Contacts of the helix formed by residues 1276 - 1293 (chain B) in PDB entry 3PT6
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 SER1276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1235B MET* 3.7 23.2 - - - +
1272B ARG* 3.8 13.1 + - - -
1273B ASN* 2.8 21.5 + - - -
1275B VAL* 1.3 86.7 - - - +
1277B TYR* 1.3 68.9 + - - +
1278B ARG 3.2 0.3 + - - -
1279B ARG* 3.0 16.2 + - - -
1280B SER* 3.2 10.5 + - - +
1347B VAL 5.8 3.1 - - - -
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Residues in contact with TYR1277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B ASP* 4.9 7.4 + - - +
704B ASP 5.2 4.7 + - - -
705B ASP* 4.5 1.9 + - - -
1229B CYS* 3.7 25.0 - - + +
1230B GLN* 5.9 0.2 - - - -
1232B PHE* 5.7 1.8 - + + +
1233B SER* 3.2 34.1 + - - -
1234B GLY* 3.2 21.5 - - - +
1235B MET* 3.7 17.3 - - + -
1271B VAL* 4.0 13.3 - - + +
1273B ASN* 2.9 38.4 + - + +
1274B PHE* 3.6 24.2 + + - +
1276B SER* 1.3 74.7 + - - +
1278B ARG* 1.3 71.7 + - + +
1280B SER* 3.0 11.1 + - - -
1281B MET 3.4 5.0 + - - -
1282B VAL* 3.9 23.0 + - + +
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Residues in contact with ARG1278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232B PHE* 3.6 25.4 + - - +
1233B SER 4.6 0.8 + - - -
1234B GLY* 2.4 44.2 + - - +
1235B MET* 3.7 0.8 - - - +
1236B ASN* 2.8 47.5 + - - +
1237B ARG* 4.0 5.4 - - - -
1238B PHE* 3.5 46.3 - - + +
1242B THR* 3.7 16.6 + - - +
1276B SER 3.2 0.8 + - - -
1277B TYR* 1.3 75.5 - - + +
1279B ARG* 1.3 71.7 + - - +
1281B MET* 3.1 30.2 + - + +
1282B VAL* 4.0 10.5 - - + -
6D T 4.6 1.4 + - - -
7D G 3.3 26.3 + - - -
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Residues in contact with ARG1279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1235B MET* 3.4 19.9 + - - +
1236B ASN* 5.2 0.2 - - - -
1237B ARG* 4.2 23.8 - - + +
1276B SER* 3.0 8.4 + - - +
1278B ARG* 1.3 78.5 - - - +
1280B SER* 1.3 70.5 + - - +
1281B MET* 3.2 4.3 + - + +
1284B LYS* 4.2 9.5 + - - -
1349B ASP* 4.8 5.2 + - - +
37J G 4.9 15.0 - - - -
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Residues in contact with SER1280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275B VAL 3.2 27.1 + - - -
1276B SER* 3.2 8.7 + - - -
1277B TYR 3.0 9.8 + - - -
1279B ARG* 1.3 78.5 - - - +
1281B MET* 1.3 59.1 + - - +
1282B VAL 3.4 2.0 - - - -
1283B LEU* 3.3 5.9 + - - +
1284B LYS* 2.8 31.3 + - - +
1347B VAL 4.2 4.2 + - - -
1348B VAL* 3.6 39.6 - - - +
1349B ASP 5.0 0.8 + - - -
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Residues in contact with MET1281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B ALA* 6.6 0.2 - - - -
811B THR* 3.5 26.5 - - + -
1237B ARG* 6.1 2.5 - - + -
1238B PHE* 3.8 29.8 - - + +
1243B TYR* 6.1 0.7 - - + -
1277B TYR 3.4 0.6 + - - -
1278B ARG* 3.1 19.3 + - + +
1279B ARG* 3.2 3.6 - - + +
1280B SER* 1.3 75.4 - - - +
1282B VAL* 1.3 58.9 + - - +
1284B LYS* 2.9 27.5 + - - +
1285B LEU* 2.6 61.5 + - + +
