Contacts of the helix formed by residues 1313 - 1328 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286A SER* 6.1 4.0 - - - +
3C UNX 3.0 26.9 - - - -
1291C GLU* 5.5 3.8 - - - +
1311C ASP 3.9 2.2 + - - -
1312C PHE* 1.3 76.2 - - - +
1314C VAL* 1.3 71.5 + - + +
1315C ASN* 3.9 11.2 - - + +
1316C THR* 3.2 24.8 + - - -
1317C VAL* 3.1 20.4 + - - +
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Residues in contact with VAL1314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271C TYR* 4.9 5.2 - - + -
1272C ILE* 4.4 10.9 - - + +
1275C THR* 4.5 10.1 - - - +
1276C GLY* 3.5 31.6 - - - +
1279C THR* 3.6 28.7 - - + +
1282C ILE* 4.2 13.0 - - + -
1312C PHE 3.5 2.7 + - - -
1313C THR* 1.3 75.5 - - + +
1315C ASN* 1.3 68.3 + - - +
1317C VAL* 3.2 8.0 + - - +
1318C ALA* 2.9 27.1 + - - +
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Residues in contact with ASN1315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C UNX 4.0 23.0 - - - -
1279C THR* 4.8 4.5 + - - -
1280C GLU 5.3 3.7 + - - +
1281C GLY 5.1 0.2 - - - -
1282C ILE* 4.2 19.9 - - - +
1283C TYR 4.3 2.4 + - - -
1285C VAL* 3.9 41.5 - - + +
1287C GLY* 4.5 17.4 + - - -
1313C THR* 3.2 2.4 - - + +
1314C VAL* 1.3 88.6 - - - +
1316C THR* 1.3 59.1 + - - +
1318C ALA* 3.7 4.6 - - - +
1319C GLY* 2.8 26.7 + - - -
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Residues in contact with THR1316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1287C GLY* 5.0 1.1 - - - -
1288C ASN* 4.4 9.9 + - - +
1291C GLU* 3.5 49.4 - - + +
1292C MET* 3.6 13.8 - - + +
1295C LEU* 4.7 2.9 - - + -
1312C PHE* 3.9 15.0 - - + -
1313C THR* 3.2 32.1 + - - -
1315C ASN* 1.3 78.3 - - - +
1317C VAL* 1.3 58.1 + - - +
1320C ALA* 2.9 30.3 + - - +
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Residues in contact with VAL1317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268C CYS* 3.7 38.9 - - + +
1271C TYR* 3.7 29.8 - - + -
1272C ILE* 3.8 10.5 - - + +
1295C LEU* 3.9 16.4 - - + -
1307C LEU* 4.9 6.7 - - + -
1312C PHE* 3.9 17.3 - - + -
1313C THR 3.1 14.1 + - - +
1314C VAL 3.7 5.6 - - - +
1316C THR* 1.3 73.8 - - - +
1318C ALA* 1.3 64.9 + - - +
1320C ALA* 3.4 1.4 + - - +
1321C MET* 3.0 22.0 + - - +
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Residues in contact with ALA1318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272C ILE* 3.5 15.4 - - + +
1282C ILE* 4.2 14.1 - - + -
1283C TYR* 3.6 37.2 - - + +
1285C VAL 6.1 0.4 - - - +
1314C VAL 2.9 17.4 + - - +
1315C ASN* 3.7 8.7 - - - +
1317C VAL* 1.3 77.0 - - - +
1319C GLY* 1.3 62.7 + - - +
1321C MET* 3.1 13.0 + - - +
1322C LYS* 3.1 12.1 + - - +
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Residues in contact with GLY1319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1286C SER* 6.4 0.2 - - - -
1287C GLY 5.6 0.9 - - - -
1292C MET* 3.4 23.8 - - - +
1315C ASN 2.8 17.1 + - - -
1318C ALA* 1.3 77.1 - - - +
1320C ALA* 1.3 56.3 + - - +
1322C LYS* 3.5 12.8 + - - +
1323C SER* 3.0 27.2 + - - -
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Residues in contact with ALA1320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247C PHE* 5.4 0.5 - - - -
1264C PHE* 3.2 25.8 - - + -
1292C MET* 3.7 19.7 - - + +
1295C LEU* 4.0 22.4 - - + -
1296C GLN* 5.5 2.0 - - + +
1316C THR 2.9 19.5 + - - +
1317C VAL 3.9 4.5 - - - +
1318C ALA 3.2 0.2 - - - -
1319C GLY* 1.3 75.2 - - - +
1321C MET* 1.3 62.8 + - - +
1323C SER* 3.5 9.2 + - - -
1324C PHE 3.3 12.5 + - - -
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Residues in contact with MET1321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264C PHE* 4.1 8.5 - - - -
1265C ILE* 3.8 14.8 - - + +
