Contacts of the helix formed by residues 1210 - 1221 (chain A) in PDB entry 1Y8Z
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 GLY1210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1201A TRP* 3.7 2.7 + - - -
1207A THR 3.2 7.7 + - - -
1208A TRP 3.1 5.1 + - - -
1209A LYS* 1.3 80.3 - - - +
1211A PHE* 1.3 65.1 + - - +
1212A TYR 3.3 2.2 - - - -
1213A GLN* 3.3 20.0 + - - +
1214A MET 3.3 15.4 + - - -
1293A LEU* 3.5 25.9 - - - +
1295A LYS* 4.7 2.9 - - - -
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Residues in contact with PHE1211 (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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1201A TRP* 3.8 11.0 - + + -
1204A ARG 4.1 10.3 - - - -
1205A THR* 4.0 10.3 - - + -
1206A THR 3.5 40.2 - - - -
1207A THR* 3.5 13.0 + - + -
1209A LYS 3.5 1.8 + - - -
1210A GLY* 1.3 78.0 - - - +
1212A TYR* 1.3 108.4 + + - +
1214A MET* 3.2 2.9 + - - +
1215A PHE* 3.0 31.4 + + + -
1231A MET* 3.6 23.5 - - + +
1234A LEU* 4.0 12.3 - - + -
1239A ALA* 5.2 5.6 - - + -
1242A ALA* 6.0 0.4 - - + -
1243A ILE* 3.4 38.1 - - + -
6C T 6.1 0.2 - - + -
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Residues in contact with TYR1212 (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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1207A THR* 4.1 18.7 + - + +
1210A GLY 3.3 0.4 - - - -
1211A PHE* 1.3 113.2 - + - +
1213A GLN* 1.3 65.1 + - - +
1215A PHE* 3.4 6.1 + - - +
1216A ASP* 3.0 28.5 + - - +
1242A ALA* 3.4 29.5 - - - +
1243A ILE* 4.5 3.6 - - + -
1246A LYS* 3.9 9.2 - - + -
1248A ILE* 3.8 28.4 - - + +
3C T 3.5 80.1 + + + +
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Residues in contact with GLN1213 (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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1207A THR 4.9 1.8 + - - +
1210A GLY* 3.3 25.4 - - - +
1211A PHE 3.3 0.2 - - - -
1212A TYR* 1.3 75.9 - - - +
1214A MET* 1.3 60.2 + - - +
1216A ASP* 3.6 6.8 - - - +
1217A PHE* 2.8 31.2 + - - +
1293A LEU* 4.1 8.1 - - + -
1295A LYS* 3.2 23.7 - - - +
1322A TRP* 3.5 28.5 - - + -
1348A PHE* 4.1 7.5 - - + -
1350A GLU* 3.0 33.8 + - + +
1353A MET* 5.0 1.5 - - - +
3C T 3.5 22.0 + - - -
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Residues in contact with MET1214 (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 ASN* 4.3 4.5 - - + +
1201A TRP* 3.7 36.1 - - + -
1210A GLY 3.3 4.7 + - - +
1211A PHE 3.2 9.3 + - - +
1213A GLN* 1.3 77.6 - - - +
1215A PHE* 1.3 65.5 + - - +
1217A PHE* 3.4 6.3 + - - +
1218A HIS* 3.0 24.1 + - - +
1222A LEU* 4.2 11.7 - - + -
1229A THR* 3.7 24.5 - - + -
1231A MET* 3.8 20.0 - - + -
1291A TYR* 3.6 55.9 - - + -
1293A LEU* 3.9 6.7 - - + +
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Residues in contact with PHE1215 (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 PHE* 3.0 29.9 + + - -
1212A TYR* 3.7 7.0 - - - +
1214A MET* 1.3 75.6 - - - +
1216A ASP* 1.3 57.5 + - - +
1218A HIS* 3.4 6.7 + - - +
1219A GLU* 3.0 32.5 + - - +
1229A THR* 6.4 0.2 - - - -
1231A MET* 3.6 28.9 - - + -
1234A LEU* 3.9 14.4 - - + -
1240A PHE* 6.0 0.7 - + - -
1243A ILE* 4.1 28.7 - - + -
1248A ILE* 3.5 46.7 - - + -
1249A PRO 4.0 7.9 - - - -
1250A TYR* 4.2 5.2 - + + -
1269A ALA* 3.8 20.0 - - + -
1271A ILE* 3.9 9.6 - - + -
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Residues in contact with ASP1216 (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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1212A TYR 3.0 18.0 + - - +
1213A GLN* 3.6 7.9 - - - +
1214A MET 3.2 0.2 - - - -
1215A PHE* 1.3 74.7 - - - +
1217A PHE* 1.3 60.2 + - - +
1219A GLU* 3.3 11.4 + - - +
1220A LYS* 2.9 72.7 + - - +
1353A MET* 3.6 15.7 - - - +
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Residues in contact with PHE1217 (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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1213A GLN 2.8 19.1 + - - +
1214A MET* 3.8 7.0 - - - +
1216A ASP* 1.3 76.3 - - - +
1218A HIS* 1.3 57.4 + - - +
1221A PHE* 2.8 37.6 + + + -
1222A LEU* 3.1 31.4 + - + -
1291A TYR* 3.5 32.8 - + - -
1348A PHE* 3.6 24.7 - + + -
1353A MET* 3.7 44.4 - - + -
1356A THR* 3.9 11.9 - - + -
1357A PHE* 4.0 14.8 - + + -
1360A ILE* 3.9 16.8 - - + -
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Residues in contact with HIS1218 (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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1214A MET 3.0 18.1 + - - +
1215A PHE* 3.7 5.5 + - - +
1217A PHE* 1.3 79.5 - - - +
1219A GLU* 1.3 62.4 + - - +
1222A LEU* 3.4 21.3 + - + -
1223A LYS* 2.6 54.7 + - + +
1227A LYS 4.1 6.4 + - - -
1228A SER* 4.7 0.2 - - - -
1229A THR* 2.8 46.9 + - + +
1267A GLN 3.0 28.8 + - - -
1268A PRO* 3.7 2.7 - - + +
1269A ALA* 3.6 25.3 + - + +
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Residues in contact with GLU1219 (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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1215A PHE 3.0 19.2 + - - +
1216A ASP* 3.8 12.2 - - - +
1218A HIS* 1.3 80.1 - - - +
1220A LYS* 1.3 60.0 + - + +
1223A LYS* 4.4 13.3 - - + +
1224A PRO* 3.3 18.9 - - - +
1249A PRO* 5.4 15.0 - - + +
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Residues in contact with LYS1220 (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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1216A ASP* 2.9 50.6 + - - +
1219A GLU* 1.3 85.5 - - + +
1221A PHE* 1.3 81.3 + - + +
1224A PRO* 3.6 12.1 - - - +
1353A MET* 4.1 15.4 - - + +
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Residues in contact with PHE1221 (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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1217A PHE* 2.8 40.9 + + + +
1219A GLU 3.6 0.4 - - - -
1220A LYS* 1.3 100.0 - - + +
1222A LEU* 1.3 65.8 + - - +
1224A PRO* 3.4 4.7 - - - +
1225A ALA* 3.1 26.2 + - - +
1353A MET* 3.5 24.5 - - + -
1354A GLU* 3.5 41.3 - - + -
1357A PHE* 4.0 32.4 - + + -
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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