Contacts of the helix formed by residues 1313 - 1328 (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 THR1313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A UNX 3.0 27.0 - - - -
1291A GLU* 5.5 2.9 - - - +
1311A ASP 3.9 2.0 + - - -
1312A PHE* 1.3 76.8 - - - +
1314A VAL* 1.3 71.2 + - + +
1315A ASN* 3.9 15.9 - - + +
1316A THR* 3.2 23.6 + - - -
1317A VAL* 3.2 20.4 + - - +
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Residues in contact with VAL1314 (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* 4.8 4.9 + - + -
1272A ILE* 4.4 11.1 - - + +
1275A THR* 4.4 9.4 - - - +
1276A GLY* 3.4 31.9 - - - +
1279A THR* 3.6 28.0 - - + +
1282A ILE* 4.2 13.9 - - + -
1312A PHE 3.5 2.3 + - - -
1313A THR* 1.3 76.4 - - + +
1315A ASN* 1.3 68.7 + - - +
1317A VAL* 3.2 7.7 + - - +
1318A ALA* 2.9 27.6 + - - +
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Residues in contact with ASN1315 (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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1279A THR* 4.8 3.3 + - - -
1280A GLU 5.2 4.1 + - - +
1281A GLY 5.1 0.2 - - - -
1282A ILE* 4.2 20.7 - - - +
1283A TYR 4.4 2.6 + - - -
1285A VAL* 3.8 42.4 - - + +
1287A GLY* 4.5 21.2 + - - -
1313A THR* 3.3 12.9 - - + +
1314A VAL* 1.3 88.6 - - - +
1316A THR* 1.3 57.9 + - - +
1318A ALA* 3.7 4.2 - - - +
1319A GLY* 2.8 27.5 + - - -
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Residues in contact with THR1316 (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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1287A GLY* 4.9 1.0 - - - -
1288A ASN* 4.4 10.6 + - - +
1291A GLU* 3.6 48.9 - - + +
1292A MET* 3.6 13.9 - - + +
1295A LEU* 4.7 3.8 - - + -
1312A PHE* 3.9 14.6 - - + -
1313A THR* 3.2 32.5 + - - -
1315A ASN* 1.3 79.0 - - - +
1317A VAL* 1.3 57.5 + - - +
1319A GLY 3.6 0.2 + - - -
1320A ALA* 2.9 28.1 + - - +
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Residues in contact with VAL1317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268A CYS* 3.6 35.9 - - + +
1271A TYR* 3.7 25.1 - - + -
1272A ILE* 3.8 9.9 - - + -
1295A LEU* 3.9 15.0 - - + -
1307A LEU* 3.8 14.6 - - + -
1312A PHE* 3.9 17.0 - - + -
1313A THR 3.2 14.4 + - - +
1314A VAL 3.2 5.8 + - - +
1316A THR* 1.3 72.2 - - - +
1318A ALA* 1.3 66.1 + - - +
1320A ALA* 3.8 1.2 - - - +
1321A MET* 3.0 22.3 + - - +
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Residues in contact with ALA1318 (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* 3.5 15.6 - - + +
1282A ILE* 4.2 15.0 - - + -
1283A TYR* 3.6 37.1 - - + +
1285A VAL 6.1 0.4 - - - +
1314A VAL 2.9 16.6 + - - +
1315A ASN* 3.7 9.0 - - - +
1317A VAL* 1.3 76.9 - - - +
1319A GLY* 1.3 61.5 + - - +
1321A MET* 3.2 5.0 + - - +
1322A LYS* 3.1 20.1 + - - +
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Residues in contact with GLY1319 (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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1283A TYR* 6.1 0.2 - - - +
1286A SER* 6.4 0.4 - - - -
1287A GLY 5.6 0.9 - - - -
1292A MET* 3.4 23.5 - - - +
1315A ASN 2.8 17.4 + - - -
1318A ALA* 1.3 76.4 - - - +
1320A ALA* 1.3 56.5 + - - +
1322A LYS* 3.5 12.2 + - - +
1323A SER* 2.9 27.7 + - - -
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Residues in contact with ALA1320 (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* 3.2 26.2 - - + -
1292A MET* 3.7 20.8 - - + +
1295A LEU* 3.9 22.9 - - + -
1296A GLN* 3.6 5.7 + - - +
1316A THR 2.9 18.6 + - - +
1317A VAL 3.9 4.3 - - - +
1319A GLY* 1.3 76.0 - - - +
1321A MET* 1.3 62.0 + - - +
1323A SER* 3.5 8.4 + - - -
1324A PHE 3.3 12.5 + - - -
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Residues in contact with MET1321 (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* 4.2 8.3 - - - -
1265A ILE* 3.9 14.9 - - + +
1268A CYS* 3.8 20.0 - - + -
1269A ILE* 3.5 35.4 - - + -
1272A ILE* 4.6 1.8 - - + -
1283A TYR* 4.4 13.7 - - - +
1317A VAL 3.0 17.9 + - - +
1318A ALA* 3.2 6.9 + - - +
