Contacts of the helix formed by residues 1086 - 1094 (chain D) in PDB entry 3LW0
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 ASP1086 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1084D ARG 4.4 0.7 - - - +
1085D GLY* 1.3 74.9 - - - -
1087D LEU* 1.3 58.0 + - - +
1088D LYS* 3.0 14.4 + - - +
1089D SER* 2.6 46.9 + - - -
1090D TYR* 3.0 25.9 + - - +
1139D ARG* 3.6 20.0 - - - +
1141D CYS 3.4 8.3 - - - +
1142D MET* 4.3 9.6 - - + +
1156D MET* 3.6 22.6 - - + +
1161D TYR* 3.7 3.6 - - - -
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Residues in contact with LEU1087 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085D GLY 3.8 0.8 + - - -
1086D ASP* 1.3 70.5 - - - +
1088D LYS* 1.3 60.7 + - - +
1090D TYR* 4.2 7.9 - - + -
1091D LEU* 2.9 49.6 + - + +
1115D MET* 4.2 20.2 - - - -
1119D ILE* 4.2 19.3 - - + -
1138D ALA* 3.3 21.7 + - + +
1141D CYS* 2.9 31.3 + - + +
1143D VAL* 3.9 24.0 - - + +
1149D VAL* 4.3 8.1 - - + -
1201D VAL* 4.8 1.1 - - + -
1205D ILE* 4.4 15.3 - - + -
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Residues in contact with LYS1088 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086D ASP* 3.0 9.5 + - - +
1087D LEU* 1.3 77.2 - - - +
1089D SER* 1.3 61.3 + - - +
1091D LEU* 3.4 1.6 + - - +
1092D ARG* 3.0 59.6 + - - +
1138D ALA* 3.3 12.9 + - + -
1139D ARG* 3.7 18.4 - - + +
1161D TYR* 3.7 32.9 - - + +
1164D ASP* 2.9 35.0 + - - +
1178D TRP* 4.1 11.7 - - - -
1204D GLU* 4.2 10.6 + - - +
1209D ALA* 3.9 17.6 + - + +
1210D GLU 5.2 3.8 + - - -
1211D GLN* 5.3 3.8 - - - +
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Residues in contact with SER1089 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084D ARG 6.1 0.2 - - - -
1086D ASP* 2.6 37.7 + - - -
1088D LYS* 1.3 72.4 - - - +
1090D TYR* 1.3 63.6 + - - +
1092D ARG* 3.3 4.7 + - - +
1093D SER* 3.0 24.1 + - - -
1160D ILE* 4.8 4.7 - - - +
1161D TYR* 2.7 25.4 + - - -
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Residues in contact with TYR1090 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A ASP* 4.5 6.2 + - - +
1084D ARG* 4.4 28.2 + - + +
1086D ASP 3.0 17.8 + - - +
1087D LEU* 3.6 15.9 - - + +
1089D SER* 1.3 76.5 - - - +
1091D LEU* 1.3 65.9 + - - +
1093D SER* 2.7 30.6 + - - -
1094D LEU* 3.5 29.1 + - + +
1143D VAL* 4.4 12.6 - - + -
1147D PHE* 3.2 33.8 - + - -
1287D CCX 3.5 41.8 - + - -
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Residues in contact with LEU1091 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087D LEU* 2.9 41.7 + - + +
1088D LYS 3.8 3.4 - - - +
1090D TYR* 1.3 78.7 - - - +
1092D ARG* 1.3 61.8 + - - +
1094D LEU* 3.2 20.7 + - + +
1095D ARG 3.9 0.5 + - - -
1107D PRO* 4.9 1.3 - - + -
1115D MET* 5.1 0.2 - - + -
1138D ALA* 4.5 7.0 - - + -
1204D GLU 3.9 20.6 - - - +
1205D ILE* 3.9 27.4 - - + +
1208D LEU* 3.8 42.8 - - + +
1209D ALA* 4.1 8.1 - - + -
1287D CCX 3.8 24.9 - - - +
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Residues in contact with ARG1092 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D LYS* 3.0 52.8 + - - +
1089D SER* 3.8 5.6 - - - +
1091D LEU* 1.3 76.1 - - - +
1093D SER* 1.3 62.3 + - - +
1095D ARG* 3.2 48.0 + - - +
1161D TYR* 4.0 20.7 - - - +
1208D LEU 3.8 11.2 - - - +
1209D ALA* 2.9 25.7 + - + +
1210D GLU* 4.6 0.4 - - - +
1211D GLN* 4.0 17.4 - - - +
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Residues in contact with SER1093 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D SER 3.0 12.8 + - - -
1090D TYR* 2.7 29.0 + - - -
1092D ARG* 1.3 76.4 - - - +
1094D LEU* 1.3 65.6 + - - +
1095D ARG 3.2 8.6 + - - +
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Residues in contact with LEU1094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090D TYR* 3.5 51.1 - - + +
1091D LEU* 3.2 12.0 + - - +
1093D SER* 1.3 79.9 - - - +
1095D ARG* 1.3 62.4 + - - +
1096D PRO* 3.8 3.6 - - - +
1106D PRO 5.3 10.0 - - - -
1107D PRO* 4.0 20.4 - - + -
1208D LEU* 4.3 15.8 - - + +
1287D CCX 3.9 16.6 - - + +
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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