Contacts of the helix formed by residues 1313 - 1328 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B UNX 3.3 25.1 - - - -
1291B GLU* 5.5 3.5 - - - +
1311B ASP 3.9 1.6 + - - -
1312B PHE* 1.3 76.6 - - - +
1314B VAL* 1.3 70.3 + - + +
1315B ASN* 3.9 14.4 - - + +
1316B THR* 3.2 23.8 + - - -
1317B VAL* 3.2 20.4 + - - +
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Residues in contact with VAL1314 (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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1271B TYR* 4.8 5.8 - - + -
1272B ILE* 4.4 11.3 - - + +
1275B THR* 4.4 8.7 - - - +
1276B GLY* 3.4 32.1 - - - +
1279B THR* 3.6 26.7 - - + +
1282B ILE* 4.1 14.8 - - + -
1312B PHE 3.5 2.0 + - - -
1313B THR* 1.3 77.8 - - + +
1315B ASN* 1.3 69.3 + - - +
1317B VAL* 3.2 7.0 + - - +
1318B ALA* 2.9 27.5 + - - +
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Residues in contact with ASN1315 (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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2B UNX 4.6 3.1 - - - -
1279B THR* 4.8 2.9 + - - -
1280B GLU 5.2 4.1 + - - +
1281B GLY 5.1 0.2 - - - -
1282B ILE* 4.2 19.4 - - - +
1283B TYR 4.4 2.4 + - - -
1285B VAL* 3.7 43.4 - - + +
1287B GLY* 4.4 20.8 + - - -
1313B THR* 3.3 12.6 - - + +
1314B VAL* 1.3 89.7 - - - +
1316B THR* 1.3 57.9 + - - +
1318B ALA* 3.7 4.8 - - - +
1319B GLY* 2.9 26.2 + - - -
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Residues in contact with THR1316 (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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1287B GLY* 5.0 0.8 - - - -
1288B ASN* 4.4 10.9 + - - +
1291B GLU* 3.6 48.8 - - + +
1292B MET* 3.6 13.9 - - + +
1295B LEU* 4.6 3.6 - - + -
1312B PHE* 4.0 15.3 - - + -
1313B THR* 3.2 31.7 + - - -
1314B VAL 3.2 0.8 - - - -
1315B ASN* 1.3 79.0 - - - +
1317B VAL* 1.3 59.3 + - - +
1320B ALA* 2.9 27.5 + - - +
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Residues in contact with VAL1317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268B CYS* 3.6 35.3 - - + +
1271B TYR* 3.7 26.9 - - + -
1272B ILE* 3.8 9.0 - - + -
1295B LEU* 3.9 20.9 - - + -
1307B LEU* 3.8 14.6 - - + -
1312B PHE* 3.9 12.1 - - + -
1313B THR 3.2 13.4 + - - +
1314B VAL 3.2 7.0 + - - +
1316B THR* 1.3 73.0 - - - +
1318B ALA* 1.3 65.4 + - - +
1320B ALA* 3.9 1.0 - - - +
1321B MET* 3.0 22.0 + - - +
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Residues in contact with ALA1318 (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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1272B ILE* 3.5 15.4 - - + +
1282B ILE* 4.2 14.4 - - + -
1283B TYR* 3.6 37.6 - - + +
1285B VAL 6.1 0.7 - - - +
1314B VAL 2.9 15.9 + - - +
1315B ASN* 3.7 9.4 - - - +
1317B VAL* 1.3 78.6 - - - +
1319B GLY* 1.3 61.2 + - - +
1321B MET* 3.2 5.0 + - - +
1322B LYS* 3.1 20.1 + - - +
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Residues in contact with GLY1319 (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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1286B SER* 6.4 0.4 - - - -
1287B GLY 5.6 0.9 - - - -
1292B MET* 3.5 23.6 - - - +
1315B ASN 2.9 17.0 + - - -
1318B ALA* 1.3 76.8 - - - +
1320B ALA* 1.3 57.0 + - - +
1322B LYS* 3.5 12.1 + - - +
1323B SER* 2.9 27.9 + - - -
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Residues in contact with ALA1320 (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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1264B PHE* 3.2 27.8 - - + -
1292B MET* 3.7 19.4 - - + +
1295B LEU* 3.9 23.3 - - + -
1296B GLN* 3.6 5.3 + - - +
1316B THR 2.9 19.3 + - - +
1317B VAL 3.9 3.6 - - - +
1319B GLY* 1.3 74.0 - - - +
1321B MET* 1.3 64.7 + - - +
1323B SER* 3.6 8.6 - - - -
1324B PHE 3.3 12.3 + - - -
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Residues in contact with MET1321 (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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1264B PHE* 4.2 8.0 - - - -
