Contacts of the helix formed by residues 1151 - 1165 (chain A) in PDB entry 1MUK
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 GLN1151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ASP* 5.0 1.0 - - - +
983A GLU* 5.0 4.0 + - - -
987A ARG* 3.5 37.3 - - - +
1146A LEU* 4.1 0.2 - - - -
1150A LEU* 1.3 73.4 - - - +
1152A GLU* 1.3 69.8 + - + +
1153A SER* 3.8 24.6 + - - +
1154A GLU* 2.8 42.7 + - + +
1155A ALA 2.8 8.5 + - - -
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Residues in contact with GLU1152 (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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987A ARG* 5.6 1.0 - - - +
990A ARG* 2.8 50.8 + - + +
1142A THR* 4.9 3.7 - - + +
1146A LEU* 3.4 32.9 - - + +
1151A GLN* 1.3 72.0 - - + +
1153A SER* 1.3 56.5 + - - +
1155A ALA* 3.8 2.0 - - - -
1156A ASP* 2.8 34.9 + - - +
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Residues in contact with SER1153 (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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1151A GLN* 2.8 28.0 + - - +
1152A GLU* 1.3 77.5 - - - +
1154A GLU* 1.3 63.3 + - - -
1156A ASP* 3.9 3.8 - - - +
1157A ALA* 3.1 20.8 + - - +
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Residues in contact with GLU1154 (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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444A ASP* 3.4 22.5 - - - +
1150A LEU* 4.4 20.1 - - + +
1151A GLN* 2.8 34.6 + - - +
1153A SER* 1.3 70.9 - - - +
1155A ALA* 1.3 56.9 + - - +
1157A ALA* 3.7 4.8 - - - +
1158A LEU* 2.7 39.1 + - + +
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Residues in contact with ALA1155 (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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1142A THR* 3.9 26.9 - - + +
1145A LEU* 3.4 21.8 - - + +
1146A LEU* 4.0 9.2 - - + -
1150A LEU* 4.2 7.3 - - + +
1151A GLN 2.8 11.8 + - - +
1152A GLU* 3.4 14.8 - - - +
1154A GLU* 1.3 76.9 - - - +
1156A ASP* 1.3 58.1 + - - +
1159A ALA* 2.9 32.2 + - - +
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Residues in contact with ASP1156 (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* 3.6 31.4 + - - -
1139A LYS* 6.0 1.7 - - - +
1142A THR* 3.7 20.3 + - + +
1152A GLU 2.8 19.8 + - - +
1153A SER* 3.9 3.8 - - - +
1155A ALA* 1.3 73.7 - - - +
1157A ALA* 1.3 60.8 + - - +
1159A ALA* 3.7 0.5 - - - +
1160A GLY* 3.0 22.2 + - - -
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Residues in contact with ALA1157 (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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1153A SER 3.1 17.7 + - - +
1154A GLU* 3.7 6.1 - - - +
1156A ASP* 1.3 78.7 + - - +
1158A LEU* 1.3 68.4 + - - +
1160A GLY* 3.1 2.8 + - - -
1161A LYS* 2.9 23.0 + - - +
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Residues in contact with LEU1158 (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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1111A PHE* 4.3 20.6 - - + +
1112A MET* 3.8 29.6 - - + -
1128A LEU* 5.2 0.2 - - + -
1145A LEU* 3.6 28.0 - - + -
1150A LEU* 4.3 7.0 - - + -
1154A GLU 2.7 21.1 + - - +
1157A ALA* 1.3 72.2 - - - +
1159A ALA* 1.3 57.4 + - - +
1161A LYS* 3.0 27.8 + - + +
1162A ILE* 2.8 51.0 + - + +
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Residues in contact with ALA1159 (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* 3.9 6.1 - - + +
1141A LEU* 3.8 15.6 - - + +
1142A THR* 3.3 40.2 - - - +
1145A LEU* 3.8 5.1 - - + +
1155A ALA 2.9 13.6 + - - +
1156A ASP 3.7 2.7 - - - +
1158A LEU* 1.3 76.9 - - - +
1160A GLY* 1.3 57.6 + - - +
1162A ILE* 3.0 8.8 + - - +
1163A MET* 2.8 34.1 + - - +
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Residues in contact with GLY1160 (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* 3.8 22.3 - - - +
1156A ASP 3.0 15.7 + - - -
1157A ALA* 3.7 2.9 - - - -
1159A ALA* 1.3 76.2 - - - +
1161A LYS* 1.3 61.9 + - - +
1163A MET* 3.5 5.8 + - - +
1164A LEU* 3.5 28.4 + - - +
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Residues in contact with LYS1161 (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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1111A PHE* 5.5 6.4 + - + -
1157A ALA 2.9 12.5 + - - +
1158A LEU* 3.0 27.6 + - + +
1160A GLY* 1.3 75.8 - - - +
1162A ILE* 1.3 65.6 + - + +
1164A LEU* 3.2 5.1 + - - +
1165A GLN* 3.0 49.3 + - - +
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Residues in contact with ILE1162 (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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1111A PHE* 3.5 54.1 - - + -
1128A LEU* 3.8 32.8 - - + +
1129A LEU* 4.9 2.7 - - + -
1132A ARG* 2.8 36.4 + - - +
1141A LEU* 3.4 21.3 - - + -
1145A LEU* 4.8 0.4 - - + -
1158A LEU* 2.8 35.2 + - + +
1159A ALA* 3.4 7.4 - - - +
1161A LYS* 1.3 78.3 - - - +
1163A MET* 1.3 57.0 + - - +
1164A LEU 3.2 0.5 + - - -
1165A GLN* 3.4 8.5 + - - +
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Residues in contact with MET1163 (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 ARG* 4.1 28.2 + - + +
1136A ALA 3.9 18.4 - - - +
1137A ASP* 4.9 0.7 - - - -
1138A LYS* 4.0 38.4 - - + +
1141A LEU* 4.0 24.9 - - + -
1159A ALA 2.8 20.1 + - - +
1160A GLY* 3.7 8.3 - - - +
1161A LYS 3.2 0.2 - - - -
1162A ILE* 1.3 77.2 - - - +
1164A LEU* 1.3 68.9 + - + +
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Residues in contact with LEU1164 (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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1160A GLY 3.5 15.9 + - - +
1161A LYS* 3.2 5.7 + - - +
1163A MET* 1.3 88.7 - - + +
1165A GLN* 1.3 63.7 + - - +
1166A ASP* 3.7 1.7 + - - +
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Residues in contact with GLN1165 (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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1111A PHE* 3.3 26.1 - - + -
1132A ARG* 2.9 26.8 + - - +
1161A LYS* 3.0 45.9 + - + +
1162A ILE* 3.4 10.0 + - - +
1164A LEU* 1.3 79.4 - - - +
1166A ASP* 1.3 74.4 + - - +
1167A VAL* 3.2 11.9 + - + +
1171A GLN* 4.4 7.4 - - - +
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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