1320A ALA* 1.3 75.8 - - - +
1322A LYS* 1.3 66.7 + - - +
1324A PHE* 3.4 16.3 + - - +
1325A PHE* 3.4 37.9 - - + -
1375A VAL* 3.9 16.6 - - + -
1378A HIS* 5.1 2.0 - - + -
1400A PHE* 4.4 15.0 - - + -
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Residues in contact with LYS1322 (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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1283A TYR* 3.6 29.0 + - + +
1318A ALA 3.1 13.3 + - - +
1319A GLY* 3.8 12.1 - - - +
1321A MET* 1.3 78.3 - - - +
1323A SER* 1.3 63.4 + - - +
1325A PHE* 2.9 18.8 + - - +
1326A SER* 3.1 13.7 + - - +
1399A CYS* 3.3 24.6 + - - +
1400A PHE* 3.5 34.1 - - + -
1403A THR* 3.5 27.0 + - + +
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Residues in contact with SER1323 (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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1292A MET* 5.1 6.5 - - - -
1296A GLN* 3.4 16.4 + - - -
1319A GLY 2.9 17.8 + - - -
1320A ALA* 3.6 5.4 - - - -
1321A MET 3.2 0.4 - - - -
1322A LYS* 1.3 77.7 - - - +
1324A PHE* 1.3 61.5 + - - +
1326A SER* 3.2 11.0 + - - -
1327A GLU* 2.9 47.9 + - - +
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Residues in contact with PHE1324 (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* 4.1 31.2 - + - -
1247A PHE* 3.7 24.5 - + + -
1248A GLY 5.5 1.0 + - - -
1251A LEU* 4.5 2.0 - - + -
1254A VAL* 4.0 10.5 - - + -
1262A PRO* 4.0 21.8 - - + -
1264A PHE* 4.0 20.9 - + + -
1265A ILE* 3.7 24.5 - - + -
1296A GLN* 3.8 1.7 - - - +
1320A ALA 3.3 4.2 + - - -
1321A MET 3.5 9.9 - - - +
1322A LYS 3.2 0.4 - - - -
1323A SER* 1.3 79.3 - - - +
1325A PHE* 1.3 84.3 + + - +
1327A GLU* 3.4 10.9 + - - +
1328A LEU* 3.3 44.3 + - + +
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Residues in contact with PHE1325 (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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1251A LEU* 5.4 0.2 - - + -
1265A ILE* 3.6 18.6 - - + -
1321A MET* 3.4 45.8 - - + -
1322A LYS* 2.9 9.4 + - - +
1324A PHE* 1.3 86.1 - + - +
1326A SER* 1.3 60.3 + - - +
1327A GLU 3.1 5.2 + - - -
1328A LEU* 3.4 33.9 + - + +
1330A ASP 5.0 0.5 - - - +
1331A PRO* 5.2 2.1 - - - +
1332A LEU* 3.7 22.2 + - + +
1371A VAL* 3.5 34.5 - - + -
1375A VAL* 3.5 14.4 - - + -
1400A PHE* 5.3 2.5 - + - -
1403A THR* 3.8 19.6 - - + +
1404A LEU* 4.3 13.7 - - + -
1406A ARG* 3.6 8.0 + - - -
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Residues in contact with SER1326 (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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1322A LYS* 3.1 12.0 + - - +
1323A SER* 3.2 17.0 + - - -
1325A PHE* 1.3 75.7 - - - +
1327A GLU* 1.3 60.8 + - - +
1328A LEU 4.2 0.5 - - - +
1403A THR* 3.9 18.2 - - - +
1406A ARG* 3.3 22.1 + - - +
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Residues in contact with GLU1327 (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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1242A TRP* 5.4 3.9 + - - -
1247A PHE* 3.5 22.3 - - - +
1248A GLY* 3.1 29.9 - - - +
1296A GLN* 3.1 28.1 + - - +
1323A SER* 2.9 33.6 + - - +
1324A PHE 3.7 4.0 - - - +
1325A PHE 3.1 0.4 - - - -
1326A SER* 1.3 80.6 - - - +
1328A LEU* 1.3 66.1 + - - +
1329A PRO* 3.4 1.4 - - - +
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Residues in contact with LEU1328 (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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1248A GLY* 4.8 2.0 - - - +
1249A VAL 3.5 22.2 - - - +
1251A LEU* 4.1 33.9 - - + +
1254A VAL* 5.4 0.2 - - + -
1324A PHE* 3.3 37.0 + - + +
1325A PHE* 3.4 36.4 + - + +
1326A SER 4.2 0.3 - - - +
1327A GLU* 1.3 79.1 - - - +
1329A PRO* 1.3 62.1 - - + +
1330A ASP 3.3 19.1 - - - +
1332A LEU* 4.6 11.2 - - + +
1406A ARG* 2.5 30.5 + - - -
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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
------------------------------------------------------------
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