Contacts of the helix formed by residues 1181 - 1201 (chain B) in PDB entry 4DM8
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 GLU1181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180B TYR* 1.3 87.1 - - + +
1182B MET* 1.3 64.4 + - + +
1184B ALA* 3.2 12.0 + - - +
1185B GLU* 2.8 57.6 + - - +
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Residues in contact with MET1182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180B TYR 3.3 5.0 - - - +
1181B GLU* 1.3 76.7 - - + +
1183B THR* 1.3 59.8 + - - +
1185B GLU* 3.8 18.9 - - - +
1186B LEU* 2.8 78.8 + - + +
1356B PRO* 5.9 4.3 - - + -
1359B GLU* 5.6 5.6 - - + -
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Residues in contact with THR1183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180B TYR* 3.3 25.3 + - + +
1181B GLU 3.2 0.4 - - - -
1182B MET* 1.3 78.4 - - - +
1184B ALA* 1.3 58.0 + - - +
1186B LEU* 3.7 5.8 - - - +
1187B ASP* 2.8 54.0 + - - +
1363B ILE* 5.6 6.9 - - + +
1367B LYS* 5.3 15.2 + - - +
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Residues in contact with ALA1184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180B TYR* 3.1 16.7 + - + +
1181B GLU* 3.4 17.5 - - - +
1183B THR* 1.3 81.8 - - - +
1185B GLU* 1.3 63.5 + - + +
1187B ASP* 3.7 7.5 - - - +
1188B ASP* 2.9 25.4 + - - +
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Residues in contact with GLU1185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181B GLU* 2.8 50.4 + - - +
1182B MET* 3.8 18.5 - - - +
1184B ALA* 1.3 76.2 - - + +
1186B LEU* 1.3 64.7 + - + +
1188B ASP* 3.3 8.3 + - - +
1189B LEU* 2.9 27.7 + - - +
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Residues in contact with LEU1186 (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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1182B MET* 2.8 59.4 + - + +
1183B THR 3.7 3.1 - - - +
1185B GLU* 1.3 75.7 - - + +
1187B ASP* 1.3 55.9 + - - +
1189B LEU* 3.1 9.0 + - + +
1190B THR* 2.7 39.4 + - - -
1356B PRO* 4.3 24.7 - - + +
1359B GLU* 4.3 9.6 - - + -
1360B ALA* 4.5 17.0 - - - +
1363B ILE* 3.4 34.5 - - + -
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Residues in contact with ASP1187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183B THR* 2.8 44.4 + - - +
1184B ALA* 3.7 5.6 + - - +
1186B LEU* 1.3 74.2 - - - +
1188B ASP* 1.3 63.2 + - - +
1190B THR* 3.3 9.1 + - - -
1191B GLU* 3.0 25.1 + - - +
1363B ILE* 5.1 10.2 - - - +
1367B LYS* 5.6 4.9 - - - +
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Residues in contact with ASP1188 (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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1184B ALA 2.9 17.7 + - - +
1185B GLU* 3.4 9.0 - - - +
1187B ASP* 1.3 78.6 - - - +
1189B LEU* 1.3 61.6 + - - +
1191B GLU* 3.4 6.5 + - - +
1192B LYS* 3.2 34.8 + - - +
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Residues in contact with LEU1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185B GLU 2.9 14.5 + - - +
1186B LEU* 3.4 12.8 - - + +
1188B ASP* 1.3 74.7 - - - +
1190B THR* 1.3 67.1 + - - +
1192B LYS* 3.1 6.1 + - - +
1193B ILE* 3.0 38.8 + - + +
1249B PRO* 3.4 42.0 - - + -
1356B PRO* 3.8 41.3 - - + +
1357B LEU* 4.1 13.9 - - + -
1360B ALA* 4.7 5.8 - - + -
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Residues in contact with THR1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186B LEU 2.7 23.7 + - - -
1187B ASP* 3.3 9.7 + - - -
1189B LEU* 1.3 73.7 - - - +
1191B GLU* 1.3 58.8 + - - +
1193B ILE* 3.4 6.8 + - - +
1194B ARG* 2.9 28.1 + - + +
1326B THR* 3.3 32.8 - - + +
1330B LEU* 4.5 6.3 - - + -
1360B ALA* 3.8 23.0 + - - +
1364B TYR* 4.2 15.1 - - + +
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Residues in contact with GLU1191 (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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1187B ASP 3.0 16.8 + - - +
1188B ASP* 3.7 6.7 - - - +
1190B THR* 1.3 75.0 - - - +
1192B LYS* 1.3 61.3 + - - +
1194B ARG* 2.6 46.1 + - - -
1195B LYS* 2.9 39.1 + - + +
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Residues in contact with LYS1192 (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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1188B ASP* 3.2 23.9 + - - +
1189B LEU* 3.1 11.0 + - + +
1191B GLU* 1.3 76.6 - - - +
1193B ILE* 1.3 52.8 + - - +
1195B LYS* 3.2 25.6 + - - +
1196B ALA* 2.7 37.7 + - - +
1247B ARG 4.5 9.2 + - - +
1249B PRO* 3.3 41.0 - - + +
