Contacts of the helix formed by residues 1137 - 1147 (chain A) in PDB entry 1MWH
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 ASP1137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998A TYR* 4.1 13.2 + - + +
1002A ILE* 5.1 0.2 - - - +
1135A GLY 3.6 1.5 + - - -
1136A ALA* 1.3 75.2 - - - +
1138A LYS* 1.3 69.4 + - - +
1139A LYS* 3.2 40.5 + - - +
1140A ALA* 2.7 35.6 + - + +
1141A LEU* 3.5 5.1 + - - +
1163A MET* 5.0 1.9 - - - +
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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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1136A ALA 4.1 0.4 + - - -
1137A ASP* 1.3 82.4 + - - +
1139A LYS* 1.3 60.7 + - + +
1141A LEU* 2.8 24.0 + - - +
1142A THR* 3.0 13.3 + - - +
1156A ASP* 3.3 48.6 + - - +
1159A ALA 4.3 1.6 - - - -
1160A GLY* 3.6 20.3 - - - +
1163A MET* 3.9 36.5 - - + +
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Residues in contact with LYS1139 (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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994A GLU* 4.2 11.3 - - - +
998A TYR* 3.4 50.2 + - + +
1137A ASP* 3.1 24.9 + - - +
1138A LYS* 1.3 82.9 - - + +
1140A ALA* 1.3 57.6 + - - +
1142A THR* 3.3 13.9 - - + +
1143A ALA* 2.9 26.0 + - - +
1156A ASP* 6.0 1.3 - - - +
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Residues in contact with ALA1140 (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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995A TRP* 3.8 5.5 - - - -
998A TYR* 3.6 35.9 - - + +
999A GLY* 4.1 6.1 - - - +
1131A LEU* 4.4 5.6 - - + -
1136A ALA* 3.9 17.5 - - + -
1137A ASP 2.7 23.5 + - - +
1139A LYS* 1.3 71.1 - - - +
1141A LEU* 1.3 63.6 + - + +
1143A ALA* 3.1 7.6 + - - +
1144A GLN* 3.0 21.0 + - - +
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Residues in contact with LEU1141 (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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1128A LEU* 3.6 37.0 - - + +
1131A LEU* 3.7 25.6 - - + -
1132A ARG* 4.1 8.1 - - + +
1136A ALA* 4.8 1.3 - - + +
1137A ASP 3.9 12.8 - - - +
1138A LYS* 2.8 8.5 + - - +
1140A ALA* 1.3 78.5 - - + +
1142A THR* 1.3 61.9 + - - +
1144A GLN* 3.1 5.3 + - - +
1145A LEU* 3.0 28.2 + - - +
1159A ALA* 3.8 13.9 - - + +
1162A ILE* 3.5 38.4 - - + -
1163A MET* 4.2 20.9 - - - -
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Residues in contact with THR1142 (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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990A ARG* 6.2 0.4 - - - +
994A GLU* 5.2 4.5 - - - +
1138A LYS* 3.0 15.7 + - - +
1139A LYS* 3.3 18.8 - - + +
1141A LEU* 1.3 79.1 - - - +
1143A ALA* 1.3 62.1 + - - +
1145A LEU* 3.4 0.9 + - - -
1146A LEU* 3.1 34.1 + - + +
1152A GLU* 4.8 4.5 - - + +
1155A ALA* 3.7 23.9 - - + +
1156A ASP* 3.8 20.6 + - + +
1159A ALA* 3.3 17.9 - - - +
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Residues in contact with ALA1143 (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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991A GLY* 3.7 7.5 - - - +
994A GLU* 3.7 25.8 - - + +
995A TRP* 3.8 17.7 - - + +
1139A LYS 2.9 14.2 + - - +
1140A ALA* 3.3 10.3 - - - +
1142A THR* 1.3 78.9 - - - +
1144A GLN* 1.3 60.9 + - - +
1146A LEU* 3.2 14.1 + - - +
1147A MET* 3.0 29.3 + - - +
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Residues in contact with GLN1144 (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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995A TRP* 4.2 11.5 - - + -
1003A ILE* 4.1 6.2 - - - +
1006A PRO* 3.7 9.5 - - - +
1007A PRO* 2.9 58.6 + - - +
1124A ILE* 4.9 5.5 - - + +
1127A ALA* 3.4 13.3 - - + +
1128A LEU* 3.9 23.1 - - + -
1131A LEU* 4.1 13.4 - - + +
1140A ALA 3.0 12.4 + - - +
1141A LEU 3.1 8.5 + - - +
1143A ALA* 1.3 78.0 - - - +
1145A LEU* 1.3 62.7 + - - +
1147A MET* 3.3 13.3 + - - +
1148A VAL* 3.4 14.2 + - - +
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Residues in contact with LEU1145 (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 MET* 4.0 15.7 - - - -
1124A ILE* 5.0 0.9 - - + -
1128A LEU* 3.8 33.2 - - + -
1141A LEU 3.0 20.2 + - - +
1142A THR 3.9 3.8 - - - +
1143A ALA 3.3 0.2 - - - -
1144A GLN* 1.3 72.8 - - - +
1146A LEU* 1.3 64.4 + - - +
1148A VAL* 3.1 21.8 - - + +
1150A LEU* 3.1 31.5 + - + +
1155A ALA* 3.4 31.2 - - + +
1158A LEU* 3.8 26.7 - - + -
1159A ALA* 3.6 17.3 - - + +
1162A ILE* 4.7 0.2 - - + -
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Residues in contact with LEU1146 (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* 3.6 19.3 - - + +
988A VAL* 3.6 14.0 + - - -
990A ARG* 4.4 15.7 - - + +
991A GLY* 3.6 22.7 - - - +
994A GLU* 4.6 5.8 - - + -
1142A THR* 3.1 35.0 + - + +
1143A ALA* 3.2 7.4 + - - +
1145A LEU* 1.3 76.7 - - - +
1147A MET* 1.3 62.9 + - - +
1148A VAL 3.1 2.8 + - - -
1149A GLY* 3.1 12.3 + - - -
1150A LEU 3.5 20.5 + - - +
1151A GLN 4.2 0.4 - - - -
1152A GLU* 3.5 39.0 - - + +
1155A ALA* 4.1 5.8 - - + -
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Residues in contact with MET1147 (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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988A VAL* 3.8 14.5 - - + +
991A GLY* 3.5 17.5 - - - +
992A ARG* 3.4 27.8 - - + +
995A TRP* 3.8 38.6 - - + -
1006A PRO* 5.0 10.3 - - + -
1007A PRO 4.0 11.0 - - - +
1008A SER* 3.6 24.9 + - - +
1009A LEU* 3.0 29.3 + - - +
1143A ALA 3.0 17.1 + - - +
1144A GLN* 3.6 10.5 - - - +
1145A LEU 3.3 0.2 - - - -
1146A LEU* 1.3 77.3 - - - +
1148A VAL* 1.3 56.9 + - - +
1149A GLY 3.4 0.9 - - - -
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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