Contacts of the helix formed by residues 1217 - 1233 (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 TRP1217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A ARG* 5.8 2.7 - - - +
1133A THR* 3.2 36.0 + - + +
1172A LEU* 3.6 36.3 - - + +
1175A VAL* 4.8 4.2 - - + +
1214A ARG 3.4 18.8 + - - -
1215A MET* 3.4 22.2 - - + +
1216A GLY* 1.3 76.0 - - - +
1218A LEU* 1.3 76.0 + - + +
1219A ARG 3.2 0.2 - - - -
1220A ALA* 3.3 19.4 + - - +
1221A ILE* 3.8 25.8 + - + +
1253A GLY* 3.5 34.1 - - - -
1256A PHE* 4.0 3.8 - - + -
1257A MET* 3.9 16.9 - - + -
1260A MET* 3.4 28.0 - - + -
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Residues in contact with LEU1218 (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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1211A ILE* 4.4 12.3 - - + -
1212A PRO* 4.3 6.5 - - + -
1215A MET* 2.9 30.3 + - + +
1217A TRP* 1.3 92.5 - - + +
1219A ARG* 1.3 54.2 + - - +
1221A ILE* 2.9 9.3 + - + +
1222A LEU* 2.8 45.0 + - + +
1245A ILE* 5.5 0.7 - - + -
1249A GLY* 3.5 33.9 - - - +
1252A LEU* 4.4 9.9 - - + -
1253A GLY* 4.2 8.3 - - - +
1256A PHE* 3.8 35.4 - - + -
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Residues in contact with ARG1219 (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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1199A LEU* 3.8 24.6 - - + +
1211A ILE* 3.5 38.7 + - + +
1216A GLY* 3.3 31.7 + - - +
1218A LEU* 1.3 77.6 - - - +
1220A ALA* 1.3 56.0 + - - +
1222A LEU* 3.7 4.8 - - - +
1223A ARG* 2.9 63.6 + - - +
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Residues in contact with ALA1220 (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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1169A THR* 3.7 35.2 - - - +
1172A LEU* 3.9 24.2 - - + -
1173A ALA* 4.1 5.4 - - - +
1216A GLY 4.5 0.4 + - - -
1217A TRP 3.3 13.0 + - - +
1218A LEU 3.1 0.6 - - - -
1219A ARG* 1.3 73.1 - - - +
1221A ILE* 1.3 68.3 - - + +
1223A ARG* 3.1 16.8 + - - +
1224A PHE* 3.3 18.9 + - - -
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Residues in contact with ILE1221 (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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1056A TYR* 4.0 18.6 - - + -
1172A LEU 5.6 0.2 - - - +
1173A ALA* 5.0 4.7 - - - -
1175A VAL* 4.5 9.4 - - + -
1176A VAL* 3.9 27.4 - - + -
1178A LEU* 4.1 11.4 - - + -
1217A TRP* 3.9 38.1 - - + +
1218A LEU* 2.9 8.1 + - + +
1220A ALA* 1.3 77.1 - - + +
1222A LEU* 1.3 67.5 + - + +
1224A PHE* 3.0 15.3 + - - +
1225A LEU* 3.2 15.2 + - + +
1256A PHE* 3.9 35.9 - - + -
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Residues in contact with LEU1222 (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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1059A VAL* 3.8 38.8 - - + -
1061A TRP* 3.2 16.1 - - + -
1199A LEU* 3.9 16.8 - - + -
1211A ILE* 4.1 26.0 - - + -
1218A LEU* 2.8 27.4 + - + +
1219A ARG* 3.7 8.1 - - - +
1221A ILE* 1.3 80.1 - - + +
1223A ARG* 1.3 63.9 + - - +
1225A LEU* 3.3 7.1 + - + +
1226A GLY 3.1 18.5 + - - -
1242A LEU* 4.2 19.3 - - + -
1245A ILE* 4.5 7.9 - - + -
1252A LEU* 4.6 9.9 - - + -
1256A PHE* 6.5 0.2 - - + -
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Residues in contact with ARG1223 (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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1169A THR* 2.9 38.7 + - + +
1193A PHE* 3.6 35.7 + - + +
1194A LYS* 5.5 3.7 + - - +
1197A VAL* 3.9 16.4 + - + +
1199A LEU* 4.0 16.1 - - + +
1219A ARG* 2.9 53.0 + - - +
1220A ALA* 3.1 7.9 + - - +
1222A LEU* 1.3 76.8 - - - +
1224A PHE* 1.3 64.5 + - - +
1226A GLY* 3.4 0.9 + - - -
1227A ALA* 3.0 24.4 + - - +
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Residues in contact with PHE1224 (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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897A LEU* 3.9 27.2 - - + +
1169A THR* 4.0 10.8 - - + -
1170A VAL* 4.2 8.1 - - + -
1173A ALA* 3.2 33.0 - - + -
1178A LEU* 3.8 24.2 - - + -
1179A ALA 3.5 28.3 - - - -
1180A VAL* 3.8 19.5 - - + -
1181A PRO* 4.9 1.3 - - + -
1184A TRP* 4.8 2.4 - + - -
1193A PHE* 3.6 37.9 - + - -
1220A ALA 3.3 10.7 + - - -
1221A ILE 3.0 9.0 + - - +
1223A ARG* 1.3 80.5 - - - +
1225A LEU* 1.3 56.6 + - - +
1227A ALA* 3.2 2.4 + - - +
1228A GLY* 2.7 28.4 + - - -
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Residues in contact with LEU1225 (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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897A LEU* 3.8 13.0 - - + -
900A TYR* 3.6 31.7 - - + -
1056A TYR* 3.5 64.4 - - + +
