Contacts of the helix formed by residues 1313 - 1328 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1286B SER* 5.3 14.2 + - - -
4D UNX 3.1 26.4 - - - -
1291D GLU* 5.5 3.8 + - - +
1311D ASP 3.9 1.8 + - - -
1312D PHE* 1.3 75.6 - - - +
1314D VAL* 1.3 70.9 + - + +
1315D ASN* 3.9 11.9 - - + +
1316D THR* 3.1 32.1 + - - -
1317D VAL* 3.1 13.3 + - - +
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Residues in contact with VAL1314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271D TYR* 4.8 4.9 - - + -
1272D ILE* 4.4 11.5 - - + +
1275D THR* 4.5 9.4 - - - +
1276D GLY* 3.4 31.4 - - - +
1279D THR* 3.6 28.3 - - + +
1282D ILE* 4.2 13.7 - - + -
1312D PHE 3.5 2.7 + - - -
1313D THR* 1.3 76.0 - - + +
1315D ASN* 1.3 68.9 + - - +
1317D VAL* 3.2 8.5 + - - +
1318D ALA* 2.9 27.1 + - - +
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Residues in contact with ASN1315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D UNX 4.2 20.3 - - - -
1279D THR* 4.8 3.9 + - - -
1280D GLU 5.2 4.7 + - - +
1282D ILE* 4.2 20.4 + - - +
1283D TYR 4.3 2.3 + - - -
1285D VAL* 3.9 41.6 - - + +
1287D GLY* 4.5 17.9 + - - -
1313D THR* 3.2 3.0 - - + +
1314D VAL* 1.3 87.4 - - - +
1316D THR* 1.3 60.7 + - - +
1318D ALA* 3.7 4.6 - - - +
1319D GLY* 2.8 26.7 + - - -
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Residues in contact with THR1316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1287D GLY* 5.0 1.1 - - - -
1288D ASN* 4.4 10.4 + - - +
1291D GLU* 3.5 48.6 - - + +
1292D MET* 3.6 15.1 - - + +
1295D LEU* 4.7 2.9 - - + -
1312D PHE* 3.9 15.3 - - + -
1313D THR* 3.1 33.0 + - - -
1315D ASN* 1.3 80.0 - - - +
1317D VAL* 1.3 56.6 + - - +
1320D ALA* 2.9 30.0 + - - +
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Residues in contact with VAL1317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268D CYS* 3.7 36.8 - - + +
1271D TYR* 3.7 26.0 - - + -
1272D ILE* 3.8 11.9 - - + -
1295D LEU* 3.9 15.0 - - + -
1307D LEU* 3.9 11.4 - - + -
1312D PHE* 3.9 17.5 - - + -
1313D THR 3.1 14.2 + - - +
1314D VAL 3.2 6.3 + - - +
1316D THR* 1.3 73.6 - - - +
1318D ALA* 1.3 61.0 + - - +
1320D ALA* 3.4 1.9 + - - +
1321D MET* 3.0 26.5 + - - +
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Residues in contact with ALA1318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272D ILE* 3.5 15.8 - - + +
1282D ILE* 4.2 16.4 - - + -
1283D TYR* 3.6 37.7 - - + +
1285D VAL 6.2 0.4 - - - +
1314D VAL 2.9 17.0 + - - +
1315D ASN* 3.7 7.0 - - - +
1316D THR 3.3 0.2 - - - -
1317D VAL* 1.3 76.3 - - - +
1319D GLY* 1.3 62.2 + - - +
1321D MET* 3.2 6.1 + - - +
1322D LYS* 3.1 19.1 + - - +
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Residues in contact with GLY1319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283D TYR* 6.5 0.2 - - - -
1286D SER* 6.4 0.4 - - - -
1287D GLY 5.6 0.7 - - - -
1292D MET* 3.4 24.6 - - - +
1315D ASN 2.8 17.4 + - - -
1318D ALA* 1.3 76.9 - - - +
1320D ALA* 1.3 55.5 + - - +
1322D LYS* 3.5 11.8 + - - +
1323D SER* 3.0 27.5 + - - -
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Residues in contact with ALA1320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264D PHE* 3.2 25.5 - - + -
1292D MET* 3.7 19.0 - - + +
1295D LEU* 3.9 23.1 - - + -
1296D GLN* 4.4 5.2 + - + -
1316D THR 2.9 19.8 + - - +
1317D VAL 3.8 4.9 - - - +
1318D ALA 3.2 0.2 - - - -
1319D GLY* 1.3 74.3 - - - +
1321D MET* 1.3 64.7 + - - +
1322D LYS 3.4 0.2 - - - -
1323D SER* 3.5 9.3 + - - -
1324D PHE* 3.3 12.6 + - - -
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Residues in contact with MET1321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264D PHE* 4.1 8.5 - - - -
1265D ILE* 3.8 15.8 - - + +
1268D CYS* 3.7 19.1 - - + -
