Contacts of the helix formed by residues 1280 - 1294 (chain A) 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 SER1280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1275A VAL 2.8 29.0 + - - -
1276A SER* 3.3 12.0 + - - +
1277A TYR 3.0 10.8 + - - -
1279A ARG* 1.3 81.3 - - - +
1281A MET* 1.3 57.7 + - - +
1282A VAL 3.2 2.5 - - - +
1283A LEU* 3.7 4.8 + - - +
1284A LYS* 3.0 30.6 + - - +
1347A VAL 4.1 11.8 + - - -
1348A VAL* 3.8 24.9 - - - +
1349A ASP 5.6 0.2 - - - -
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Residues in contact with MET1281 (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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810A ALA* 6.5 0.2 - - - -
811A THR* 3.4 28.5 - - + -
1237A ARG* 6.3 2.2 - - + -
1238A PHE* 3.5 30.3 - - + +
1243A TYR* 5.6 1.6 - - + -
1277A TYR 3.4 0.2 + - - -
1278A ARG* 3.1 19.6 + - + +
1279A ARG* 3.2 3.5 - - + +
1280A SER* 1.3 77.2 - - - +
1282A VAL* 1.3 60.4 + - - +
1284A LYS* 3.6 27.4 - - - +
1285A LEU* 2.8 58.3 + - + +
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Residues in contact with VAL1282 (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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1229A CYS* 4.5 2.9 - - - -
1232A PHE* 3.9 20.9 - - + -
1238A PHE* 4.8 3.6 - - + -
1246A PHE* 3.8 26.8 - - + -
1251A VAL* 5.3 0.9 - - + -
1274A PHE* 4.0 32.8 - - + +
1277A TYR* 3.0 40.2 - - + +
1278A ARG* 4.0 9.4 - - + -
1280A SER 3.2 0.2 - - - -
1281A MET* 1.3 78.3 - - - +
1283A LEU* 1.3 56.4 + - - +
1285A LEU* 3.8 0.9 - - - +
1286A THR* 2.7 37.3 + - + +
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Residues in contact with LEU1283 (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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807A VAL* 5.3 2.9 - - + -
1274A PHE* 4.0 22.7 + - + -
1275A VAL* 3.9 37.5 - - + +
1280A SER 3.7 7.2 + - - +
1281A MET 3.4 0.2 - - - -
1282A VAL* 1.3 77.6 - - - +
1284A LYS* 1.3 66.4 + - + +
1286A THR* 3.2 4.2 + - - +
1287A LEU* 3.0 43.5 + - + +
1299A PHE* 3.7 48.9 - - + -
1318A ILE* 4.3 7.6 - - + -
1348A VAL* 4.4 10.8 - - + -
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Residues in contact with LYS1284 (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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807A VAL* 3.1 32.8 - - + +
808A LEU* 3.5 14.7 - - - +
809A GLY* 4.5 0.7 - - - -
810A ALA* 5.2 6.7 - - - +
811A THR* 3.7 17.3 + - + +
1279A ARG 4.1 8.8 + - - -
1280A SER 3.0 27.0 + - - +
1281A MET* 3.6 26.8 - - - +
1283A LEU* 1.3 76.6 - - + +
1285A LEU* 1.3 58.6 + - - +
1287A LEU* 3.9 7.3 - - - +
1288A ARG* 3.0 29.3 + - - +
1348A VAL* 4.3 12.3 - - + -
1349A ASP* 3.6 29.0 + - - +
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Residues in contact with LEU1285 (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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811A THR* 4.0 21.5 - - + -
1238A PHE* 3.9 11.4 - - + -
1243A TYR* 3.8 32.8 - - + +
1246A PHE* 4.0 22.2 - - + -
1255A LEU* 5.1 0.8 - - - +
1281A MET* 2.8 45.4 + - + +
1282A VAL 3.9 2.9 - - - +
1284A LYS* 1.3 76.7 - - - +
1286A THR* 1.3 62.8 + - - +
1288A ARG* 3.6 8.9 - - + +
1289A CYS* 3.1 21.1 + - - +
1292A ARG* 6.1 1.1 - - - +
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Residues in contact with THR1286 (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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1246A PHE* 4.9 3.6 - - + -
1251A VAL* 4.2 19.1 - - + -
1255A LEU* 4.1 23.2 - - + +
1268A LEU* 5.3 4.4 - - + +
1274A PHE* 3.7 22.9 - - + -
1282A VAL* 2.7 26.4 + - + +
1283A LEU* 3.4 6.9 + - - -
1285A LEU* 1.3 73.8 - - - +
1287A LEU* 1.3 69.8 + - - +
1289A CYS* 3.0 5.2 + - - +
1290A LEU* 3.0 28.9 + - - +
1318A ILE* 4.4 17.3 - - - +
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Residues in contact with LEU1287 (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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807A VAL* 4.4 19.1 - - + -
