Contacts of the helix formed by residues 1246 - 1263 (chain B) in PDB entry 2WIN
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 SER1246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B ILE* 6.1 0.8 - - - +
1205B LEU* 4.7 5.4 - - - -
1239B TYR* 3.0 25.1 - - - -
1242B GLY* 3.1 23.5 + - - -
1243B GLY 2.6 22.0 + - - -
1244B TYR 4.6 0.7 - - - -
1245B GLY* 1.3 77.8 - - - +
1247B THR* 1.3 63.3 + - - +
1248B GLN 3.5 2.2 - - - -
1249B ALA* 4.0 9.2 - - - +
1250B THR* 2.8 23.6 + - - -
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Residues in contact with THR1247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B ILE* 3.3 29.5 - - - +
997B THR* 3.5 19.6 - - + +
1059B TYR* 3.2 33.4 - - + +
1106B GLU 5.0 0.4 + - - -
1107B MET* 3.6 39.1 + - + +
1245B GLY* 3.5 3.4 - - - -
1246B SER* 1.3 78.5 + - - +
1248B GLN* 1.3 59.7 + - - +
1251B PHE* 3.2 28.4 + - - +
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Residues in contact with GLN1248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055B TRP* 3.0 30.2 - - - -
1059B TYR* 3.0 31.4 - - - -
1062B LYS* 5.0 0.3 - - - +
1107B MET 3.1 17.6 + - - +
1108B ILE 3.3 18.6 - - - +
1109B GLY* 4.2 4.9 - - - -
1124B PHE* 3.6 20.0 - - - -
1209B GLU* 3.3 25.6 - - - +
1213B TYR* 3.8 9.4 + - - -
1245B GLY 5.5 0.4 + - - -
1247B THR* 1.3 74.6 - - - +
1249B ALA* 1.3 66.9 + - - +
1250B THR 3.2 0.4 - - - -
1251B PHE* 4.8 1.0 - - - +
1252B MET* 3.1 37.7 + - - +
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Residues in contact with ALA1249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205B LEU* 3.9 31.4 - - + +
1208B VAL* 4.4 5.1 - - + +
1209B GLU* 4.5 13.1 + - - +
1212B SER* 5.1 0.3 + - - -
1239B TYR* 3.5 27.6 - - + +
1245B GLY 5.2 0.9 - - - +
1246B SER* 3.8 9.8 + - - +
1247B THR 3.4 0.4 - - - -
1248B GLN* 1.3 79.4 - - - +
1250B THR* 1.3 57.3 + - - +
1253B VAL* 3.0 29.3 + - - +
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Residues in contact with THR1250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981B LEU* 3.9 25.6 - - + -
997B THR* 5.3 2.2 - - + -
998B PRO* 4.8 5.8 - - + -
1001B ILE* 4.2 10.7 - - + +
1239B TYR* 3.4 3.9 + - - -
1241B GLY* 3.2 6.4 - - - -
1242B GLY 3.1 20.7 + - - +
1246B SER* 2.8 23.0 + - - -
1247B THR* 4.3 1.6 - - - -
1249B ALA* 1.3 75.7 - - - +
1251B PHE* 1.3 65.3 + - - +
1252B MET 3.2 2.0 - - - -
1253B VAL* 3.3 9.1 - - - +
1254B PHE* 3.1 44.1 + - + +
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Residues in contact with PHE1251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B THR* 3.6 20.6 - - + +
1000B VAL* 4.7 7.0 - - + -
1001B ILE* 3.4 30.0 - - + +
1059B TYR* 3.9 11.0 - + + +
1062B LYS* 3.5 39.7 - - + -
1063B VAL* 3.9 23.6 - - + -
1066B LEU* 3.6 26.2 - - + -
1247B THR 3.2 18.2 + - - +
1248B GLN* 4.3 2.9 - - - +
1250B THR* 1.3 78.8 - - - +
1252B MET* 1.3 68.6 + - + +
