Contacts of the helix formed by residues 1133 - 1145 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091A ARG* 5.1 13.2 - - - +
1094A ARG* 5.5 1.6 - - - +
1131A VAL 3.5 2.6 + - - -
1132A ALA* 1.3 71.8 - - - +
1134A PRO* 1.3 85.5 - - + +
1135A GLY* 2.6 39.5 + - - -
1136A GLN* 2.8 20.1 + - + +
1137A ARG 2.8 18.2 + - - -
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Residues in contact with PRO1134 (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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1132A ALA 3.6 3.5 - - - +
1133A GLU* 1.3 93.9 - - + +
1135A GLY* 1.3 62.2 + - - +
1137A ARG* 3.8 20.3 - - + +
1138A LYS* 3.2 21.8 + - - +
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Residues in contact with GLY1135 (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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1133A GLU* 2.6 29.2 + - - -
1134A PRO* 1.3 71.2 - - - +
1136A GLN* 1.3 60.9 + - - -
1138A LYS* 3.2 22.8 - - - +
1139A ILE* 3.3 13.1 + - - +
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Residues in contact with GLN1136 (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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1094A ARG* 4.8 1.6 - - - +
1095A ALA* 3.0 49.6 + - - +
1098A ILE* 3.2 43.8 - - + +
1099A ASP* 3.5 10.7 - - - +
1102A CYS* 5.6 0.8 - - - -
1132A ALA* 4.2 5.7 - - + +
1133A GLU* 2.8 24.1 + - + +
1135A GLY* 1.3 69.0 - - - -
1137A ARG* 1.3 66.2 + - - +
1139A ILE* 3.0 17.5 + - + +
1140A VAL* 2.9 22.2 + - + +
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Residues in contact with ARG1137 (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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1129A ILE* 2.8 23.8 + - + +
1130A ASP* 2.9 29.1 + - - +
1132A ALA* 3.5 26.4 + - + +
1133A GLU 2.8 19.4 + - - +
1134A PRO* 3.8 18.1 - - + +
1136A GLN* 1.3 72.2 - - - +
1138A LYS* 1.3 58.0 + - - +
1140A VAL* 3.3 6.1 + - - +
1141A MET* 2.9 49.8 + - + +
1167A TYR* 4.1 34.0 + - - -
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Residues in contact with LYS1138 (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 PRO 3.2 10.9 + - - +
1135A GLY* 3.2 14.6 - - - +
1136A GLN 3.1 0.2 - - - -
1137A ARG* 1.3 80.3 - - - +
1139A ILE* 1.3 71.9 + - - +
1141A MET* 3.3 7.7 + - - +
1142A HIS* 3.1 26.3 + - - +
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Residues in contact with ILE1139 (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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1102A CYS* 4.6 15.0 - - + -
1135A GLY 3.3 13.4 + - - +
1136A GLN* 3.0 18.9 + - + +
1138A LYS* 1.3 85.8 - - - +
1140A VAL* 1.3 63.6 + - - +
1142A HIS* 3.2 9.2 + - + +
1143A LYS* 3.1 38.5 + - + +
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Residues in contact with VAL1140 (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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1098A ILE* 3.6 30.3 - - + -
1102A CYS* 3.7 15.9 - - - -
1112A LEU* 4.2 11.7 - - + -
1125A VAL* 5.0 4.7 - - + +
1128A MET* 5.6 5.6 - - + +
1129A ILE* 4.0 22.2 - - + +
1132A ALA* 5.2 3.6 - - + -
1136A GLN* 2.9 18.1 + - + +
1137A ARG* 3.6 11.7 - - - +
1139A ILE* 1.3 75.8 - - - +
1141A MET* 1.3 65.1 + - - +
1143A LYS* 3.2 4.5 + - - +
1144A ILE* 3.0 45.2 + - + +
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Residues in contact with MET1141 (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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1129A ILE* 3.4 42.8 - - + -
1137A ARG* 2.9 32.2 + - + +
1138A LYS* 3.6 8.3 - - + +
1140A VAL* 1.3 74.6 - - - +
1142A HIS* 1.3 53.7 + - - +
1144A ILE* 3.2 9.2 + - - +
1145A ARG* 2.7 35.0 + - - +
1164A LEU* 3.8 23.8 - - + -
1167A TYR* 3.9 27.4 - - + -
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Residues in contact with HIS1142 (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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1138A LYS* 3.1 16.1 + - - +
1139A ILE* 3.2 11.6 + - + +
1141A MET* 1.3 75.1 - - - +
1143A LYS* 1.3 72.3 + - + +
1145A ARG* 3.6 22.8 + - + +
1146A PRO* 3.1 22.6 - - + +
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Residues in contact with LYS1143 (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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1102A CYS* 3.2 39.2 - - + +
1105A ASN* 5.8 0.8 - - - +
1110A SER* 3.6 29.0 + - - +
1112A LEU* 3.8 14.8 - - + -
1116A MET* 4.9 0.7 - - - +
1139A ILE* 3.1 23.7 + - + +
1140A VAL 3.2 6.3 + - - +
1142A HIS* 1.3 87.4 - - + +
1144A ILE* 1.3 62.4 + - - +
1146A PRO* 3.9 5.6 - - - +
1147A HIS* 3.4 21.2 + - - -
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Residues in contact with ILE1144 (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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1112A LEU* 4.2 9.0 - - + -
1116A MET* 3.6 35.2 - - - -
1125A VAL* 4.2 7.2 - - + -
1129A ILE* 4.0 20.9 - - + -
1140A VAL* 3.0 35.2 + - + +
1141A MET* 3.5 10.1 - - - +
1143A LYS* 1.3 79.8 - - - +
1145A ARG* 1.3 65.0 + - - +
1147A HIS* 3.0 19.9 + - - +
1148A ILE* 3.5 4.6 + - + -
1151A LEU* 4.3 5.6 - - + -
1160A ILE* 4.7 2.7 - - + -
1164A LEU* 4.0 35.4 - - + -
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Residues in contact with ARG1145 (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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1141A MET 2.7 19.5 + - - +
1142A HIS* 3.6 24.6 + - - +
1144A ILE* 1.3 70.6 - - - +
1146A PRO* 1.3 69.6 - - + +
1147A HIS 2.8 6.8 + - - -
1148A ILE* 2.9 37.5 + - + +
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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