Contacts of the helix formed by residues 1202 - 1219 (chain A) in PDB entry 1YW2
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 GLN1202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142A HIS* 3.3 76.7 + - + +
1145A ASP* 4.0 16.0 + - - +
1146A ILE 4.0 11.4 + - - +
1147A ILE* 4.0 18.3 - - + +
1201A ASN* 1.3 72.2 - - + +
1203A THR* 1.3 60.0 + - + +
1204A VAL 2.9 7.9 + - - -
1205A ASP* 2.9 16.3 + - - +
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Residues in contact with THR1203 (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 ASN* 2.6 37.0 + - + +
1202A GLN* 1.3 73.9 - - + +
1204A VAL* 1.3 64.3 + - - +
1205A ASP 3.1 0.7 - - - -
1206A ILE* 3.0 23.1 + - + -
1207A TRP 3.2 5.5 + - - -
1293A SER* 3.2 14.4 + - - +
1296A ARG* 2.8 49.7 + - - +
1297A ILE 4.5 4.7 - - - +
1298A THR* 5.1 10.1 - - + -
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Residues in contact with VAL1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A ILE* 3.7 23.6 - - + -
1149A ARG* 4.6 4.3 - - - -
1190A ALA* 3.8 6.9 + - + +
1192A GLU* 3.6 26.2 - - + +
1193A ILE* 3.7 24.6 - - + +
1200A TYR* 3.4 22.4 - - + -
1201A ASN* 3.0 22.6 + - - +
1202A GLN 2.9 1.4 + - - +
1203A THR* 1.3 78.1 + - - +
1205A ASP* 1.3 68.4 + - - +
1206A ILE 3.2 0.3 + - - -
1207A TRP* 3.2 14.7 + - - +
1208A SER* 3.2 11.8 + - - -
1296A ARG* 3.6 6.1 - - - +
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Residues in contact with ASP1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A LEU* 3.8 16.1 - - + +
1142A HIS* 2.7 27.0 + - + +
1147A ILE* 3.6 3.9 - - - -
1148A HIS* 2.6 35.4 + - - +
1149A ARG* 2.5 31.2 + - - -
1150A ASP 4.5 0.2 + - - -
1151A LEU* 3.7 6.5 - - + +
1202A GLN 2.9 10.8 + - - +
1204A VAL* 1.3 82.2 - - - +
1206A ILE* 1.3 60.5 + - - +
1208A SER* 3.4 9.5 + - - -
1209A VAL* 3.1 26.9 + - - +
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Residues in contact with ILE1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135A LEU* 4.5 11.4 - - + -
1138A LEU* 4.1 16.2 - - + -
1142A HIS* 4.8 3.8 - - + -
1202A GLN 4.6 2.0 - - - +
1203A THR* 3.0 23.9 + - + +
1205A ASP* 1.3 74.2 - - - +
1207A TRP* 1.3 65.4 + - - +
1209A VAL* 3.2 5.7 + - + +
1210A GLY* 2.9 19.6 + - - -
1288A MET* 3.9 29.8 - - + +
1296A ARG* 4.1 9.9 - - + -
1297A ILE* 3.4 28.7 - - + +
1298A THR* 4.0 2.5 - - - -
1299A ALA* 3.6 33.2 - - + +
1302A ALA* 5.4 0.2 - - + -
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Residues in contact with TRP1207 (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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1187A TRP 5.2 0.6 + - - -
1188A TYR 3.6 2.9 - - - -
1189A ARG 3.4 30.4 + - - -
1190A ALA* 3.6 13.5 - - + -
1191A PRO* 3.5 18.4 - - + -
1203A THR 3.2 5.7 + - - -
1204A VAL 3.4 10.3 - - - +
1206A ILE* 1.3 76.3 - - - +
1208A SER* 1.3 62.9 + - - +
1210A GLY* 3.0 4.0 + - - -
1211A CYS* 2.9 41.5 + - - -
1223A PHE* 3.7 17.4 - + - -
1235A ILE* 3.7 38.1 - - + +
1239A VAL* 3.9 15.9 - - + -
1288A MET 4.3 4.9 - - - -
1289A LEU* 3.5 31.8 - - + +
1290A VAL 3.3 28.5 - - - -
1291A LEU* 4.4 1.8 - - + -
1296A ARG* 3.8 14.8 - - - +