1255B GLN* 3.2 48.5 + - - +
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Residues in contact with MET1252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062B LYS* 4.4 9.9 - - - +
1127B ILE* 6.2 0.4 - - + -
1172B TYR* 5.6 0.9 - - + -
1209B GLU* 4.4 4.0 - - + -
1212B SER* 3.4 22.6 - - - -
1213B TYR* 3.5 57.4 - - + +
1216B LEU* 3.7 24.2 - - + -
1248B GLN* 3.1 25.8 + - - +
1251B PHE* 1.3 87.6 - - + +
1253B VAL* 1.3 63.9 + - - +
1254B PHE 3.2 2.2 - - - -
1255B GLN* 3.4 26.0 - - - +
1256B ALA* 3.1 20.1 + - - +
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Residues in contact with VAL1253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208B VAL* 3.9 20.2 - - + -
1212B SER* 3.2 14.7 + - - +
1234B LEU* 4.9 14.9 - - + +
1239B TYR* 4.2 17.9 - - + +
1249B ALA 3.0 25.3 + - - +
1250B THR* 3.3 11.4 - - - +
1252B MET* 1.3 79.1 - - - +
1254B PHE* 1.3 80.9 + - + +
1256B ALA* 4.1 2.1 - - - +
1257B LEU* 3.2 37.4 + - + +
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Residues in contact with PHE1254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B VAL* 3.7 24.9 - - + -
978B LEU* 3.6 26.7 - - + -
981B LEU* 4.1 13.5 - - + -
1001B ILE* 3.5 26.0 - - + +
1005B TYR* 3.2 36.4 - + + -
1239B TYR 4.2 7.6 - - - -
1240B TYR* 4.1 18.2 - - - -
1241B GLY 4.2 0.7 - - - -
1250B THR* 3.1 38.2 + - + -
1252B MET 3.2 0.2 - - - -
1253B VAL* 1.3 95.0 - - + +
1255B GLN* 1.3 62.0 + - - +
1256B ALA 3.3 1.1 - - - -
1257B LEU* 4.0 3.4 - - + -
1258B ALA* 3.0 29.1 + - - +
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Residues in contact with GLN1255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B ILE* 3.8 10.1 - - + +
1004B HIS* 4.9 4.9 + - - +
1062B LYS* 4.9 1.8 - - - +
1066B LEU* 4.1 20.5 - - + +
1131B GLU* 3.2 30.7 + - - -
1172B TYR* 4.6 1.4 + - - -
1216B LEU* 3.8 23.5 - - + +
1251B PHE* 3.2 39.2 + - - +
1252B MET* 3.3 19.7 + - - +
1254B PHE* 1.3 79.1 - - - +
1256B ALA* 1.3 58.5 + - - +
1258B ALA* 4.0 3.6 - - - +
1259B GLN* 3.1 27.9 + - + +
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Residues in contact with ALA1256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212B SER* 3.7 25.1 - - - +
1215B LEU* 3.6 25.9 - - + +
1216B LEU* 3.6 16.4 - - + +
1219B LEU* 4.0 1.9 - - - +
1234B LEU* 5.3 1.1 - - + -
1252B MET 3.1 16.1 + - - +
1253B VAL* 4.4 3.6 - - - +
1255B GLN* 1.3 76.5 - - - +
1257B LEU* 1.3 59.7 + - + +
1258B ALA 3.2 0.2 - - - -
1259B GLN* 3.5 1.7 + - - +
1260B TYR* 2.8 28.8 + - - +
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Residues in contact with LEU1257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971B ASP 6.1 0.2 - - - +
972B ALA* 5.9 2.2 - - + -
973B VAL* 4.3 12.3 - - + -
1005B TYR* 3.4 31.4 + - + +
1215B LEU* 4.5 3.6 - - + -
1231B VAL* 4.0 22.0 - - + -
1234B LEU* 4.1 24.5 - - + -
1235B ASN* 3.9 25.1 - - - +