1269D ILE* 3.5 34.8 - - + -
1272D ILE* 4.6 2.0 - - + -
1283D TYR* 4.3 16.2 - - - +
1317D VAL 3.0 16.7 + - - +
1318D ALA* 3.2 6.5 + - - +
1320D ALA* 1.3 75.1 - - - +
1322D LYS* 1.3 67.4 + - - +
1324D PHE* 3.3 12.8 + - - +
1325D PHE* 3.4 41.3 - - + -
1375D VAL* 3.9 16.6 - - + -
1378D HIS* 5.1 1.3 - - + -
1400D PHE* 4.4 15.5 - - + -
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Residues in contact with LYS1322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283D TYR* 3.6 29.6 + - + +
1284D ARG 5.8 0.2 + - - -
1318D ALA 3.1 13.5 + - - +
1319D GLY* 3.8 12.6 - - - +
1320D ALA 3.4 0.2 - - - -
1321D MET* 1.3 78.3 - - - +
1323D SER* 1.3 63.8 + - - +
1325D PHE* 2.9 18.1 + - - +
1326D SER* 3.1 14.1 + - - -
1399D CYS* 3.3 30.0 + - - +
1400D PHE* 3.5 33.9 - - + -
1403D THR* 3.5 22.0 + - + +
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Residues in contact with SER1323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292D MET* 5.1 5.6 - - - -
1296D GLN* 3.6 11.9 + - - -
1319D GLY 3.0 18.2 + - - -
1320D ALA* 3.6 11.4 - - - -
1321D MET 3.2 0.2 - - - -
1322D LYS* 1.3 77.7 - - - +
1324D PHE* 1.3 63.8 + - - +
1326D SER* 3.2 11.0 + - - -
1327D GLU* 2.9 50.1 + - - +
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Residues in contact with PHE1324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246D TYR* 4.2 30.5 - + - -
1247D PHE* 3.7 25.6 - + + -
1248D GLY 5.5 1.2 + - - -
1251D LEU* 4.5 2.2 - - + -
1254D VAL* 4.0 10.8 - - + -
1262D PRO* 4.0 27.8 - - + -
1264D PHE* 4.0 22.0 - + + -
1265D ILE* 3.8 17.7 - - + -
1296D GLN* 4.2 0.4 - - - +
1320D ALA 3.3 3.6 + - - -
1321D MET 3.5 9.6 - - - +
1322D LYS 3.1 0.8 - - - -
1323D SER* 1.3 78.9 - - - +
1325D PHE* 1.3 85.3 + + - +
1327D GLU* 3.3 11.0 + - - +
1328D LEU* 3.2 45.3 + - + +
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Residues in contact with PHE1325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251D LEU* 5.5 0.4 - - + -
1265D ILE* 3.6 19.3 - - + -
1321D MET* 3.4 47.8 - - + -
1322D LYS* 2.9 10.5 + - - +
1324D PHE* 1.3 86.6 - + - +
1326D SER* 1.3 60.4 + - - +
1327D GLU 3.1 5.0 + - - -
1328D LEU* 3.4 34.0 + - + +
1330D ASP 5.0 0.3 - - - +
1331D PRO* 5.2 2.4 - - - +
1332D LEU* 3.7 22.4 + - + -
1371D VAL* 3.5 25.1 - - + -
1375D VAL* 3.5 23.1 - - + -
1400D PHE* 5.3 2.7 - + - -
1403D THR* 3.8 19.3 - - + +
1404D LEU* 4.3 13.7 - - + -
1406D ARG* 3.7 7.3 + - - -
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Residues in contact with SER1326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322D LYS* 3.1 13.3 + - - +
1323D SER* 3.2 19.1 + - - -
1325D PHE* 1.3 75.9 - - - +
1327D GLU* 1.3 60.2 + - - +
1328D LEU 4.2 0.3 - - - +
1403D THR* 3.9 17.6 - - - +
1406D ARG* 3.3 21.9 + - - +
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Residues in contact with GLU1327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247D PHE* 3.5 18.7 - - - +
1248D GLY* 3.2 31.4 - - - +
1296D GLN* 2.7 34.4 + - - +
1323D SER* 2.9 30.9 + - - +
1324D PHE* 3.7 4.4 - - - +
1325D PHE 3.1 0.4 - - - -
1326D SER* 1.3 79.1 - - - +
1328D LEU* 1.3 65.4 + - - +
1329D PRO* 3.4 1.6 - - - +
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Residues in contact with LEU1328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248D GLY* 4.9 1.8 - - - +
1249D VAL 3.5 22.0 - - - +
1251D LEU* 4.1 31.4 - - + +
1254D VAL* 5.4 0.2 - - + -
1324D PHE* 3.2 43.0 + - + +
1325D PHE* 3.4 33.4 + - + +
1326D SER 4.2 0.5 - - - +
1327D GLU* 1.3 79.3 - - - +
1329D PRO* 1.3 61.8 - - + +
1330D ASP 3.4 18.6 - - - +
1332D LEU* 4.7 12.1 - - + +
1406D ARG* 2.5 31.0 + - - -
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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