1265B ILE* 3.9 13.1 - - + +
1268B CYS* 3.7 22.4 - - + -
1269B ILE* 3.5 35.0 - - + -
1272B ILE* 4.6 1.8 - - + -
1283B TYR* 4.4 13.9 - - - +
1317B VAL 3.0 18.6 + - - +
1318B ALA* 3.2 6.7 + - - +
1320B ALA* 1.3 74.5 - - - +
1322B LYS* 1.3 70.7 + - - +
1324B PHE* 3.3 16.1 + - - +
1325B PHE* 3.4 36.7 - - + -
1375B VAL* 4.0 16.6 - - + -
1378B HIS* 5.0 2.0 - - + -
1400B PHE* 4.5 12.3 - - + -
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Residues in contact with LYS1322 (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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1283B TYR* 3.6 30.1 + - + -
1318B ALA 3.1 14.4 + - - +
1319B GLY* 3.8 12.6 - - - +
1320B ALA 3.4 0.2 - - - -
1321B MET* 1.3 77.4 - - - +
1323B SER* 1.3 58.2 + - - +
1325B PHE* 2.8 26.4 + - - +
1326B SER* 3.1 12.5 + - - +
1399B CYS* 3.3 24.7 + - - +
1400B PHE* 3.5 33.7 - - + -
1403B THR* 3.6 25.9 + - + +
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Residues in contact with SER1323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292B MET* 5.1 6.3 - - - -
1296B GLN* 3.3 16.0 + - - -
1319B GLY 2.9 19.0 + - - -
1320B ALA* 3.6 5.4 - - - -
1321B MET 3.2 0.4 - - - -
1322B LYS* 1.3 76.3 - - - +
1324B PHE* 1.3 62.1 + - - +
1326B SER* 3.3 10.9 + - - -
1327B GLU* 2.9 52.8 + - - +
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Residues in contact with PHE1324 (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 TYR* 4.1 30.7 - + - -
1247B PHE* 3.7 24.2 - + + -
1248B GLY 5.5 1.1 + - - -
1251B LEU* 4.5 2.0 - - + -
1254B VAL* 4.0 14.1 - - + -
1262B PRO* 4.0 22.2 - - + -
1264B PHE* 4.0 21.8 - + + -
1265B ILE* 3.7 24.9 - - + -
1296B GLN* 3.8 1.5 - - - +
1320B ALA 3.3 3.8 + - - -
1321B MET 3.6 9.6 - - - +
1322B LYS 3.1 0.6 - - - -
1323B SER* 1.3 79.6 - - - +
1325B PHE* 1.3 83.9 + + - +
1327B GLU* 3.4 10.9 + - - +
1328B LEU* 3.3 39.7 + - + +
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Residues in contact with PHE1325 (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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1251B LEU* 5.4 0.2 - - + -
1265B ILE* 3.6 18.6 - - + -
1321B MET* 3.4 46.2 - - + -
1322B LYS* 2.8 10.3 + - - +
1324B PHE* 1.3 87.7 - + - +
1326B SER* 1.3 59.0 + - - +
1327B GLU 3.1 5.5 + - - -
1328B LEU* 3.4 33.1 + - + +
1330B ASP 5.0 0.5 - - - +
1331B PRO* 5.2 2.3 - - - +
1332B LEU* 3.7 21.6 + - + -
1371B VAL* 3.5 24.7 - - + -
1375B VAL* 3.5 24.7 - - + -
1400B PHE* 5.3 2.5 - + - -
1403B THR* 3.8 19.9 - - + +
1404B LEU* 4.3 13.7 - - + -
1406B ARG* 3.6 8.0 + - - -
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Residues in contact with SER1326 (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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1322B LYS* 3.1 11.3 + - - +
1323B SER* 3.3 17.0 + - - -
1325B PHE* 1.3 76.3 - - - +
1327B GLU* 1.3 60.0 + - - +
1328B LEU 4.2 0.3 - - - +
1403B THR* 3.8 19.3 - - - +
1406B ARG* 3.3 21.5 + - - +
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Residues in contact with GLU1327 (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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1242B TRP* 5.5 4.1 - - - -
1247B PHE* 3.5 21.9 - - - +
1248B GLY* 3.1 30.5 - - - +
1296B GLN* 3.2 26.1 + - - +
1323B SER* 2.9 35.3 + - - +
1324B PHE 3.8 4.0 - - - +
1325B PHE 3.1 0.2 - - - -
1326B SER* 1.3 79.7 - - - +
1328B LEU* 1.3 66.5 + - - +
1329B PRO* 3.4 1.6 - - - +
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Residues in contact with LEU1328 (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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1248B GLY* 4.8 2.0 - - - +
1249B VAL 3.4 21.3 - - - +
1251B LEU* 4.1 33.2 - - + +
1324B PHE* 3.3 38.3 + - + +
1325B PHE* 3.4 35.6 + - + +
1326B SER 4.2 0.3 - - - +
1327B GLU* 1.3 79.1 - - - +
1329B PRO* 1.3 63.2 - - + +
1330B ASP 3.4 18.6 - - - +
1332B LEU* 4.7 11.0 - - + +
1406B 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