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Residues in contact with VAL1282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229B CYS* 5.0 2.2 - - - -
1232B PHE* 4.4 15.0 - - + -
1238B PHE* 4.3 6.2 - - + -
1246B PHE* 3.9 33.9 - - + -
1251B VAL* 5.0 0.9 - - + -
1274B PHE* 3.7 39.7 - - + +
1277B TYR* 3.9 26.7 - - + +
1278B ARG* 4.0 14.8 - - + -
1281B MET* 1.3 77.4 - - - +
1283B LEU* 1.3 60.1 + - - +
1286B THR* 3.1 32.5 + - + +
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Residues in contact with LEU1283 (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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807B VAL* 4.8 3.6 - - + -
1274B PHE* 4.0 24.0 + - + +
1275B VAL* 4.0 35.9 - - + +
1280B SER* 3.3 9.2 + - - +
1281B MET 3.1 0.4 - - - -
1282B VAL* 1.3 78.3 - - - +
1284B LYS* 1.3 68.0 + - + +
1286B THR* 3.6 1.2 + - - +
1287B LEU* 3.2 40.8 + - + +
1299B PHE* 3.5 48.5 - - + -
1318B ILE* 4.5 6.7 - - + -
1346B VAL* 4.9 0.2 - - + -
1348B VAL* 4.7 12.8 - - + -
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Residues in contact with LYS1284 (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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807B VAL* 3.0 32.1 - - + +
808B LEU* 3.4 23.0 + - - +
810B ALA* 4.7 10.5 - - - +
811B THR* 3.7 11.7 + - + +
1279B ARG 4.2 6.5 + - - -
1280B SER* 2.8 26.6 + - - +
1281B MET* 3.6 29.5 - - - +
1283B LEU* 1.3 75.0 - - + +
1285B LEU* 1.3 57.8 + - - +
1287B LEU* 3.9 5.3 + - - -
1288B ARG* 3.1 26.2 + - - +
1348B VAL* 3.9 11.4 - - + -
1349B ASP* 2.9 34.1 + - - +
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Residues in contact with LEU1285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B THR* 3.6 29.4 - - + -
1238B PHE* 4.2 7.6 - - + -
1243B TYR* 4.0 23.1 - - + +
1246B PHE* 3.7 31.2 - - + -
1281B MET* 2.6 39.0 + - + +
1282B VAL 4.1 2.9 - - - +
1284B LYS* 1.3 73.4 - - - +
1286B THR* 1.3 60.7 + - - +
1288B ARG* 3.1 9.2 + - + +
1289B CYS* 2.9 27.4 + - - +
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Residues in contact with THR1286 (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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1246B PHE* 4.8 9.4 - - + -
1251B VAL* 4.1 25.6 - - + -
1252B VAL* 6.4 0.7 - - + -
1255B LEU* 3.8 27.6 - - + +
1268B LEU* 5.0 3.0 - - - +
1274B PHE* 4.1 16.7 - - + -
1282B VAL* 3.1 18.8 + - + +
1283B LEU* 3.6 9.0 + - - +
1285B LEU* 1.3 72.6 - - - +
1287B LEU* 1.3 68.8 + - - +
1289B CYS* 3.4 2.6 + - - +
1290B LEU* 3.1 30.2 + - - +
1318B ILE* 4.9 10.0 - - - +
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Residues in contact with LEU1287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B VAL* 4.6 16.6 - - + -
808B LEU* 4.1 10.7 - - + +
878B ALA 5.8 0.2 - - - +
880B PHE* 4.9 11.3 - - + -
1283B LEU* 3.2 30.7 + - + +
1284B LYS* 4.0 4.9 - - - +
1286B THR* 1.3 83.4 + - - +
1288B ARG* 1.3 59.5 + - - +
1290B LEU* 3.4 9.7 + - + +
1291B VAL* 3.2 23.9 + - - +
1297B CYS* 3.5 37.4 - - + -
1298B THR* 4.0 19.7 - - - +
1299B PHE* 3.8 29.4 - - + -
