Contacts of the helix formed by residues 1413 - 1431 (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 ASP1413 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412C MET* 1.3 72.5 - - - +
1414C ALA* 1.3 72.3 + - - +
1415C LEU* 3.3 13.1 + - - +
1416C THR* 3.3 36.8 + - + +
1417C ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409C PHE* 3.8 34.4 - - + +
1412C MET 3.4 3.4 + - - -
1413C ASP* 1.3 76.0 + - - +
1415C LEU* 1.3 53.6 + - + +
1417C ALA* 3.9 1.4 - - - +
1418C THR* 2.6 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1413C ASP* 3.3 11.7 + - - +
1414C ALA* 1.3 80.3 - - + +
1416C THR* 1.3 63.8 + - + +
1418C THR* 3.2 23.2 + - + +
1419C ARG* 3.2 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412C MET* 5.6 0.9 - - - +
1413C ASP* 3.3 32.4 + - + +
1415C LEU* 1.3 74.6 - - + +
1417C ALA* 1.3 67.9 + - - +
1419C ARG* 3.3 7.2 + - - +
1420C THR* 3.1 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409C PHE* 3.2 32.8 - - + -
1412C MET* 3.6 24.7 - - + -
1413C ASP 2.9 13.0 + - - +
1416C THR* 1.3 78.3 + - - +
1418C THR* 1.3 60.7 + - - +
1420C THR* 4.4 4.7 - - - -
1421C TYR* 3.0 39.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1418 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1401C TRP* 3.8 31.8 + - + +
1409C PHE* 4.4 3.1 - - - -
1414C ALA* 2.6 26.1 + - - +
1415C LEU* 3.3 19.4 - - + +
1416C THR 3.0 0.4 - - - -
1417C ALA* 1.3 78.5 - - - +
1419C ARG* 1.3 63.5 + - - +
1421C TYR* 4.1 0.2 - - - -
1422C GLN* 3.0 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1419 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345C HIS* 5.6 0.2 - - - -
1415C LEU 3.2 9.0 + - - +
1416C THR* 3.3 7.8 + - - +
1418C THR* 1.3 79.5 - - - +
1420C THR* 1.3 61.7 + - - +
1422C GLN* 3.9 8.4 - - - +
1423C THR* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1420 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342C VAL* 4.1 27.4 - - + -
1345C HIS* 4.0 24.6 + - + -
1416C THR* 3.1 18.3 + - - -
1417C ALA* 3.8 7.1 - - - -
1418C THR 3.2 0.2 - - - -
1419C ARG* 1.3 76.2 - - - +
1421C TYR* 1.3 68.9 + - + +
1423C THR* 3.5 1.9 + - - -
1424C ILE* 3.1 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1421 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1338C GLN* 3.6 29.7 + - + +
1341C LEU* 6.4 0.4 - - + -
1342C VAL* 3.8 29.4 - - + +
1401C TRP* 3.6 27.4 - + + -
1405C MET* 3.5 21.8 - - + -
1407C PRO* 3.6 33.1 - - + +
1412C MET* 3.6 30.8 - - - +
1417C ALA* 3.0 32.6 + - + +
1420C THR* 1.3 74.4 - - + +
1422C GLN* 1.3 66.7 + - - +
1424C ILE* 3.2 7.8 + - + +
1425C ILE* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394C GLU* 3.6 32.3 + - - +
1397C SER* 3.3 22.1 + - - +
1398C ILE* 3.7 25.6 - - + +
1401C TRP* 3.5 22.3 + - + +
1418C THR* 3.0 31.2 + - - +
1419C ARG* 3.9 7.6 - - - +
1421C TYR* 1.3 78.8 - - - +
1423C THR* 1.3 61.2 + - - +
1426C GLU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345C HIS* 3.6 28.5 + - + -
1350C ARG* 6.1 2.5 - - - +
1353C LYS* 5.6 0.9 - - - +
1419C ARG* 2.9 18.8 + - - +
1420C THR 3.9 0.4 - - - -
1422C GLN* 1.3 79.5 - - - +
1424C ILE* 1.3 66.5 + - - +
1426C GLU* 3.2 14.0 + - + +