1268C CYS* 3.7 19.7 - - + -
1269C ILE* 3.5 35.7 - - + -
1272C ILE* 4.6 2.0 - - + -
1283C TYR* 4.3 15.3 - - - +
1317C VAL 3.0 14.2 + - - +
1318C ALA* 3.1 9.6 + - - +
1320C ALA* 1.3 76.0 - - - +
1322C LYS* 1.3 66.3 + - - +
1324C PHE* 3.4 13.2 + - - +
1325C PHE* 3.4 41.1 - - + -
1375C VAL* 3.9 16.2 - - + -
1378C HIS* 5.1 1.1 - - + -
1400C PHE* 4.4 16.2 - - + -
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Residues in contact with LYS1322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283C TYR* 3.6 29.9 + - + +
1284C ARG 5.8 0.4 + - - -
1318C ALA 3.1 12.4 + - - +
1319C GLY* 3.8 13.7 - - - +
1321C MET* 1.3 75.6 - - - +
1323C SER* 1.3 66.4 + - - +
1325C PHE* 2.9 18.0 + - - +
1326C SER* 3.1 13.4 + - - -
1399C CYS* 3.3 29.5 + - - +
1400C PHE* 3.5 33.4 - - + -
1403C THR* 3.5 21.0 + - + +
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Residues in contact with SER1323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292C MET* 5.1 7.6 - - - -
1319C GLY 3.0 18.4 + - - -
1320C ALA* 3.6 11.7 - - - -
1321C MET 3.2 0.4 - - - -
1322C LYS* 1.3 77.4 - - - +
1324C PHE* 1.3 63.1 + - - +
1326C SER* 3.2 10.9 + - - -
1327C GLU* 2.9 52.7 + - - +
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Residues in contact with PHE1324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246C TYR* 4.2 30.1 - + - -
1247C PHE* 3.7 25.6 - + + -
1248C GLY 5.5 0.8 + - - -
1251C LEU* 4.5 2.2 - - + -
1254C VAL* 4.0 11.2 - - + -
1262C PRO* 4.0 28.5 - - + -
1264C PHE* 4.0 22.2 - + + -
1265C ILE* 3.7 18.8 - - + -
1320C ALA 3.3 3.8 + - - -
1321C MET 3.5 9.6 - - - +
1322C LYS 3.1 1.0 - - - -
1323C SER* 1.3 78.6 - - - +
1325C PHE* 1.3 83.8 + + - +
1327C GLU* 3.3 11.4 + - - +
1328C LEU* 3.3 44.4 + - + +
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Residues in contact with PHE1325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251C LEU* 5.5 0.4 - - + -
1265C ILE* 3.6 18.6 - - + -
1321C MET* 3.4 47.6 - - + -
1322C LYS* 2.9 9.2 + - - +
1324C PHE* 1.3 87.6 - + - +
1326C SER* 1.3 59.3 + - - +
1327C GLU 3.1 5.2 + - - -
1328C LEU* 3.4 34.6 + - + +
1330C ASP 5.0 0.3 - - - +
1331C PRO* 5.2 2.4 - - - +
1332C LEU* 3.7 22.1 + - + -
1371C VAL* 3.5 34.5 - - + -
1375C VAL* 3.5 14.1 - - + -
1400C PHE* 5.3 2.0 - + - -
1403C THR* 3.8 20.2 - - + +
1404C LEU* 4.3 13.0 - - + -
1406C ARG* 3.7 7.3 + - - -
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Residues in contact with SER1326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322C LYS* 3.1 12.6 + - - +
1323C SER* 3.2 19.2 + - - -
1325C PHE* 1.3 75.8 - - - +
1327C GLU* 1.3 60.0 + - - +
1328C LEU 3.4 0.9 - - - +
1403C THR* 3.9 16.9 - - - +
1406C ARG* 3.3 21.8 + - - +
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Residues in contact with GLU1327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247C PHE* 3.5 32.6 - - - +
1248C GLY* 3.1 30.9 - - - +
1323C SER* 2.9 37.0 + - - +
1324C PHE* 3.7 4.4 - - - +
1325C PHE 3.1 0.4 - - - -
1326C SER* 1.3 79.3 - - - +
1328C LEU* 1.3 65.9 + - - +
1329C PRO* 3.4 1.6 - - - +
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Residues in contact with LEU1328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248C GLY* 4.9 2.0 - - - +
1249C VAL 3.5 21.1 - - - +
1251C LEU* 4.1 31.0 - - + +
1254C VAL* 5.5 0.2 - - + -
1324C PHE* 3.3 41.1 + - + +
1325C PHE* 3.4 35.7 + - + +
1326C SER 4.2 0.3 - - - +
1327C GLU* 1.3 79.1 - - - +
1329C PRO* 1.3 62.1 - - + +
1330C ASP 3.3 19.3 - - - +
1332C LEU* 4.6 11.9 - - + +
1406C ARG* 2.5 31.4 + - - -
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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