1318B ILE* 4.9 3.4 - - + -
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Residues in contact with ARG1288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B LEU* 3.8 8.2 - - + +
811B THR* 3.2 39.2 + - - +
812B SER* 4.3 5.4 - - - +
813B ASP* 3.6 31.1 + - - +
816B GLU* 3.8 14.5 + - - -
1284B LYS 3.1 19.8 + - - +
1285B LEU* 3.1 13.3 + - + +
1287B LEU* 1.3 76.8 - - - +
1289B CYS* 1.3 56.9 + - - +
1291B VAL* 2.8 17.0 - - - +
1292B ARG* 2.8 84.9 + - - +
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Residues in contact with CYS1289 (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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1255B LEU* 3.7 34.3 - - + -
1259B ASP* 6.1 1.8 - - - -
1285B LEU 2.9 12.3 + - - +
1286B THR 3.8 0.2 - - - +
1287B LEU 3.3 0.2 - - - -
1288B ARG* 1.3 75.1 - - - +
1290B LEU* 1.3 64.5 + - - +
1292B ARG* 3.3 27.2 + - - +
1293B MET* 2.9 44.5 + - - +
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Residues in contact with LEU1290 (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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1255B LEU* 4.8 8.5 - - + -
1258B CYS* 4.3 16.8 - - + -
1266B PHE* 3.9 27.4 - - + -
1286B THR* 3.1 19.4 + - - +
1287B LEU* 3.7 12.6 - - - +
1288B ARG 3.4 0.2 - - - -
1289B CYS* 1.3 76.0 - - - +
1291B VAL* 1.3 58.8 + - - +
1293B MET* 3.2 10.3 + - - +
1294B GLY 3.2 5.9 + - - -
1295B TYR* 2.8 36.4 + - + +
1297B CYS* 3.8 21.8 - - + -
1318B ILE* 3.2 33.0 - - + -
1320B ALA* 4.0 8.7 - - + -
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Residues in contact with VAL1291 (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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808B LEU* 4.6 12.6 - - + -
816B GLU* 3.9 22.9 - - - +
818B PHE* 4.4 14.1 - - + -
870B GLN* 3.4 9.3 - - - +
871B LEU* 4.1 18.4 - - + -
880B PHE* 5.2 4.3 - - + -
1287B LEU 3.2 12.5 + - - +
1288B ARG* 2.8 39.5 - - - +
1290B LEU* 1.3 76.2 - - - +
1292B ARG* 1.3 58.1 + - - +
1293B MET 2.9 1.3 - - - -
1294B GLY* 2.6 23.8 + - - -
1295B TYR 4.0 11.2 + - - +
1297B CYS* 4.6 5.6 - - - -
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Residues in contact with ARG1292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B LYS* 5.5 5.9 + - - -
870B GLN* 4.8 4.6 + - - +
1288B ARG* 2.8 70.9 + - - +
1289B CYS* 3.6 36.7 - - - +
1291B VAL* 1.3 74.4 - - - +
1293B MET* 1.3 62.7 + - + +
1294B GLY* 3.3 0.5 + - - -
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Residues in contact with MET1293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B TRP* 2.9 29.1 + - - -
1255B LEU* 4.7 4.7 - - - +
1258B CYS* 3.5 9.9 - - - +
1259B ASP* 3.4 52.0 - - - +
1262B ARG* 3.5 17.1 + - - +
1289B CYS* 2.9 31.0 + - - +
1290B LEU* 3.3 12.6 - - - +
1291B VAL 2.9 0.8 - - - -
1292B ARG* 1.3 78.2 - - + +
1294B GLY* 1.3 59.6 + - - +
1295B TYR* 3.0 34.0 + - + -
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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