1427C LEU* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1424 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341C LEU* 3.8 41.5 - - + +
1342C VAL* 4.0 7.6 - - + +
1345C HIS* 4.1 18.4 - - + +
1357C LEU* 4.3 11.8 - - + +
1405C MET* 4.4 7.6 - - + -
1420C THR* 3.1 35.8 + - + +
1421C TYR* 3.2 11.6 + - + +
1423C THR* 1.3 77.3 - - - +
1425C ILE* 1.3 64.5 + - + +
1427C LEU* 3.1 18.0 + - + +
1428C PHE* 3.1 40.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1425 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372C PHE* 4.0 28.3 - - + -
1376C ILE* 4.6 6.5 - - + -
1397C SER* 3.6 26.5 - - - -
1400C PHE* 4.8 6.1 - - + -
1401C TRP* 3.7 22.2 - - + +
1404C LEU* 4.6 8.3 - - + -
1405C MET* 3.7 31.0 - - + -
1421C TYR 3.1 13.8 + - - +
1424C ILE* 1.3 71.7 - - - +
1426C GLU* 1.3 66.5 + - - +
1428C PHE* 3.2 6.5 + - + +
1429C ILE* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1426 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393C SER* 4.1 8.5 + - - -
1394C GLU* 3.5 47.6 + - - +
1397C SER* 3.5 14.6 + - - +
1422C GLN* 2.9 21.0 + - - +
1423C THR* 3.2 17.2 + - - +
1425C ILE* 1.3 77.6 - - - +
1427C LEU* 1.3 60.2 + - + +
1429C ILE* 3.3 3.9 + - - +
1430C GLN* 2.8 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345C HIS* 4.7 3.4 - - - +
1350C ARG* 3.4 31.0 - - - +
1353C LYS* 4.4 16.4 - - + -
1354C LEU* 4.4 20.2 - - + -
1357C LEU* 4.0 23.8 - - + -
1423C THR* 2.9 37.6 + - + +
1424C ILE* 3.1 8.7 + - - +
1426C GLU* 1.3 76.2 - - + +
1428C PHE* 1.3 58.2 + - - +
1430C GLN* 4.4 6.7 - - - +
1431C GLN* 2.7 46.5 + - + +
1435C PHE* 3.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341C LEU* 3.7 29.2 - - + -
1357C LEU* 4.4 15.0 - - + -
1361C LEU* 4.1 21.5 - - + -
1364C PHE* 5.5 0.4 - + - -
1372C PHE* 4.0 31.0 - + + -
1376C ILE* 3.1 24.7 - - + +
1424C ILE* 3.1 47.9 + - + -
1425C ILE* 3.2 9.4 + - + +
1427C LEU* 1.3 76.9 - - + +
1429C ILE* 1.3 57.5 + - - +
1432C CYS* 3.1 22.5 + - - -
1435C PHE* 3.7 41.6 - + + -
1436C PHE* 4.3 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376C ILE* 3.8 22.7 - - + -
1379C LEU* 3.5 33.9 - - + +
1380C ASN* 2.8 48.1 + - - +
1383C SER* 4.7 1.3 - - - -
1393C SER* 3.5 25.4 - - - +
1396C LEU* 3.9 7.4 - - + -
1397C SER* 3.9 23.3 - - - +
1425C ILE* 3.0 27.1 + - + +
1426C GLU 3.6 3.6 - - - +
1428C PHE* 1.3 77.4 - - - +
1430C GLN* 1.3 59.8 + - - +
1432C CYS* 3.3 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350C ARG* 5.9 0.9 + - - -
1380C ASN* 4.2 6.9 + - - +
1383C SER* 6.0 0.2 - - - -
1393C SER* 3.9 20.9 + - - +
1426C GLU* 2.8 33.8 + - - +
1427C LEU* 4.4 5.9 - - - +
1429C ILE* 1.3 75.0 - - - +
1431C GLN* 1.3 80.3 + - + +
1432C CYS 3.2 2.0 + - - -
1433C PRO* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C UNX 3.2 22.0 - - - -
1350C ARG* 5.2 4.4 + - - -
1354C LEU* 4.1 28.8 - - + +
1427C LEU* 2.7 31.6 + - + +
1430C GLN* 1.3 98.5 + - + +
1432C CYS* 1.3 66.1 + - - +
1433C PRO* 3.2 4.5 - - - -
1434C PHE* 2.9 19.9 + - + +
1435C PHE* 3.0 26.8 + - + -
----------------------------------------------------------
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