1253B VAL* 3.2 29.2 + - + +
1254B PHE* 5.0 3.1 - - + -
1256B ALA* 1.3 75.4 - - - +
1258B ALA* 1.3 61.9 + - - +
1260B TYR* 3.4 15.2 - - + +
1261B GLN* 3.3 21.1 + - - +
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Residues in contact with ALA1258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B HIS* 3.8 31.0 - - + +
1005B TYR* 3.7 19.4 - - + -
1008B GLU* 4.1 9.2 - - + +
1009B THR* 5.5 0.2 - - - -
1254B PHE 3.0 22.9 + - - +
1255B GLN 4.1 1.6 - - - +
1257B LEU* 1.3 75.4 - - - +
1259B GLN* 1.3 65.4 + - - +
1261B GLN* 3.0 22.7 + - - +
1262B LYS* 3.4 11.5 + - - +
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Residues in contact with GLN1259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B HIS* 5.2 4.1 + - - +
1216B LEU* 3.8 21.5 - - + -
1219B LEU* 4.1 5.2 - - + -
1220B GLN* 5.8 1.8 + - - -
1255B GLN* 3.1 21.4 + - + +
1256B ALA 3.8 0.7 - - - +
1258B ALA* 1.3 71.3 - - - +
1260B TYR* 1.3 61.0 + - - +
1261B GLN 3.0 5.1 + - - -
1262B LYS* 3.0 40.2 + - - +
1263B ASP* 2.9 48.4 + - - +
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Residues in contact with TYR1260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969B THR* 4.0 7.6 - - + -
970B GLU* 3.0 57.3 + - + +
1215B LEU* 4.8 3.8 - - + -
1219B LEU* 4.0 10.9 - - + +
1224B PHE* 6.5 0.2 - + - -
1227B VAL* 3.8 19.1 - - + -
1228B PRO* 5.6 3.9 - - + +
1231B VAL* 3.7 34.8 - - + -
1256B ALA 2.8 19.3 + - - +
1257B LEU* 3.4 12.6 - - + +
1258B ALA 3.1 0.2 - - - -
1259B GLN* 1.3 76.2 - - - +
1261B GLN* 1.3 73.7 + - - +
1263B ASP* 3.0 19.7 - - - +
1264B ALA* 3.4 17.6 - - + +
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Residues in contact with GLN1261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969B THR* 4.0 18.7 - - - +
970B GLU 3.9 11.5 + - - -
971B ASP* 5.1 0.4 - - - +
972B ALA* 3.7 25.9 - - + +
1008B GLU* 3.9 18.4 - - + +
1009B THR* 4.0 20.0 - - + -
1257B LEU 3.3 14.8 + - - +
1258B ALA 3.0 8.8 + - - +
1259B GLN 3.0 0.6 - - - -
1260B TYR* 1.3 98.5 - - - +
1262B LYS* 1.3 63.9 + - - +
1263B ASP 3.5 0.2 - - - -
1264B ALA* 3.2 16.7 - - - +
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Residues in contact with LYS1262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B HIS* 5.1 12.2 - - - -
1008B GLU* 3.2 45.0 + - + +
1258B ALA 3.9 7.4 - - - +
1259B GLN* 3.0 38.7 + - - +
1261B GLN* 1.3 75.7 - - - +
1263B ASP* 1.3 57.9 + - - +
1264B ALA 3.1 12.2 + - - +
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Residues in contact with ASP1263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219B LEU* 3.1 49.0 - - + +
1224B PHE* 3.4 30.1 - - + -
1259B GLN* 2.9 33.4 + - - +
1260B TYR* 3.0 17.5 - - - +
1262B LYS* 1.3 75.3 - - - +
1264B ALA* 1.3 63.4 + - - +
1265B PRO* 3.5 2.3 - - - +
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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