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Residues in contact with SER1208 (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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1149A ARG 5.9 1.4 - - - -
1151A LEU* 3.6 37.3 + - - +
1188A TYR* 2.9 27.0 + - - -
1189A ARG* 5.0 0.3 - - - -
1190A ALA 5.0 0.7 + - - -
1204A VAL 3.2 13.5 + - - -
1205A ASP* 3.6 7.6 + - - -
1206A ILE 3.4 0.6 - - - -
1207A TRP* 1.3 77.2 - - - +
1209A VAL* 1.3 59.4 + - - +
1211A CYS* 2.9 6.5 + - - +
1212A ILE* 2.7 35.0 + - - +
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Residues in contact with VAL1209 (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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1131A ILE* 4.2 18.7 - - + +
1134A ILE* 3.7 22.0 - - + -
1135A LEU* 3.9 13.7 - - + -
1138A LEU* 4.0 11.4 - - + -
1151A LEU* 3.5 21.3 - - + -
1205A ASP 3.1 15.4 + - - +
1206A ILE* 3.2 9.8 + - - +
1208A SER* 1.3 75.9 - - - +
1210A GLY* 1.3 63.5 + - - +
1212A ILE* 3.4 8.1 + - + +
1213A MET* 3.0 23.0 + - - +
1288A MET* 3.8 24.2 - - + -
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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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1206A ILE 2.9 13.3 + - - -
1207A TRP 3.4 3.6 - - - -
1209A VAL* 1.3 76.8 - - - +
1211A CYS* 1.3 55.1 + - - +
1213A MET* 3.2 1.8 + - - -
1214A ALA* 2.9 27.2 + - - +
1285A LEU* 3.3 16.9 - - - +
1288A MET* 4.0 18.1 - - - -
1289A LEU* 3.9 17.0 - - - -
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Residues in contact with CYS1211 (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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1187A TRP 3.8 15.9 - - - +
1188A TYR* 3.7 24.0 - - + -
1207A TRP* 2.9 47.0 + - - +
1208A SER* 2.9 8.3 + - - +
1210A GLY* 1.3 75.1 - - - +
1212A ILE* 1.3 63.2 + - - +
1214A ALA* 3.4 2.8 + - - +
1215A GLU* 3.3 19.9 + - - +
1222A LEU* 4.4 15.4 + - + +
1223A PHE* 3.8 18.6 - - + -
1289A LEU* 4.2 1.8 - - - -
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Residues in contact with ILE1212 (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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1113A LEU* 3.5 30.1 - - + -
1131A ILE* 4.6 7.6 - - + -
1134A ILE* 4.7 6.3 - - + -
1151A LEU* 4.8 7.0 - - + -
1152A LYS* 4.1 21.5 - - - +
1153A PRO* 4.0 5.6 - - + -
1156A LEU* 4.0 23.6 - - + -
1188A TYR* 3.9 22.4 - - + -
1208A SER* 2.7 28.1 + - - +
1209A VAL* 3.8 8.3 - - + +
1211A CYS* 1.3 72.4 - - - +
1213A MET* 1.3 65.1 + - - +
1215A GLU* 3.2 7.5 + - - +
1216A LEU* 3.0 29.2 + - + +
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Residues in contact with MET1213 (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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1127A VAL* 4.1 4.5 - - + -
1131A ILE* 3.3 52.5 - - + +
1209A VAL 3.0 14.9 + - - +
1210A GLY* 3.4 8.5 - - - +
1212A ILE* 1.3 78.0 - - - +
1214A ALA* 1.3 63.7 + - - +
1216A LEU* 3.0 5.1 + - - +
1217A LEU* 3.0 36.7 + - + +
1281A ALA 4.5 3.8 - - - +
1284A LEU* 3.6 23.8 - - + -
1285A LEU* 3.9 23.6 - - + -
1288A MET* 4.7 4.5 - - - +
1307A TYR* 3.5 29.2 - - + -
1308A PHE* 3.9 0.2 - - + -