808A LEU* 3.7 15.3 - - + -
878A ALA 5.9 0.7 - - - +
880A PHE* 5.1 6.3 - - + -
1283A LEU* 3.0 32.0 + - + +
1284A LYS* 3.9 1.6 - - - +
1286A THR* 1.3 82.4 + - - +
1288A ARG* 1.3 57.3 + - - +
1290A LEU* 3.1 12.0 + - + +
1291A VAL* 2.9 33.5 + - - +
1297A CYS* 3.5 31.7 - - + +
1298A THR* 4.8 10.5 - - - +
1299A PHE* 3.9 32.8 - - + -
1318A ILE* 5.0 4.0 - - + -
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Residues in contact with ARG1288 (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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808A LEU* 3.7 9.2 - - + +
811A THR* 3.2 37.4 + - - +
812A SER* 4.2 4.4 - - - +
813A ASP* 3.5 33.5 + - - +
816A GLU* 3.1 25.3 + - - -
868A PHE* 5.7 1.6 - - - -
1284A LYS 3.0 19.0 + - - +
1285A LEU* 3.6 13.0 - - + +
1287A LEU* 1.3 76.3 - - - +
1289A CYS* 1.3 57.9 + - - +
1291A VAL* 3.1 21.1 - - - +
1292A ARG* 2.9 78.0 + - - +
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Residues in contact with CYS1289 (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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1255A LEU* 3.8 27.8 - - + -
1285A LEU 3.1 13.9 + - - +
1286A THR 3.0 10.7 + - - +
1288A ARG* 1.3 73.6 - - - +
1290A LEU* 1.3 67.0 + - + +
1292A ARG* 3.0 34.7 + - - +
1293A MET* 3.1 39.9 + - + +
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Residues in contact with LEU1290 (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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1255A LEU* 5.0 5.4 - - + -
1258A CYS* 4.2 17.3 - - - -
1266A PHE* 4.1 18.8 - - + -
1286A THR* 3.0 22.3 + - - +
1287A LEU* 3.6 10.5 - - + +
1289A CYS* 1.3 76.4 - - + +
1291A VAL* 1.3 63.7 + - - +
1293A MET* 3.1 14.7 + - + +
1294A GLY 3.1 5.5 + - - -
1295A TYR* 3.1 30.9 + - + +
1297A CYS* 3.9 25.1 - - + -
1318A ILE* 3.7 29.8 - - + -
1320A ALA* 4.0 18.6 - - + -
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Residues in contact with VAL1291 (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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808A LEU* 3.8 18.2 - - + -
816A GLU* 4.1 13.5 - - - +
818A PHE* 4.1 11.9 - - + -
870A GLN* 3.2 18.1 - - - +
871A LEU* 3.5 25.6 - - + -
880A PHE* 4.9 4.7 - - + -
1287A LEU 2.9 24.8 + - - +
1288A ARG* 3.1 28.0 - - - +
1290A LEU* 1.3 74.3 - - - +
1292A ARG* 1.3 57.6 + - - +
1294A GLY* 2.8 17.8 + - - -
1295A TYR 4.1 9.9 - - - +
1297A CYS* 5.0 6.5 - - - -
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Residues in contact with ARG1292 (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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870A GLN* 4.6 5.7 + - - +
1285A LEU* 6.1 1.4 - - - +
1288A ARG* 2.9 63.8 + - - +
1289A CYS* 3.0 38.5 + - - +
1291A VAL* 1.3 79.0 - - - +
1293A MET* 1.3 62.7 + - + +
1294A GLY* 3.2 0.5 + - - -
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Residues in contact with MET1293 (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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846A TRP* 2.9 25.1 + - - -
1255A LEU* 3.5 25.1 - - + +
1258A CYS* 4.3 7.6 - - + -
1259A ASP* 3.7 37.9 - - + +
1262A ARG* 4.4 16.7 + - - +
1289A CYS* 3.1 40.6 + - - +
1290A LEU* 3.1 12.1 + - + +
1292A ARG* 1.3 79.3 - - + +
1294A GLY* 1.3 58.0 + - - +
1295A TYR* 3.9 30.1 - - + -
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Residues in contact with GLY1294 (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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842A PRO* 5.2 4.2 - - - +
846A TRP* 4.5 3.8 - - - -
870A GLN* 3.5 21.2 + - - -
871A LEU* 5.0 5.6 - - - +
1291A VAL 2.8 16.2 + - - -
1293A MET* 1.3 80.4 - - - +
1295A TYR* 1.3 63.7 + - - +
1296A GLN* 3.9 0.9 + - - +
1323A PRO* 3.6 25.5 - - - +
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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