Contacts of the helix formed by residues 1262 - 1276 (chain A) in PDB entry 3FK2
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 PRO1262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246A TYR* 3.6 13.7 - - + +
1251A LEU* 4.1 8.1 - - + -
1254A VAL* 3.7 12.6 - - + +
1255A VAL* 3.4 21.8 - - + -
1260A PRO 3.6 1.8 - - - +
1261A ILE* 1.3 88.7 - - + +
1263A ILE* 1.3 66.2 + - - +
1265A ILE* 2.9 29.4 + - + +
1266A GLU* 3.1 10.0 + - - +
1324A PHE* 4.0 28.3 - - + -
1371A VAL* 3.8 17.0 - - + -
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Residues in contact with ILE1263 (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 TYR* 3.1 11.5 + - + +
1254A VAL 5.2 4.5 - - - +
1259A LYS* 5.2 13.9 - - + +
1261A ILE 3.9 11.2 - - - +
1262A PRO* 1.3 71.9 - - + +
1264A PHE* 1.3 63.4 + - - +
1266A GLU* 3.2 17.3 + - + +
1267A ARG* 3.0 49.8 + - - +
1299A PHE* 3.8 17.0 - - + -
1303A HIS* 3.9 10.3 - - + +
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Residues in contact with PHE1264 (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 TYR* 3.3 26.2 + - + -
1247A PHE* 3.7 31.6 - + - -
1262A PRO* 3.2 1.2 - - + -
1263A ILE* 1.3 78.3 - - - +
1265A ILE* 1.3 66.2 + - + +
1267A ARG* 3.4 4.9 + - + +
1268A CYS* 3.1 48.2 + - - -
1295A LEU* 4.4 14.6 - - + -
1296A GLN* 4.2 4.5 - - + -
1299A PHE* 3.7 40.3 - + + -
1307A LEU* 6.1 0.7 - - + -
1320A ALA* 3.2 39.9 - - + -
1321A MET* 4.2 2.0 - - - -
1324A PHE* 4.0 16.4 - + + -
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Residues in contact with ILE1265 (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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1261A ILE* 4.1 6.1 - - + -
1262A PRO* 2.9 26.9 + - + +
1264A PHE* 1.3 78.4 - - + +
1266A GLU* 1.3 65.0 + - - +
1268A CYS* 3.4 2.1 + - - +
1269A ILE* 2.9 34.4 + - + +
1321A MET* 3.9 24.9 - - + +
1324A PHE* 3.7 23.1 - - + -
1325A PHE* 3.6 36.6 - - + -
1371A VAL* 5.4 1.1 - - + -
1374A TYR* 3.8 25.8 - - + -
1375A VAL* 4.8 1.1 - - + -
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Residues in contact with GLU1266 (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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1261A ILE* 4.1 29.4 - - + +
1262A PRO 3.1 7.5 + - - +
1263A ILE* 3.2 21.2 + - + +
1265A ILE* 1.3 76.1 - - - +
1267A ARG* 1.3 65.1 + - + +
1270A GLU* 2.9 47.4 + - - +
1374A TYR* 3.4 27.9 - - + +
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Residues in contact with ARG1267 (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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1263A ILE* 3.0 32.7 + - - +
1264A PHE* 3.6 9.4 - - + +
1266A GLU* 1.3 77.1 - - - +
1268A CYS* 1.3 60.0 + - - +
1270A GLU* 3.9 5.0 - - - +
1271A TYR* 2.9 32.1 + - - +
1299A PHE* 4.2 11.5 - - + -
1303A HIS 2.6 29.7 + - - -
1304A ASN* 3.7 20.8 - - - +
1305A LEU 3.2 26.3 + - - +
1306A ASP* 6.0 0.4 - - - +
1307A LEU* 3.9 17.5 - - + +
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Residues in contact with CYS1268 (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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1264A PHE* 3.1 54.0 + - - +
1265A ILE 4.0 0.4 - - - +
1267A ARG* 1.3 80.1 - - - +
1269A ILE* 1.3 59.4 + - - +
1271A TYR* 3.3 1.0 + - - +
1272A ILE* 2.7 37.4 + - + +
1295A LEU* 5.0 2.7 - - - -
1307A LEU* 4.2 6.1 - - - -
1317A VAL* 3.6 32.5 - - + -
1321A MET* 3.8 22.0 - - + -
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Residues in contact with ILE1269 (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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1265A ILE* 2.9 18.4 + - + +
