Contacts of the helix formed by residues 1413 - 1431 (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 ASP1413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A ILE* 4.6 3.4 - - - +
1412B MET* 1.3 76.0 - - - +
1414B ALA* 1.3 76.0 + - - +
1415B LEU* 3.1 13.6 + - - +
1416B THR* 3.7 19.9 - - - -
1417B ALA* 2.7 37.2 + - - +
1381D LYS* 3.1 27.8 + - - -
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Residues in contact with ALA1414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412B MET 3.9 2.0 + - - -
1413B ASP* 1.3 78.6 + - - +
1415B LEU* 1.3 57.5 + - - +
1417B ALA* 3.7 2.5 - - - +
1418B THR* 2.7 36.3 + - - -
1273D GLU* 3.2 49.1 - - + +
1274D ALA* 4.6 3.4 - - + +
1277D LEU* 4.2 3.8 - - + -
1381D LYS* 4.3 2.2 - - - +
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Residues in contact with LEU1415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1413B ASP* 3.1 8.2 + - - +
1414B ALA* 1.3 75.2 - - - +
1416B THR* 1.3 61.4 + - - +
1418B THR* 3.8 2.9 - - - -
1419B ARG* 2.9 31.4 + - - +
1277D LEU* 3.7 23.0 - - + +
1381D LYS* 4.4 17.2 - - + +
1384D HIS* 5.8 6.1 - - + -
1385D ASN* 5.8 7.2 - - + -
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Residues in contact with THR1416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412B MET* 4.8 8.1 - - - -
1413B ASP* 3.3 27.7 + - - +
1415B LEU* 1.3 80.5 - - - +
1417B ALA* 1.3 58.1 + - - +
1419B ARG* 3.6 4.7 - - - +
1420B THR* 2.9 33.6 + - - -
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Residues in contact with ALA1417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1401B TRP* 5.7 0.7 - - - -
1412B MET* 3.5 39.2 - - + +
1413B ASP 2.7 22.4 + - - +
1414B ALA* 4.1 2.5 - - - +
1416B THR* 1.3 69.9 - - - +
1418B THR* 1.3 64.0 + - - +
1420B THR* 3.8 1.5 - - - -
1421B TYR* 2.9 42.1 + - + -
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Residues in contact with THR1418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1401B TRP* 4.1 28.9 + - + +
1414B ALA 2.7 29.1 + - - -
1415B LEU* 3.8 6.7 - - - -
1417B ALA* 1.3 71.5 - - - +
1419B ARG* 1.3 67.5 + - - +
1420B THR 3.1 0.3 + - - -
1421B TYR* 4.1 0.7 - - - +
1422B GLN* 3.0 30.7 + - - +
1273D GLU 4.0 11.3 + - - -
1274D ALA* 5.0 3.6 + - - -
1277D LEU* 4.6 14.8 - - + +
1278D SER* 3.6 24.7 - - - +
1385D ASN* 5.2 3.4 - - - +
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Residues in contact with ARG1419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345B HIS* 5.0 0.6 + - - -
1415B LEU 2.9 19.7 + - - +
1416B THR* 3.6 5.4 - - - +
1418B THR* 1.3 78.3 - - - +
1420B THR* 1.3 60.7 + - - +
1422B GLN* 3.8 9.4 - - - +
1423B THR* 2.9 33.4 + - - +
1385D ASN* 6.0 2.0 - - - +
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Residues in contact with THR1420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342B VAL* 4.2 26.0 - - + -
1345B HIS* 3.8 29.8 + - + -
1412B MET* 3.9 12.6 - - + +
1416B THR* 2.9 18.6 + - - -
1417B ALA* 3.8 8.7 - - - +
1418B THR 3.1 0.4 - - - -
1419B ARG* 1.3 79.9 - - - +
1421B TYR* 1.3 64.8 + - + +
1423B THR* 3.5 2.1 + - - -
1424B ILE* 3.1 41.0 + - + +
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Residues in contact with TYR1421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1338B GLN* 4.0 26.5 + - + +
1342B VAL* 3.7 31.0 - - + +
1401B TRP* 3.9 29.4 - + + -
1405B MET* 3.8 19.5 - - + -
1407B PRO* 3.7 31.2 - - + +
1412B MET* 4.6 10.3 - - - -
1417B ALA* 2.9 39.2 + - + +
1420B THR* 1.3 74.8 - - + +
1422B GLN* 1.3 67.4 + - - +
1424B ILE* 3.2 9.1 + - + +
1425B ILE* 3.1 28.1 + - - +
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Residues in contact with GLN1422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394B GLU* 3.3 35.0 + - - +
