Contacts of the helix formed by residues 1262 - 1276 (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 PRO1262 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246D TYR* 3.7 12.6 - - - +
1251D LEU* 4.1 9.2 - - + -
1254D VAL* 3.8 13.2 - - + +
1255D VAL* 3.4 20.8 - - + -
1260D PRO 3.6 2.0 - - - +
1261D ILE* 1.3 89.6 - - + +
1263D ILE* 1.3 66.3 + - - +
1264D PHE 4.5 0.2 - - - +
1265D ILE* 2.9 32.0 + - + +
1266D GLU* 3.1 9.7 + - - +
1324D PHE* 4.0 26.7 - - + -
1371D VAL* 3.9 15.0 - - + -
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Residues in contact with ILE1263 (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* 3.1 11.4 + - + +
1254D VAL 5.2 4.7 - - - +
1259D LYS* 5.1 14.1 - - + +
1261D ILE 3.9 11.0 - - - +
1262D PRO* 1.3 72.1 - - + +
1264D PHE* 1.3 63.4 + - - +
1266D GLU* 3.2 18.6 + - + +
1267D ARG* 3.0 50.1 + - - +
1299D PHE* 3.8 17.0 - - + -
1303D HIS* 4.0 10.3 - - + +
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Residues in contact with PHE1264 (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* 3.3 26.1 + - + +
1247D PHE* 3.7 31.9 - + - -
1262D PRO* 3.2 1.0 - - + -
1263D ILE* 1.3 78.3 - - - +
1265D ILE* 1.3 66.2 + - + +
1267D ARG* 3.4 4.0 + - + +
1268D CYS* 3.1 48.8 + - - -
1295D LEU* 4.4 15.3 - - + -
1296D GLN* 4.3 3.8 - - + -
1299D PHE* 3.7 40.1 - + + -
1307D LEU* 5.9 0.9 - - + -
1320D ALA* 3.2 39.9 - - + -
1321D MET* 4.1 2.2 - - - -
1324D PHE* 4.0 16.8 - + + -
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Residues in contact with ILE1265 (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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1261D ILE* 4.1 5.8 - - + -
1262D PRO* 2.9 28.2 + - + +
1264D PHE* 1.3 77.0 - - + +
1266D GLU* 1.3 59.4 + - - +
1268D CYS* 3.4 1.5 + - - -
1269D ILE* 2.9 42.5 + - + +
1321D MET* 3.8 24.0 - - + +
1324D PHE* 3.8 22.7 - - + -
1325D PHE* 3.6 35.7 - - + -
1371D VAL* 5.4 0.9 - - + -
1374D TYR* 3.8 25.1 - - + -
1375D VAL* 4.8 1.6 - - + -
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Residues in contact with GLU1266 (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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1261D ILE* 4.1 28.5 - - + +
1262D PRO 3.1 6.7 + - - +
1263D ILE* 3.2 20.0 + - - +
1265D ILE* 1.3 78.2 - - - +
1267D ARG* 1.3 66.0 + - - +
1270D GLU* 2.9 46.8 + - - +
1374D TYR* 3.3 28.7 - - + +
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Residues in contact with ARG1267 (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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1263D ILE* 3.0 31.1 + - - +
1264D PHE* 3.6 9.2 - - + +
1265D ILE 3.4 0.2 - - - -
1266D GLU* 1.3 78.6 - - - +
1268D CYS* 1.3 60.2 + - - +
1270D GLU* 3.8 3.4 - - - +
1271D TYR* 2.9 32.2 + - - +
1299D PHE* 4.2 11.5 - - + -
1303D HIS 2.6 30.1 + - - -
1304D ASN* 3.7 9.5 - - - +
1305D LEU 3.2 25.8 + - - +
1306D ASP* 6.0 0.2 - - - +
1307D LEU* 3.6 18.2 - - + +
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Residues in contact with CYS1268 (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* 3.1 55.3 + - - +
1265D ILE 4.0 0.2 - - - +
1267D ARG* 1.3 80.9 - - - +
1269D ILE* 1.3 58.6 + - - +
1271D TYR* 3.3 1.2 + - - +
1272D ILE* 2.7 38.1 + - + +
1295D LEU* 4.9 2.7 - - - -
1307D LEU* 4.0 6.7 - - - -
1317D VAL* 3.7 31.9 - - + -
1321D MET* 3.7 22.2 - - + -
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Residues in contact with ILE1269 (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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1265D ILE* 2.9 19.4 + - + +
1268D CYS* 1.3 75.3 - - - +
1270D GLU* 1.3 59.1 + - + +
