Contacts of the helix formed by residues 1208 - 1221 (chain M) in PDB entry 3HOU
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 THR1208 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1202M MET* 4.1 2.7 - - - -
1207M LEU* 1.3 75.6 + - - +
1209M MET* 1.3 70.6 + - - +
1210M GLY* 3.3 15.9 - - - +
1211M GLN* 2.6 44.5 + - - +
1212M VAL* 3.1 5.9 + - - +
1231M ASP* 3.2 26.0 + - - +
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Residues in contact with MET1209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197M LEU* 4.0 23.6 - - + -
1202M MET* 4.1 8.9 - - - +
1208M THR* 1.3 70.3 - - - +
1210M GLY* 1.3 64.8 + - - +
1212M VAL* 3.2 6.2 + - - +
1213M GLY* 2.8 24.6 + - - -
1228M TRP* 3.6 25.1 + - + -
1229M SER* 3.5 13.5 - - - +
1230M GLU* 4.3 1.8 - - + -
1231M ASP* 2.8 34.3 + - - +
1236M LEU* 3.3 27.6 - - + -
1237M ILE* 3.1 46.2 - - - +
1238M ILE* 4.5 4.5 - - + +
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Residues in contact with GLY1210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208M THR* 2.9 13.7 + - - +
1209M MET* 1.3 79.1 - - - +
1211M GLN* 1.3 51.3 + - - +
1213M GLY* 3.7 0.5 - - - -
1214M GLU* 2.8 45.6 + - - +
1228M TRP* 3.6 20.7 - - - +
1231M ASP* 5.0 0.2 + - - -
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Residues in contact with GLN1211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206M ASP 3.7 1.6 - - - +
1207M LEU* 3.0 22.1 - - + +
1208M THR* 2.6 49.5 + - - +
1210M GLY* 1.3 64.9 - - - -
1212M VAL* 1.3 70.9 + - - +
1214M GLU* 2.9 20.9 + - - +
1215M ARG* 3.1 16.4 + - + +
1274M ARG* 4.1 26.1 + - - +
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Residues in contact with VAL1212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143M LEU* 3.5 32.5 - - + -
1197M LEU* 4.0 5.6 - - + -
1202M MET* 3.1 38.8 - - + -
1207M LEU* 4.4 4.9 - - + -
1208M THR 3.6 4.9 - - - +
1209M MET* 3.6 4.7 - - - +
1211M GLN* 1.3 80.4 - - + +
1213M GLY* 1.3 66.1 + - - +
1215M ARG* 3.0 24.1 + - - +
1216M ILE* 3.2 10.4 - - + +
1238M ILE* 3.9 17.0 - - + -
1273M LEU* 4.3 22.2 - - + +
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Residues in contact with GLY1213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209M MET 2.8 19.8 + - - -
1210M GLY 3.7 0.9 - - - -
1212M VAL* 1.3 74.0 - - - +
1214M GLU* 1.3 64.6 + - - +
1216M ILE* 2.9 17.8 + - - +
1217M LYS* 2.7 26.1 + - - +
1226M VAL* 5.2 0.8 - - - +
1228M TRP* 3.9 24.6 - - - -
1238M ILE* 5.0 2.9 - - - +
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Residues in contact with GLU1214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210M GLY* 2.8 28.4 + - - +
1211M GLN* 2.9 10.9 + - - +
1213M GLY* 1.3 69.6 - - - +
1215M ARG* 1.3 53.3 + - - +
1217M LYS* 3.1 13.6 - - - +
1218M GLN* 2.7 57.1 + - - +
1228M TRP* 3.2 31.0 - - - -
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Residues in contact with ARG1215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211M GLN* 3.6 13.5 - - + +
1212M VAL* 3.0 13.1 + - - +
1213M GLY 2.9 0.2 + - - -
1214M GLU* 1.3 78.5 - - - +
1216M ILE* 1.3 53.8 + - + +
1218M GLN* 2.8 27.8 + - - +
1219M THR* 2.5 50.8 + - - +
1271M ILE* 4.9 5.4 - - + -
1272M THR* 2.4 40.5 + - - +
1273M LEU* 3.3 32.5 + - + +
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Residues in contact with ILE1216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143M LEU* 4.3 18.2 - - + -
1195M LEU* 4.8 2.7 - - + -
1212M VAL* 3.2 21.3 - - + +
1213M GLY* 2.9 10.6 + - - +
1215M ARG* 1.3 71.8 - - + +
1217M LYS* 1.3 57.2 + - - +
1219M THR* 2.8 26.8 + - - -
1220M PHE* 3.0 40.9 + - + -
1224M LEU* 4.5 7.6 - - + -
1226M VAL* 4.8 7.0 - - + -
1238M ILE* 3.6 42.8 - - + -
1240M CYS* 4.7 6.1 - - - -
1267M MET* 3.8 15.0 - - - -
1271M ILE* 4.3 6.7 - - + +
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Residues in contact with LYS1217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1213M GLY 2.7 15.9 + - - +
1214M GLU* 3.1 25.6 - - - +
1216M ILE* 1.3 73.2 - - - +
1218M GLN* 1.3 50.2 + - + +
1220M PHE* 5.7 0.4 - - - -
1221M LYS* 2.6 53.0 + - - +
1222M ASN* 5.6 2.1 + - - -
1224M LEU 2.9 26.5 + - - -
1225M PHE* 4.4 3.6 - - - +
1226M VAL* 4.3 29.3 - - + +
1228M TRP* 4.9 10.3 - - + -
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Residues in contact with GLN1218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214M GLU* 2.7 54.3 + - - +
1215M ARG* 2.9 36.1 + - - +
1217M LYS* 1.3 72.1 - - + +
1219M THR* 1.3 61.3 + - - +
1220M PHE 3.3 0.7 - - - -
1221M LYS* 2.7 43.7 - - + +
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Residues in contact with THR1219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215M ARG* 2.5 42.4 + - - +
1216M ILE* 2.8 8.6 + - - -
1218M GLN* 1.3 75.6 - - - +
1220M PHE* 1.3 68.4 + - + +
1221M LYS* 4.8 3.3 + - - +
1266M THR* 5.3 5.8 - - + -
1270M ASN 5.0 4.0 - - - +
1271M ILE* 3.6 35.6 - - + +
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Residues in contact with PHE1220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216M ILE* 3.0 42.5 + - + +
1217M LYS* 5.7 0.2 - - - -
1219M THR* 1.3 83.0 - - + +
1221M LYS* 1.3 69.2 + - - +
1223M ASP* 2.6 32.4 - - - +
1224M LEU* 3.4 39.0 - - + -
1263M ILE* 3.7 38.1 - - + -
1266M THR* 4.3 23.1 - - + -
1267M MET* 3.7 17.3 - - + -
1271M ILE* 4.3 9.0 - - + -
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Residues in contact with LYS1221 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217M LYS* 2.6 48.5 + - - +
1218M GLN* 2.7 39.9 - - - +
1219M THR 4.8 3.3 + - - +
1220M PHE* 1.3 75.7 - - - +
1222M ASN* 1.3 68.3 + - + +
1223M ASP 3.0 8.8 + - - -
1224M LEU 3.7 5.4 + - - +
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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