Contacts of the helix formed by residues 1349 - 1363 (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 ASP1349 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347B ILE* 3.5 3.3 - - + +
1348B ASN* 1.3 76.5 - - - +
1350B ARG* 1.3 61.8 + - - +
1351B GLU* 3.5 10.3 + - - +
1352B GLN* 3.1 43.0 + - + +
1353B LYS* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1348B ASN 3.4 5.9 + - - +
1349B ASP* 1.3 75.2 + - - +
1351B GLU* 1.3 63.7 + - - +
1353B LYS* 3.2 23.8 + - - +
1354B LEU* 2.9 43.9 + - + +
1423B THR* 5.7 5.3 - - - +
1427B LEU* 3.4 29.9 - - - +
1430B GLN* 5.9 1.0 + - - -
1431B GLN* 5.3 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349B ASP* 3.5 8.0 + - - +
1350B ARG* 1.3 78.2 - - - +
1352B GLN* 1.3 69.2 + - - +
1354B LEU* 3.1 10.0 + - + +
1355B HIS* 3.0 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347B ILE* 3.5 25.6 - - + +
1349B ASP* 3.1 28.0 + - + +
1350B ARG 3.3 0.2 - - - -
1351B GLU* 1.3 82.3 - - - +
1353B LYS* 1.3 63.1 + - - +
1355B HIS* 3.2 16.4 + - - +
1356B ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1344B ALA 4.1 7.9 - - - +
1345B HIS* 2.8 58.7 + - - +
1347B ILE* 3.3 25.1 + - - +
1348B ASN* 4.8 9.8 + - - +
1349B ASP 2.8 17.9 + - - +
1350B ARG* 3.2 23.5 + - - +
1352B GLN* 1.3 75.3 - - - +
1354B LEU* 1.3 59.7 + - - +
1356B ALA* 3.3 6.2 + - - +
1357B LEU* 2.9 42.7 + - + +
1423B THR* 5.5 1.4 - - - +
1427B LEU* 4.2 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350B ARG* 2.9 37.6 + - + +
1351B GLU* 3.1 7.6 + - + +
1353B LYS* 1.3 78.4 - - - +
1355B HIS* 1.3 56.6 + - - +
1357B LEU* 3.2 10.4 + - + +
1358B LYS* 2.8 29.8 + - - +
1427B LEU* 4.2 20.4 - - + -
1431B GLN* 4.1 28.9 - - + +
1434B PHE* 3.6 24.2 - - + -
1435B PHE* 3.5 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1351B GLU* 3.0 56.6 + - + +
1352B GLN* 3.2 16.0 + - - +
1354B LEU* 1.3 73.0 - - - +
1356B ALA* 1.3 66.2 + - - +
1358B LYS* 3.0 9.0 + - + +
1359B GLU* 2.8 27.9 + - + +
1434B PHE* 3.9 24.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1344B ALA* 3.4 23.8 - - + +
1347B ILE* 3.5 27.8 - - + -
1352B GLN 3.0 6.7 + - - +
1353B LYS 3.4 7.6 - - - +
1355B HIS* 1.3 76.2 - - - +
1357B LEU* 1.3 62.6 + - - +
1359B GLU* 3.2 17.5 + - - +
1360B VAL* 3.2 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341B LEU* 3.6 46.8 - - + +
1344B ALA* 4.2 8.5 - - + -
1345B HIS* 4.8 2.9 - - - +
1353B LYS* 2.9 31.3 + - + +
1354B LEU* 3.5 12.1 - - + +
1356B ALA* 1.3 73.5 - - - +
1358B LYS* 1.3 67.0 + - - +
1360B VAL* 3.1 7.4 + - - +
1361B LEU* 3.0 19.9 + - - +
1424B ILE* 4.2 18.2 - - + -
1427B LEU* 4.0 30.1 - - + -
1428B PHE* 4.3 6.1 - - + -
1435B PHE* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354B LEU 2.8 16.9 + - - +
1355B HIS* 3.0 9.1 + - + +
1357B LEU* 1.3 76.2 - - - +
1359B GLU* 1.3 62.0 + - - +
1361B LEU* 3.0 18.9 + - + +
1362B LYS* 3.0 30.8 + - + +
1434B PHE* 2.7 49.6 + - + +
1435B PHE* 3.6 31.4 - - + +
1437B TYR 5.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1355B HIS 2.8 15.6 + - - +
1356B ALA* 3.3 13.5 - - - +
1358B LYS* 1.3 74.2 - - - +
1360B VAL* 1.3 66.0 - - + +
1362B LYS* 2.9 54.8 + - - +
1363B LYS* 3.6 9.8 + - - +
1438C ASN* 5.1 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337B MET* 3.6 30.5 - - - +
1340B ASP* 3.4 39.5 - - + +
1341B LEU* 3.7 18.6 - - + +
1344B ALA* 4.7 3.6 - - + -
1356B ALA 3.2 12.1 + - - +
1357B LEU 3.1 7.7 + - - +
1359B GLU* 1.3 75.6 - - + +
1361B LEU* 1.3 55.8 + - - +
1363B LYS* 2.7 31.6 + - - +
1364B PHE* 3.4 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341B LEU* 5.2 0.2 - - - +
1357B LEU 3.0 12.4 + - - +
1358B LYS* 3.0 15.9 + - + +
1360B VAL* 1.3 78.9 - - - +
1362B LYS* 1.3 58.9 + - - +
1363B LYS 3.4 0.5 + - - -
1364B PHE* 3.4 28.4 + - + +
1369B HIS* 3.3 42.7 + - + +
1372B PHE* 4.1 22.7 - - + -
1428B PHE* 4.0 12.1 - - + -
1435B PHE* 3.5 42.4 - - + +
1436B PHE* 3.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1358B LYS* 3.0 31.8 + - + +
1359B GLU* 2.9 41.7 + - - +
1360B VAL 3.0 0.2 - - - -
1361B LEU* 1.3 78.7 - - - +
1363B LYS* 1.3 59.2 + - + +
1364B PHE 3.3 5.0 + - - +
1369B HIS* 5.6 1.3 - - - -
1438C ASN* 5.6 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337B MET* 3.4 23.7 - - + +
1340B ASP* 4.8 12.3 - - - +
1359B GLU* 4.1 11.9 - - - +
1360B VAL* 2.7 13.8 + - - +
1362B LYS* 1.3 79.2 - - + +
1364B PHE* 1.3 67.5 + - - +
1365B PRO* 3.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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