1272D ILE* 3.4 6.4 + - - +
1273D GLU* 2.8 39.7 + - - +
1283D TYR* 4.8 0.2 - - - +
1321D MET* 3.5 36.3 - - + -
1374D TYR* 3.4 41.5 - - + +
1375D VAL* 4.4 4.5 - - - -
1378D HIS* 3.3 47.6 - - + +
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Residues in contact with GLU1270 (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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1266D GLU* 2.9 47.9 + - - +
1267D ARG* 4.0 4.0 - - - +
1269D ILE* 1.3 78.2 - - + +
1271D TYR* 1.3 57.7 + - - +
1273D GLU* 3.9 9.1 - - - +
1274D ALA* 3.2 26.9 + - - +
1374D TYR* 3.8 10.4 + - - +
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Residues in contact with TYR1271 (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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1267D ARG 2.9 19.1 + - - +
1268D CYS 3.7 1.3 - - - +
1270D GLU* 1.3 76.2 - - - +
1272D ILE* 1.3 62.6 + - + +
1274D ALA* 3.2 5.7 + - + -
1275D THR* 2.8 55.1 + - - -
1307D LEU* 3.6 45.3 + - + -
1308D ALA* 3.8 13.9 - - + -
1311D ASP* 5.3 1.6 - - - -
1312D PHE 3.4 20.2 + - - -
1314D VAL* 4.8 7.4 - - + -
1317D VAL* 3.7 35.7 - - + -
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Residues in contact with ILE1272 (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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1268D CYS* 2.7 29.6 + - + +
1269D ILE* 3.8 4.3 - - - +
1271D TYR* 1.3 74.3 - - + +
1273D GLU* 1.3 58.6 + - - +
1276D GLY* 2.7 30.4 + - - +
1277D LEU* 3.4 7.6 + - + +
1282D ILE* 3.4 26.9 - - + -
1283D TYR* 3.5 23.8 - - + +
1314D VAL* 4.4 10.1 - - + +
1317D VAL* 3.8 18.6 - - + +
1318D ALA* 3.5 36.1 - - + +
1321D MET* 4.6 2.7 - - + -
1378D HIS* 4.1 9.2 - - + -
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Residues in contact with GLU1273 (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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1414B ALA* 3.2 27.2 - - + +
1418B THR* 4.0 6.8 + - - -
1269D ILE* 2.8 29.8 + - - +
1270D GLU* 3.9 9.7 - - - +
1271D TYR 3.2 0.2 - - - -
1272D ILE* 1.3 76.8 - - - +
1274D ALA* 1.3 58.7 + - - +
1275D THR 3.8 0.2 + - - -
1277D LEU* 3.6 21.6 - - + +
1378D HIS* 2.8 38.4 + - + +
1381D LYS* 3.2 42.9 + - + +
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Residues in contact with ALA1274 (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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1401B TRP* 4.1 20.8 - - - -
1402B PRO* 5.8 0.7 - - - +
1414B ALA* 4.9 4.0 - - + +
1418B THR* 5.0 4.2 + - - -
1270D GLU 3.2 16.3 + - - +
1271D TYR* 3.2 8.0 + - + +
1273D GLU* 1.3 78.9 - - - +
1275D THR* 1.3 57.7 + - - +
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Residues in contact with THR1275 (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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1401B TRP* 5.7 5.0 - - - -
1402B PRO* 5.5 8.9 - - - +
1271D TYR* 2.8 44.2 + - - -
1272D ILE* 4.9 0.4 - - - -
1274D ALA* 1.3 80.3 - - - +
1276D GLY* 1.3 56.6 + - - +
1277D LEU 3.9 0.9 - - - -
1278D SER 5.4 0.3 + - - -
1279D THR* 4.3 5.5 - - - +
1314D VAL* 4.5 8.7 - - - +
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Residues in contact with GLY1276 (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 2.7 19.7 + - - -
1275D THR* 1.3 74.9 - - - +
1277D LEU* 1.3 56.1 + - - +
1278D SER 2.9 12.0 + - - -
1279D THR* 3.1 32.4 + - - +
1282D ILE* 3.5 14.9 - - - +
1314D VAL* 3.4 14.5 - - - +
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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
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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