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Residues in contact with ILE1193 (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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1189B LEU* 3.0 37.8 + - + +
1190B THR 3.8 4.0 - - - +
1192B LYS* 1.3 75.4 - - - +
1194B ARG* 1.3 57.7 + - - +
1196B ALA* 3.3 5.1 + - - +
1197B HIS* 2.8 30.7 + - - +
1244B PHE* 4.2 7.6 - - + -
1248B LEU* 3.3 24.0 - - + -
1249B PRO* 3.9 9.4 - - + -
1326B THR 4.9 0.4 - - - +
1329B GLY* 3.3 38.4 - - - +
1330B LEU* 3.6 24.7 - - + +
1333B ALA* 4.3 1.3 - - + -
1357B LEU* 4.2 9.9 - - + -
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Residues in contact with ARG1194 (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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1190B THR* 2.9 18.1 + - + +
1191B GLU* 2.6 40.1 + - - +
1193B ILE* 1.3 77.0 - - - +
1195B LYS* 1.3 75.2 - - - +
1197B HIS* 3.2 2.4 + - - +
1198B GLN* 2.6 82.8 + - - +
1325B ASP* 4.1 4.2 - - + +
1326B THR* 3.2 42.1 - - - +
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Residues in contact with LYS1195 (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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1191B GLU* 2.9 27.9 + - + +
1192B LYS* 3.4 27.6 - - - +
1194B ARG* 1.3 90.9 - - - +
1196B ALA* 1.3 63.7 + - - +
1198B GLN* 3.1 2.9 + - - -
1199B GLU* 2.9 53.8 + - + +
1247B ARG* 5.7 4.5 - - - +
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Residues in contact with ALA1196 (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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1192B LYS 2.7 20.5 + - - +
1193B ILE* 3.6 7.2 - - - +
1195B LYS* 1.3 74.7 - - - +
1197B HIS* 1.3 59.9 + - - +
1199B GLU 4.0 0.2 - - - -
1200B THR* 2.9 31.7 + - - +
1244B PHE* 3.6 20.9 - - + +
1247B ARG* 3.7 40.4 - - + +
1248B LEU* 4.9 3.1 - - + -
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Residues in contact with HIS1197 (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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1193B ILE 2.8 20.9 + - - +
1194B ARG 3.6 2.9 - - - +
1196B ALA* 1.3 74.7 - - - +
1198B GLN* 1.3 64.2 + - - +
1200B THR* 3.1 4.4 + - - -
1201B PHE* 3.0 58.3 + + + +
1244B PHE* 3.7 10.4 - - + -
1274B ARG* 4.1 18.1 + - + -
1277B THR* 5.6 0.4 + - - -
1325B ASP* 3.3 44.2 + - - +
1328B THR* 3.6 28.1 - - + +
1329B GLY* 3.9 19.6 - - - -
1332B SER* 4.8 3.7 + - - -
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Residues in contact with GLN1198 (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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1194B ARG* 2.6 48.7 + - - +
1195B LYS* 3.8 3.1 - - - +
1197B HIS* 1.3 77.9 - - - +
1199B GLU* 1.3 64.0 + - + +
1200B THR 3.3 0.7 + - - -
1201B PHE 3.6 18.8 + - - +
1202B PRO* 4.4 3.1 - - - +
1203B SER* 6.5 0.7 - - - -
1206B GLN* 5.4 4.4 + - - +
1325B ASP* 2.5 47.7 + - + +
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Residues in contact with GLU1199 (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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1195B LYS* 2.9 39.4 + - + +
1198B GLN* 1.3 79.5 - - + +
1200B THR* 1.3 60.6 + - - +
1201B PHE 3.6 0.2 - - - -
1240B LYS* 4.3 10.9 + - - -
1243B GLU* 4.6 3.1 - - - +
1247B ARG* 2.5 42.3 + - - +
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Residues in contact with THR1200 (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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1196B ALA 2.9 23.1 + - - +
1197B HIS 3.1 3.2 + - - -
1199B GLU* 1.3 81.5 - - - +
1201B PHE* 1.3 58.4 + - - +
1202B PRO* 4.3 4.6 - - - +
1240B LYS* 3.2 48.5 - - - +
1243B GLU* 3.9 25.4 - - + +
1244B PHE* 3.6 10.5 - - - +
1247B ARG* 4.3 6.5 - - - -
1274B ARG* 3.0 34.8 + - - -
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Residues in contact with PHE1201 (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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1197B HIS* 3.0 37.8 + + + +
1198B GLN* 3.6 13.7 + - - +
1199B GLU 3.6 0.4 - - - -
1200B THR* 1.3 82.0 - - - +
1202B PRO* 1.3 71.6 - - - +
1203B SER* 3.6 1.4 + - - -
1237B CYS* 4.3 3.8 - - - -
1274B ARG* 3.4 72.7 - - + +
1275B ILE 4.5 0.2 - - - -
1277B THR* 3.9 10.1 - - - -
1278B ARG* 3.2 35.7 - - - -
1289B SER* 3.8 4.7 - - - -
1325B ASP* 5.1 2.3 - - - +
1501B REA 3.2 25.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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