LEU1193 (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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931A ILE* 3.9 14.4 - - + +
934A ILE* 4.1 15.5 - - + -
935A GLN* 3.6 29.2 - - + +
938A LEU* 3.9 22.4 - - + -
1189A VAL* 3.0 28.1 + - + +
1190A ALA 3.8 0.4 - - - +
1191A LYS 3.2 0.8 - - - -
1192A ASN* 1.3 71.5 - - - +
1194A ASN* 1.3 59.6 + - - +
1195A GLU 3.1 2.0 - - - -
1196A SER* 2.9 29.0 + - - +
1197A LEU* 3.6 9.2 + - - +
930B ALA* 3.9 37.7 - - + +
933B LYS* 4.0 14.4 - - + +
934B ILE* 4.6 6.7 - - + -
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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