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Residues in contact with ALA1214 (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 2.9 12.4 + - - +
1211A CYS 3.7 3.4 - - - +
1212A ILE 3.2 0.2 - - - -
1213A MET* 1.3 76.0 - - - +
1215A GLU* 1.3 52.6 + - - +
1217A LEU* 3.4 4.2 + - - +
1218A THR* 2.8 40.5 + - - -
1220A ARG 4.5 0.7 - - - -
1222A LEU* 3.5 28.3 - - + -
1274A PHE* 3.3 36.3 - - + -
1285A LEU* 4.1 5.6 - - + +
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Residues in contact with GLU1215 (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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1114A ASN* 4.8 3.5 - - - +
1117A VAL* 5.9 0.8 - - - +
1118A LYS* 3.9 19.9 + - - -
1120A GLN* 2.5 28.0 + - - +
1153A PRO* 4.5 6.7 - - - +
1188A TYR* 2.9 31.7 + - + -
1211A CYS 3.3 7.6 + - - +
1212A ILE* 3.2 9.6 + - - +
1213A MET 3.2 0.4 - - - -
1214A ALA* 1.3 80.2 - - - +
1216A LEU* 1.3 52.5 + - + +
1219A GLY* 2.6 24.6 + - - -
1220A ARG* 3.3 32.5 + - - +
1221A THR* 4.1 17.5 + - - +
1222A LEU 4.8 0.6 - - - +
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Residues in contact with LEU1216 (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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1113A LEU* 4.2 31.6 - - + -
1117A VAL* 3.6 23.3 - - + -
1120A GLN* 2.5 34.4 - - - +
1121A LYS* 3.3 12.5 - - - -
1122A LEU* 3.8 10.5 + - + -
1127A VAL* 4.0 22.2 - - + +
1130A LEU* 4.4 20.0 - - + -
1131A ILE* 4.5 10.1 - - + -
1134A ILE* 6.1 0.2 - - + -
1212A ILE* 3.0 26.2 + - + +
1213A MET 3.0 6.7 + - - +
1215A GLU* 1.3 81.2 - - + +
1217A LEU* 1.3 61.0 + - - +
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Residues in contact with LEU1217 (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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1121A LYS* 2.8 33.9 + - - +
1124A ASP* 3.7 13.7 - - - +
1127A VAL* 3.7 18.8 - - + -
1213A MET* 3.0 28.0 + - + +
1214A ALA* 3.8 3.6 - - - +
1216A LEU* 1.3 76.4 - - - +
1218A THR* 1.3 57.5 + - - +
1274A PHE* 5.1 4.5 - - + -
1275A ILE* 3.1 28.7 - - + +
1277A ALA* 4.6 8.7 - - + -
1281A ALA* 3.9 13.9 - - + -
1282A VAL* 6.1 0.9 - - + -
1285A LEU* 3.5 31.6 - - + -
1307A TYR* 3.6 22.4 - - - +
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Residues in contact with THR1218 (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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1121A LYS* 4.1 8.0 - - - +
1214A ALA 2.8 18.8 + - - -
1217A LEU* 1.3 79.4 - - - +
1219A GLY* 1.3 59.2 + - - +
1220A ARG* 3.0 50.3 - - + +
1222A LEU* 6.3 0.9 - - + -
1273A VAL 4.9 2.1 + - - -
1274A PHE* 3.9 16.2 - - + -
1275A ILE* 3.9 23.0 - - + +
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Residues in contact with GLY1219 (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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1118A LYS* 6.0 1.4 - - - +
1120A GLN* 3.3 34.7 + - - +
1121A LYS* 4.2 5.1 - - - +
1215A GLU* 2.6 22.1 + - - -
1217A LEU 3.8 0.2 - - - -
1218A THR* 1.3 72.5 - - - +
1220A ARG* 1.3 63.1 + - - +
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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