1268A CYS* 1.3 77.7 - - - +
1270A GLU* 1.3 59.4 + - + +
1272A ILE* 3.3 6.0 + - - +
1273A GLU* 2.8 39.2 + - - +
1283A TYR* 4.7 0.4 - - - +
1321A MET* 3.5 36.1 - - + -
1374A TYR* 3.4 41.1 - - + +
1375A VAL* 4.4 3.6 - - - -
1378A HIS* 3.3 47.3 - - + +
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Residues in contact with GLU1270 (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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1266A GLU* 2.9 47.3 + - - +
1267A ARG* 4.1 3.9 - - - +
1269A ILE* 1.3 77.0 - - + +
1271A TYR* 1.3 60.8 + - - +
1273A GLU* 3.9 8.9 - - - +
1274A ALA* 3.2 23.4 + - - +
1374A TYR* 3.9 9.8 + - - +
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Residues in contact with TYR1271 (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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1267A ARG 2.9 20.6 + - - +
1268A CYS 3.7 2.0 - - - +
1270A GLU* 1.3 74.9 - - - +
1272A ILE* 1.3 64.2 + - + +
1274A ALA* 3.2 5.1 + - + +
1275A THR* 2.8 55.3 + - - -
1307A LEU* 3.7 41.6 + - + -
1308A ALA* 3.9 13.3 - - + -
1311A ASP* 5.3 1.2 - - - -
1312A PHE* 3.4 21.5 + - + -
1314A VAL* 4.8 7.9 - - + -
1317A VAL* 3.7 35.9 - - + -
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Residues in contact with ILE1272 (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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1268A CYS* 2.7 29.8 + - + +
1269A ILE* 3.8 4.5 - - - +
1271A TYR* 1.3 74.7 - - + +
1273A GLU* 1.3 60.7 + - - +
1276A GLY* 2.7 30.6 + - - +
1277A LEU* 3.4 6.9 + - + +
1282A ILE* 3.5 25.6 - - + -
1283A TYR* 3.5 24.7 - - + +
1314A VAL* 4.4 11.0 - - + +
1317A VAL* 3.8 17.5 - - + +
1318A ALA* 3.5 36.6 - - + +
1321A MET* 4.6 2.5 - - + -
1378A HIS* 4.0 11.0 - - + -
1382A VAL* 5.2 0.2 - - + -
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Residues in contact with GLU1273 (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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1269A ILE* 2.8 27.9 + - - +
1270A GLU* 3.9 9.2 - - - +
1272A ILE* 1.3 76.6 - - - +
1274A ALA* 1.3 58.9 + - - +
1275A THR 3.7 0.2 + - - -
1277A LEU* 3.5 30.7 + - + +
1378A HIS* 2.9 39.2 + - + +
1381A LYS* 3.2 42.5 + - + +
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Residues in contact with ALA1274 (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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1270A GLU 3.2 17.4 + - - +
1271A TYR* 3.2 6.3 + - + +
1273A GLU* 1.3 77.2 - - - +
1275A THR* 1.3 59.5 + - - +
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Residues in contact with THR1275 (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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1271A TYR* 2.8 45.2 + - - -
1272A ILE* 4.9 0.4 - - - -
1274A ALA* 1.3 81.0 - - - +
1276A GLY* 1.3 57.4 + - - +
1277A LEU 3.9 0.9 - - - -
1278A SER 5.4 0.3 + - - -
1279A THR* 4.2 5.7 - - - +
1314A VAL* 4.4 8.2 - - - +
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Residues in contact with GLY1276 (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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1272A ILE 2.7 19.7 + - - -
1275A THR* 1.3 75.7 - - - +
1277A LEU* 1.3 59.7 + - - +
1278A SER 3.0 7.4 + - - -
1279A THR* 3.1 28.7 + - - +
1282A ILE* 3.4 19.7 - - - +
1314A VAL* 3.4 14.1 - - - +
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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
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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