Contacts of the helix formed by residues 1208 - 1221 (chain A) in PDB entry 1Y1V
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1202A MET* 4.6 0.9 - - - -
1207A LEU* 1.3 78.1 + - - +
1209A MET* 1.3 71.5 + - - +
1210A GLY* 3.4 14.1 - - - +
1211A GLN* 2.5 43.9 + - + +
1212A VAL* 3.2 6.0 + - - -
1231A ASP* 3.5 26.1 + - - +
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Residues in contact with MET1209 (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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1197A LEU* 4.6 7.9 - - + -
1202A MET* 4.3 19.0 - - - +
1208A THR* 1.3 70.4 - - - +
1210A GLY* 1.3 69.8 + - - +
1212A VAL* 3.0 14.3 + - - +
1213A GLY* 3.1 12.1 + - - -
1228A TRP* 4.0 14.8 + - + +
1229A SER* 3.4 30.3 - - - +
1230A GLU* 4.5 0.7 - - - -
1231A ASP* 3.4 27.6 + - - +
1236A LEU* 3.6 25.6 - - + -
1237A ILE 3.1 45.1 - - - +
1238A ILE* 4.5 6.6 - - + +
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Residues in contact with GLY1210 (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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1208A THR* 2.6 14.0 + - - +
1209A MET* 1.3 78.2 - - - +
1211A GLN* 1.3 65.9 + - - -
1214A GLU* 2.7 34.9 + - - +
1228A TRP* 4.0 17.5 - - - +
1231A ASP* 5.0 0.4 + - - -
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Residues in contact with GLN1211 (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 LEU* 3.2 25.7 - - + +
1208A THR* 2.5 43.6 + - + +
1210A GLY* 1.3 68.7 - - - +
1212A VAL* 1.3 68.8 + - - +
1214A GLU* 3.0 7.7 - - - +
1215A ARG* 2.8 20.6 + - - +
1274A ARG* 3.6 19.1 + - - +
4E GLU* 5.9 1.0 + - - -
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Residues in contact with VAL1212 (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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1143A LEU* 4.6 11.4 - - + -
1146A VAL* 5.6 0.2 - - + -
1197A LEU* 4.1 11.9 - - + -
1202A MET* 3.3 36.1 - - + -
1207A LEU* 4.5 6.7 - - + +
1208A THR 4.1 4.3 - - - +
1209A MET* 3.0 11.2 + - - +
1211A GLN* 1.3 80.7 - - - +
1213A GLY* 1.3 68.9 + - - +
1215A ARG* 2.7 19.1 + - - +
1216A ILE* 3.1 12.0 + - + +
1238A ILE* 3.7 22.7 - - + -
1273A LEU* 4.4 24.7 - - + +
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Residues in contact with GLY1213 (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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1209A MET 3.1 8.3 + - - -
1210A GLY 4.0 0.4 - - - -
1212A VAL* 1.3 79.3 - - - +
1214A GLU* 1.3 53.9 + - - +
1215A ARG 2.5 2.6 + - - -
1216A ILE* 2.4 45.4 + - - -
1217A LYS* 2.7 12.0 + - - -
1226A VAL* 5.2 2.0 - - - -
1228A TRP* 4.4 19.5 - - - -
1238A ILE* 4.3 6.8 - - - +
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Residues in contact with GLU1214 (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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1210A GLY* 2.7 36.8 + - - +
1211A GLN* 3.0 11.4 - - - +
1213A GLY* 1.3 68.7 - - - +
1215A ARG* 1.3 58.5 + - - +
1217A LYS* 3.6 12.3 + - - +
1218A GLN* 3.2 35.1 + - - +
1228A TRP* 4.3 19.2 - - + -
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Residues in contact with ARG1215 (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 GLN 2.8 8.8 + - - +
1212A VAL* 2.7 15.1 + - - +
1213A GLY 2.5 3.8 + - - -
1214A GLU* 1.3 68.5 - - - +
1216A ILE* 1.3 60.3 + - + +
1217A LYS 3.0 1.6 - - - -
1218A GLN* 2.9 30.9 + - - +
1219A THR* 2.4 37.3 + - - +
1271A ILE* 5.2 3.6 - - + -
1272A THR* 3.5 32.1 + - - +
1273A LEU* 3.0 34.4 + - + +
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Residues in contact with ILE1216 (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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1143A LEU* 4.4 15.7 - - + -
1195A LEU* 5.3 0.9 - - + -
1212A VAL* 3.4 16.6 - - + +
1213A GLY* 2.4 31.1 + - - +
1215A ARG* 1.3 72.9 - - + +
1217A LYS* 1.3 59.2 + - - +
1219A THR* 2.9 26.5 + - - -
1220A PHE* 3.3 21.3 - - + -
1224A LEU* 5.4 1.5 - - + +
1226A VAL* 5.1 14.5 - - + +
1238A ILE* 3.4 33.2 - - + -
1267A MET* 3.9 25.8 - - - -
1271A ILE* 4.0 12.5 - - + +
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Residues in contact with LYS1217 (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 GLY 2.7 13.4 + - - +
1214A GLU* 3.7 17.5 - - - +
1216A ILE* 1.3 70.3 - - - +
1218A GLN* 1.3 51.5 + - - +
1219A THR 2.9 4.8 + - - -
1220A PHE* 4.6 0.3 - - - +
1221A LYS* 2.6 47.2 + - - +
1224A LEU 5.2 5.2 - - - +
1225A PHE* 4.8 13.8 - - - +
1226A VAL* 4.1 41.3 + - + +
1228A TRP* 4.6 20.2 - - + -
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Residues in contact with GLN1218 (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 GLU* 3.2 30.2 + - - +
1215A ARG* 2.9 31.8 + - - +
1217A LYS* 1.3 76.6 - - - +
1219A THR* 1.3 57.7 + - - +
1220A PHE 3.7 0.2 - - - -
1221A LYS* 4.1 23.1 - - + +
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Residues in contact with THR1219 (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 ARG* 2.4 33.1 + - - +
1216A ILE* 2.9 17.4 + - - -
1217A LYS 2.9 0.2 - - - -
1218A GLN* 1.3 82.3 - - - +
1220A PHE* 1.3 72.2 + - + +
1221A LYS* 4.9 1.4 - - - +
1266A THR* 5.4 4.7 - - + +
1270A ASN 5.7 2.5 - - - +
1271A ILE* 3.4 29.7 - - + +
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Residues in contact with PHE1220 (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 ILE* 3.3 24.0 - - + +
1217A LYS* 3.4 1.4 + - - +
1219A THR* 1.3 89.3 - - + +
1221A LYS* 1.3 67.7 + - - +
1223A ASP* 2.5 32.3 - - - +
1224A LEU* 3.7 33.9 - - + -
1263A ILE* 3.4 39.5 - - + -
1266A THR* 4.1 27.4 - - + -
1267A MET* 3.7 22.0 - - + -
1271A ILE* 4.7 1.8 - - + -
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Residues in contact with LYS1221 (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 LYS* 2.6 31.8 + - - +
1218A GLN* 4.1 24.2 - - - +
1219A THR 4.9 1.6 - - - +
1220A PHE* 1.3 78.4 - - - +
1222A ASN* 1.3 68.6 + - - +
1223A ASP* 3.0 8.2 + - - +
1224A LEU 4.1 12.5 + - - +
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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