Contacts of the helix formed by residues 1133 - 1145 (chain B) in PDB entry 1M8X
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 GLU1133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091B ARG* 3.3 45.9 + - - +
1094B ARG* 5.1 8.8 + - - +
1095B ALA* 5.8 2.4 - - - +
1131B VAL 3.4 5.3 + - - +
1132B ALA* 1.3 74.3 - - - +
1134B PRO* 1.3 70.1 - - + +
1135B GLY 3.2 3.1 - - - +
1136B GLN* 3.0 14.0 + - + +
1137B ARG* 2.6 30.5 + - - +
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Residues in contact with PRO1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132B ALA 3.8 0.6 - - - +
1133B GLU* 1.3 89.2 - - + +
1135B GLY* 1.3 63.9 + - - +
1137B ARG* 3.7 10.5 - - + +
1138B LYS* 3.1 25.1 + - - +
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Residues in contact with GLY1135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133B GLU* 3.2 3.0 - - - +
1134B PRO* 1.3 84.0 - - - +
1136B GLN* 1.3 60.6 + - - +
1138B LYS* 3.5 11.7 + - - +
1139B ILE* 3.5 17.9 - - - +
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Residues in contact with GLN1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094B ARG* 5.3 2.3 - - - +
1095B ALA* 2.8 50.1 + - - +
1098B ILE* 3.4 30.2 - - + +
1099B ASP* 3.4 21.4 - - - +
1102B CYS* 5.5 1.7 - - - -
1132B ALA* 4.4 5.6 - - + +
1133B GLU* 3.0 17.6 + - + +
1135B GLY* 1.3 71.7 - - - +
1137B ARG* 1.3 66.5 + - - +
1138B LYS 3.0 2.0 - - - -
1139B ILE* 3.0 25.4 + - + +
1140B VAL* 3.1 15.5 + - + +
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Residues in contact with ARG1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B ILE* 3.8 43.0 + - + +
1130B ASP* 5.0 6.6 + - - +
1132B ALA* 3.8 19.3 + - + +
1133B GLU 2.6 21.5 + - - +
1134B PRO* 3.7 10.3 - - + +
1136B GLN* 1.3 72.4 - - - +
1138B LYS* 1.3 56.5 + - - +
1140B VAL* 3.5 6.6 + - + +
1141B MET* 3.1 37.2 + - + +
1163B LYS* 5.6 3.8 + - - +
1166B LYS* 4.4 22.4 - - - +
1167B TYR* 3.9 28.1 - - - +
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Residues in contact with LYS1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134B PRO 3.1 16.0 + - - +
1135B GLY* 3.7 6.7 - - - +
1136B GLN 3.0 0.6 - - - -
1137B ARG* 1.3 76.3 - - - +
1139B ILE* 1.3 59.8 + - + +
1141B MET* 3.5 2.9 + - + +
1142B HIS* 2.9 29.5 + - + +
1145B ARG* 5.7 7.8 + - - +
1167B TYR* 4.2 14.8 + - + +
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Residues in contact with ILE1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B CYS* 4.9 16.6 - - + -
1135B GLY 3.5 17.9 - - - +
1136B GLN* 3.0 15.0 + - + +
1138B LYS* 1.3 74.3 - - + +
1140B VAL* 1.3 61.8 + - + +
1142B HIS* 3.3 11.5 + - + +
1143B LYS* 2.9 37.5 + - + +
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Residues in contact with VAL1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098B ILE* 3.6 29.4 - - + -
1102B CYS* 3.8 14.8 - - - -
1112B LEU* 3.8 20.1 - - + +
1125B VAL* 5.2 2.5 - - + +
1128B MET* 5.3 4.9 - - + +
1129B ILE* 4.1 27.1 - - + +
1132B ALA* 5.0 3.8 - - + -
1136B GLN 3.1 16.7 + - - +
1137B ARG* 3.6 11.2 - - - +
1139B ILE* 1.3 76.2 - - - +
1141B MET* 1.3 63.6 + - + +
1143B LYS* 3.1 12.0 + - - +
1144B ILE* 3.2 25.0 + - + +
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Residues in contact with MET1141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B ILE* 4.6 28.3 - - + -
1137B ARG* 3.1 21.9 + - + +
1138B LYS* 3.8 4.3 - - + +
1139B ILE 3.3 0.2 - - - -
1140B VAL* 1.3 75.1 - - - +
1142B HIS* 1.3 56.4 + - - +
1144B ILE* 2.7 28.5 + - - +
1145B ARG* 2.8 12.6 + - - +
1163B LYS 4.6 4.5 - - - +
1164B LEU* 3.3 52.7 - - + +
1166B LYS* 4.9 2.2 - - + -
1167B TYR* 3.2 44.6 - - + +
1168B TYR* 3.9 21.1 + - + +
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Residues in contact with HIS1142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138B LYS* 2.9 19.9 + - + +
1139B ILE* 3.3 15.3 - - + +
1141B MET* 1.3 75.8 - - - +
1143B LYS* 1.3 60.4 + - + +
1145B ARG* 2.8 53.9 + - - +
1146B PRO* 2.9 25.8 - - - +
1168B TYR* 4.0 5.0 + - - -
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Residues in contact with LYS1143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B CYS* 3.1 35.4 + - + +
1103B THR* 5.2 1.2 - - - +
1110B SER* 4.0 26.1 + - - -
1112B LEU* 3.8 19.2 - - + +
1116B MET* 4.9 1.1 - - - +
1139B ILE* 2.9 20.6 + - + +
1140B VAL* 3.5 10.1 - - - +
1141B MET 3.1 0.4 + - - -
1142B HIS* 1.3 80.6 - - + +
1144B ILE* 1.3 59.0 + - - +
1146B PRO* 3.7 3.6 - - + +
1147B HIS* 2.8 37.1 + - - +
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Residues in contact with ILE1144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112B LEU* 4.1 7.6 - - + -
1116B MET* 3.4 31.9 - - + -
1125B VAL* 4.6 5.6 - - + -
1129B ILE* 4.4 16.6 - - + -
1140B VAL* 3.2 31.6 - - + +
1141B MET* 2.7 11.2 + - - +
1143B LYS* 1.3 75.8 - - - +
1145B ARG* 1.3 68.6 + - - +
1146B PRO 3.5 0.4 - - - -
1147B HIS* 3.4 3.2 + - - -
1148B ILE* 3.3 18.2 + - + +
1151B LEU* 3.6 21.8 - - + -
1160B ILE* 4.5 11.7 - - + -
1164B LEU* 4.5 24.7 - - + -
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Residues in contact with ARG1145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138B LYS* 5.9 7.1 - - - +
1141B MET 2.8 9.9 + - - +
1142B HIS* 2.8 48.6 + - - +
1144B ILE* 1.3 75.7 - - - +
1146B PRO* 1.3 66.0 - - + +
1148B ILE* 3.0 29.8 - - - +
1164B LEU* 5.8 0.8 - - - +
1168B TYR* 3.1 41.6 + - + +
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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