1059A VAL* 3.9 24.7 - - + -
1061A TRP* 4.0 7.2 - - + -
1178A LEU* 5.1 2.2 - - + -
1221A ILE* 3.2 16.0 + - + +
1222A LEU* 3.7 13.2 - - + +
1224A PHE* 1.3 76.3 - - - +
1226A GLY* 1.3 63.1 + - - +
1228A GLY* 3.1 9.9 + - - -
1229A MET* 3.3 10.9 + - - +
1256A PHE* 5.6 0.9 - - + -
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Residues in contact with GLY1226 (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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1061A TRP* 3.4 30.2 - - - -
1197A VAL* 4.2 1.3 - - - -
1222A LEU 3.1 10.5 + - - -
1223A ARG 3.9 1.8 - - - -
1225A LEU* 1.3 77.2 - - - +
1227A ALA* 1.3 63.6 + - - +
1229A MET 3.3 2.1 + - - -
1230A VAL* 3.1 25.5 + - - +
1240A ILE* 3.7 19.3 - - - +
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Residues in contact with ALA1227 (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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1184A TRP* 3.7 12.1 - - + -
1192A MET* 3.9 22.2 - - + -
1193A PHE* 3.5 28.5 - - + -
1197A VAL* 3.9 6.3 - - + +
1223A ARG 3.0 17.7 + - - +
1224A PHE 3.6 2.0 - - - +
1226A GLY* 1.3 71.9 - - - +
1228A GLY* 1.3 67.2 + - - +
1230A VAL* 3.2 1.5 + - - -
1231A MET* 2.9 29.3 + - - +
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Residues in contact with GLY1228 (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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893A PRO* 4.0 17.2 - - - +
897A LEU* 4.6 3.8 - - - -
901A SER* 2.8 17.9 - - - -
1184A TRP* 3.9 3.1 - - - -
1224A PHE 2.7 15.8 + - - -
1225A LEU 3.1 4.0 + - - -
1227A ALA* 1.3 77.4 - - - +
1229A MET* 1.3 55.0 + - - +
1231A MET* 3.4 0.9 + - - +
1232A THR* 2.7 35.5 + - - -
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Residues in contact with MET1229 (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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900A TYR* 4.2 7.2 - - + -
901A SER* 3.2 12.9 + - - +
904A SER* 3.5 49.6 - - - +
905A LEU* 3.6 9.6 - - + +
1061A TRP* 3.7 34.5 - - + +
1063A MET* 3.5 30.0 - - + +
1225A LEU 3.3 11.3 + - - +
1226A GLY 3.8 6.1 - - - +
1227A ALA 3.3 0.2 - - - -
1228A GLY* 1.3 72.4 - - - +
1230A VAL* 1.3 67.6 + - - +
1232A THR* 3.3 2.6 + - - -
1233A ALA* 3.1 25.8 + - - +
1240A ILE* 4.0 11.9 - - + -
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Residues in contact with VAL1230 (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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1063A MET* 5.0 4.0 - - - -
1091A LYS* 3.8 4.9 - - - -
1192A MET* 4.2 14.8 - - + -
1196A HIS 5.1 1.3 - - - +
1197A VAL* 5.4 0.9 - - + -
1226A GLY 3.1 17.6 + - - +
1227A ALA* 3.2 10.3 + - - +
1229A MET* 1.3 77.7 - - - +
1231A MET* 1.3 63.0 + - - +
1232A THR 3.5 0.2 + - - -
1233A ALA* 3.5 18.8 + - - +
1236A VAL 5.2 0.7 - - - +
1237A ALA* 3.9 15.0 - - + -
1238A VAL* 3.4 47.9 + - + +
1240A ILE* 3.5 28.3 - - + -
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Residues in contact with MET1231 (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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889A SER* 3.5 12.8 + - - -
891A TYR* 3.6 28.9 - - + +
1091A LYS* 3.5 29.2 - - + +
1095A VAL* 3.9 18.6 - - + -
1184A TRP* 3.5 34.1 - - + +
1187A LEU* 3.8 29.2 - - + -
1192A MET* 3.4 35.2 - - + +
1227A ALA 2.9 18.5 + - - +
1228A GLY 4.0 0.2 - - - +
1230A VAL* 1.3 77.3 - - - +
1232A THR* 1.3 61.2 + - - +
1233A ALA 3.4 0.2 - - - -
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Residues in contact with THR1232 (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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887A ILE 3.5 0.2 - - - +
888A PHE* 3.3 18.9 - - + -
889A SER* 2.8 26.9 + - - -
892A MET* 3.6 27.3 - - + +
893A PRO* 3.1 22.7 - - - +
901A SER* 3.2 13.6 - - - -
902A TRP* 4.2 4.7 - - + +
905A LEU* 3.5 20.2 - - + -
1228A GLY 2.7 21.4 + - - -
1229A MET 3.3 1.3 + - - -
1231A MET* 1.3 75.5 - - - +
1233A ALA* 1.3 60.8 + - - +
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Residues in contact with ALA1233 (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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887A ILE 3.6 5.6 - - - +
889A SER* 4.4 0.2 - - - -
905A LEU* 3.9 19.3 - - + +
1063A MET* 4.8 8.5 - - - -
1091A LYS* 2.7 28.4 + - - -
1229A MET 3.1 16.3 + - - +
1230A VAL* 3.7 6.7 - - - +
1231A MET 3.4 0.4 - - - -
1232A THR* 1.3 75.5 - - - +
1234A THR* 1.3 61.3 + - - +
1235A GLY 4.1 1.2 - - - +
1236A VAL 4.9 2.9 - - - +
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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