Contacts of the helix formed by residues 1183 - 1192 (chain I) in PDB entry 6LTJ
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 ASP1183 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1173I ILE* 3.9 22.9 - - - +
1175I ASP 4.9 0.2 - - - +
1180I PRO* 3.8 6.7 - - - +
1181I HIS 2.7 0.2 - - - -
1182I GLN* 1.3 112.2 + - - +
1184I LEU* 1.3 52.4 + - - +
1185I GLN 3.5 0.4 - - - -
1186I ALA* 3.5 7.2 - - + +
1187I GLN* 2.8 52.2 + - - +
1203I ARG* 4.6 11.8 + - - -
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Residues in contact with LEU1184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781I MET* 6.5 0.9 - - - -
818I TRP* 5.3 13.0 - - + +
1161I LEU* 5.9 4.0 - - + -
1180I PRO 3.9 1.2 + - - +
1181I HIS* 2.8 49.3 + - + +
1183I ASP* 1.3 78.3 - - - +
1185I GLN* 1.3 57.5 + - - +
1187I GLN* 3.2 24.4 + - - +
1188I ASP* 2.9 45.8 + - - +
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Residues in contact with GLN1185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102I PHE* 5.3 5.7 - - - -
1155I SER 4.9 4.4 + - - -
1156I THR* 2.9 26.9 + - - +
1157I ARG* 4.8 2.7 - - - +
1158I ALA 5.4 0.6 + - - -
1159I GLY 3.4 21.2 + - - +
1160I GLY* 4.5 7.2 - - - -
1161I LEU* 4.4 13.4 - - + +
1181I HIS 3.1 9.3 + - - +
1182I GLN* 4.4 7.3 - - - +
1184I LEU* 1.3 78.9 - - - +
1186I ALA* 1.3 65.8 + - - +
1188I ASP* 3.0 21.7 + - - +
1189I ARG* 3.0 55.1 + - - +
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Residues in contact with ALA1186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102I PHE* 5.1 11.7 - - + -
1171I VAL* 4.8 12.3 - - - +
1173I ILE* 4.1 24.7 - - + -
1182I GLN 3.2 21.9 + - - +
1183I ASP* 3.3 10.7 + - + +
1184I LEU 3.2 0.8 - - - -
1185I GLN* 1.3 86.2 + - - +
1187I GLN* 1.3 62.4 + - - +
1189I ARG* 4.2 10.8 - - - +
1190I ALA* 5.0 0.5 + - - +
1201I VAL* 5.6 3.4 - - - +
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Residues in contact with GLN1187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991I LYS* 3.9 42.2 + - + +
1183I ASP* 2.8 43.1 + - - +
1184I LEU* 3.3 28.1 - - - +
1186I ALA* 1.3 75.9 - - - +
1188I ASP* 1.3 60.1 + - - +
1189I ARG 2.8 13.7 + - - -
1190I ALA* 3.4 7.6 + - - +
1191I HIS* 3.2 18.7 + - + +
1199I VAL* 5.3 5.0 - - - +
1201I VAL* 5.9 6.3 - - + -
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Residues in contact with ASP1188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161I LEU* 2.9 40.1 - - + +
1164I ASN* 4.1 11.4 + - - +
1184I LEU* 2.9 32.8 + - - +
1185I GLN 3.0 1.5 + - - +
1187I GLN* 1.3 79.9 - - - +
1189I ARG* 1.3 67.0 + - - +
1190I ALA 3.6 0.2 - - - -
1191I HIS* 4.0 14.5 + - - +
1192I ARG* 4.2 20.7 + - + +
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Residues in contact with ARG1189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100I LEU* 5.7 7.9 - - + -
1102I PHE* 5.5 9.2 - - + -
1159I GLY* 2.9 19.9 + - - -
1160I GLY 2.7 30.1 + - - -
1161I LEU* 3.3 16.0 - - - +
1162I GLY 3.2 14.8 - - - +
1163I LEU* 3.3 40.3 - - + +
1164I ASN* 2.9 38.6 + - - +
1165I LEU 4.3 8.7 + - - +
1166I GLN* 4.0 1.0 - - - +
1185I GLN* 3.0 39.6 + - - +
1186I ALA* 4.2 10.5 - - - +
1187I GLN 2.8 2.8 + - - -
1188I ASP* 1.3 76.9 + - - +
1190I ALA* 1.3 60.5 + - + +
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Residues in contact with ALA1190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100I LEU* 5.6 5.4 - - + -
1164I ASN* 4.7 0.2 - - - -
1165I LEU 5.1 1.1 - - - +
1166I GLN* 3.9 29.1 - - + +
1169I ASP* 5.9 1.6 - - - +
1171I VAL* 5.3 11.7 - - + -
1186I ALA 5.0 0.4 + - - -
1187I GLN 3.4 3.4 + - - +
1189I ARG* 1.3 78.8 - - + +
1191I HIS* 1.3 60.1 + - - +
1192I ARG 3.7 4.1 - - - +
1195I GLN* 3.7 25.1 - - + +
1199I VAL* 4.0 22.0 - - + +
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Residues in contact with HIS1191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990I GLU* 5.0 2.9 - - - -
991I LYS* 3.5 54.3 + - + -
1187I GLN* 3.2 24.2 + - + +
1188I ASP* 4.0 7.4 - - - +
1189I ARG 3.4 2.4 - - - -
1190I ALA* 1.3 76.0 - - - +
1192I ARG* 1.3 68.2 + - + +
1195I GLN 4.5 5.2 - - - +
1196I GLN* 5.0 13.6 + - - -
1199I VAL* 3.8 21.7 - - + +
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Residues in contact with ARG1192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781I MET* 6.4 0.4 - - - +
821I GLU* 3.6 27.1 + - - -
825I TRP* 3.4 39.8 - - - +
1161I LEU* 5.4 11.8 - - - +
1164I ASN* 4.1 22.9 + - - +
1166I GLN* 5.2 0.3 - - - +
1188I ASP* 4.2 22.6 + - - +
1190I ALA 4.0 3.3 - - - +
1191I HIS* 1.3 85.1 - - + +
1193I ILE* 1.3 75.7 + - + +
1194I GLY 3.3 2.4 + - - -
1195I GLN 3.8 10.9 + - - +
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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