Contacts of the helix formed by residues 1146 - 1154 (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 PRO1146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142B HIS 2.9 27.1 - - - +
1143B LYS* 3.7 2.9 - - + +
1144B ILE 3.6 1.1 - - - -
1145B ARG* 1.3 82.3 - - + +
1147B HIS* 1.3 90.0 + - + +
1148B ILE* 2.9 17.4 + - + +
1149B ALA* 4.0 6.2 + - - +
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Residues in contact with HIS1147 (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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1109B HIS* 6.0 2.7 - - + -
1110B SER* 3.5 32.8 + - - -
1112B LEU* 6.2 0.2 - - + -
1113B TYR* 3.2 41.8 - + + -
1116B MET* 4.4 6.9 - - + +
1143B LYS* 2.8 32.2 + - - +
1144B ILE* 3.4 7.2 + - - +
1146B PRO* 1.3 90.0 - - + +
1148B ILE* 1.3 61.5 + - - +
1149B ALA* 3.2 5.0 + - - +
1150B THR 4.4 0.9 + - - -
1151B LEU* 3.6 16.6 + - - +
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Residues in contact with ILE1148 (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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1144B ILE* 3.3 7.9 + - + +
1145B ARG* 3.0 21.8 - - - +
1146B PRO 2.9 8.2 + - - +
1147B HIS* 1.3 76.9 - - - +
1149B ALA* 1.3 76.1 + - + +
1151B LEU* 2.9 28.6 - - + +
1152B ARG* 3.9 8.7 + - + +
1161B LEU* 3.7 30.3 - - + -
1164B LEU* 6.0 7.2 - - + -
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Residues in contact with ALA1149 (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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1146B PRO 4.0 6.0 + - - +
1147B HIS* 3.2 2.0 - - - -
1148B ILE* 1.3 90.1 - - + +
1150B THR* 1.3 67.3 + - + +
1151B LEU 2.8 3.1 + - - -
1152B ARG* 3.4 17.8 + - - +
1153B LYS* 5.0 4.3 - - - +
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Residues in contact with THR1150 (chain B).
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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1113B TYR* 2.6 37.5 + - - +
1147B HIS 4.4 0.6 + - - -
1149B ALA* 1.3 81.6 - - + +
1151B LEU* 1.3 62.1 + - - +
1152B ARG 3.2 1.3 - - - -
1153B LYS* 3.1 47.4 + - + +
1154B TYR* 3.1 28.9 - - - -
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Residues in contact with LEU1151 (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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1113B TYR* 6.1 0.9 - - - -
1116B MET* 3.5 33.9 - - + -
1117B LYS* 6.2 1.1 - - - -
1144B ILE* 3.6 20.2 - - + -
1147B HIS 3.6 5.4 + - - +
1148B ILE* 2.9 33.4 - - + +
1149B ALA 2.8 1.2 + - - -
1150B THR* 1.3 79.8 + - - +
1152B ARG* 1.3 57.7 + - - +
1153B LYS 3.3 0.7 + - - -
1154B TYR* 4.1 12.8 + - - -
1157B GLY* 3.4 34.4 - - - +
1160B ILE* 4.6 8.5 - - + +
1161B LEU* 3.4 30.7 - - + +
1164B LEU* 6.0 1.1 - - + -
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Residues in contact with ARG1152 (chain B).
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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1148B ILE* 4.2 9.4 - - + +
1149B ALA 3.4 12.4 + - - +
1150B THR 3.2 1.4 - - - -
1151B LEU* 1.3 77.6 - - - +
1153B LYS* 1.3 57.3 + - + +
1154B TYR 3.1 13.7 + - - +
1157B GLY 6.1 0.2 - - - -
1161B LEU* 4.2 33.2 - - + +
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Residues in contact with LYS1153 (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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1149B ALA 5.0 2.7 - - - +
1150B THR* 3.1 50.7 + - - +
1152B ARG* 1.3 78.8 - - + +
1154B TYR* 1.3 80.1 + - + +
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Residues in contact with TYR1154 (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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1113B TYR* 5.3 0.3 + - - -
1117B LYS* 3.3 57.6 - - + -
1150B THR* 3.1 37.6 - - - -
1151B LEU* 4.1 7.9 + - - +
1152B ARG 3.1 8.2 + - - +
1153B LYS* 1.3 93.9 - - + +
1155B THR* 1.3 63.5 + - - +
1156B TYR* 2.9 20.8 + + + +
1157B GLY* 3.1 23.5 + - - +
1158B LYS* 3.4 10.2 + - - -
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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