1397B SER* 3.3 21.4 + - - +
1398B ILE* 3.9 16.7 - - + +
1401B TRP* 3.6 21.3 + - + +
1418B THR* 3.0 22.2 + - - +
1419B ARG* 3.8 7.8 - - - +
1421B TYR* 1.3 78.8 - - - +
1423B THR* 1.3 61.6 + - - +
1425B ILE 3.4 0.2 + - - -
1426B GLU* 2.9 31.0 + - - +
1278D SER* 3.2 21.8 + - - -
1385D ASN* 4.9 3.8 + - - +
1388D VAL* 4.0 9.1 - - - +
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Residues in contact with THR1423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345B HIS* 3.8 26.6 + - + -
1350B ARG* 5.7 4.9 - - - +
1353B LYS* 5.5 1.1 - - - +
1419B ARG* 2.9 20.6 + - - +
1420B THR 4.0 0.2 - - - -
1422B GLN* 1.3 77.6 + - - +
1424B ILE* 1.3 67.3 + - - +
1426B GLU* 3.5 14.6 + - + +
1427B LEU* 2.9 37.3 + - + +
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Residues in contact with ILE1424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341B LEU* 3.8 41.1 - - + +
1342B VAL* 4.0 11.2 - - + +
1345B HIS* 4.0 23.8 - - + +
1357B LEU* 4.2 13.4 - - + +
1405B MET* 4.5 7.9 - - + -
1420B THR* 3.1 27.3 + - + +
1421B TYR* 3.2 10.9 + - + +
1423B THR* 1.3 78.4 - - - +
1425B ILE* 1.3 65.1 + - + +
1427B LEU* 3.1 15.9 + - - +
1428B PHE* 3.2 40.9 + - + -
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Residues in contact with ILE1425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372B PHE* 4.0 27.1 - - + -
1376B ILE* 4.6 7.2 - - + -
1379B LEU* 5.4 0.2 - - + -
1397B SER* 3.5 29.4 - - - +
1400B PHE* 4.9 6.5 - - + -
1401B TRP* 3.7 22.0 - - + +
1404B LEU* 4.7 7.6 - - + -
1405B MET* 3.7 31.4 - - + -
1421B TYR 3.1 14.2 + - - +
1424B ILE* 1.3 74.8 - - - +
1426B GLU* 1.3 63.2 + - - +
1428B PHE* 3.1 6.4 + - + +
1429B ILE* 2.9 34.1 + - + +
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Residues in contact with GLU1426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1393B SER* 4.2 9.2 + - - -
1394B GLU* 3.6 46.4 + - - +
1397B SER* 3.6 12.4 + - - +
1422B GLN* 2.9 22.3 + - - +
1423B THR* 3.2 18.1 + - - +
1425B ILE* 1.3 75.8 - - - +
1427B LEU* 1.3 60.6 + - + +
1429B ILE* 3.3 3.1 + - - +
1430B GLN* 2.8 42.9 + - - +
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Residues in contact with LEU1427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345B HIS* 4.8 1.6 - - - +
1350B ARG* 3.4 31.2 - - - +
1353B LYS* 4.2 19.7 - - + +
1354B LEU* 4.2 21.8 - - + -
1357B LEU* 4.0 24.0 - - + -
1423B THR* 2.9 34.8 + - + +
1424B ILE* 3.1 8.9 + - - +
1426B GLU* 1.3 77.1 - - + +
1428B PHE* 1.3 57.3 + - + +
1430B GLN* 4.7 5.6 - - - +
1431B GLN* 2.7 47.8 + - + +
1435B PHE* 3.5 3.5 - - + -
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Residues in contact with PHE1428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341B LEU* 3.7 29.6 - - + -
1357B LEU* 4.3 14.8 - - + -
1361B LEU* 4.0 23.3 - - + -
1364B PHE* 5.6 0.4 - + - -
1372B PHE* 4.0 29.6 - + + -
1376B ILE* 3.1 24.7 - - + +
1424B ILE* 3.2 46.0 + - + -
1425B ILE* 3.1 11.3 + - + +
1427B LEU* 1.3 77.7 - - + +
1429B ILE* 1.3 62.2 + - - +
1432B CYS* 3.1 17.8 + - - -
1435B PHE* 3.7 42.3 - + + -
1436B PHE* 4.3 4.2 - + - -
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Residues in contact with ILE1429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376B ILE* 3.8 18.8 - - + -
1379B LEU* 3.6 35.4 - - + +
1380B ASN* 2.8 47.6 + - - +
1383B SER* 4.5 2.0 - - - +
1393B SER* 3.4 27.6 - - - +
1396B LEU* 3.9 7.9 - - + -
1397B SER 3.9 22.9 - - - +
1425B ILE* 2.9 26.2 + - + +
1426B GLU 3.6 3.8 - - - +
1428B PHE* 1.3 77.9 - - - +
1430B GLN* 1.3 60.8 + - - +
1432B CYS* 3.4 7.3 - - - +
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Residues in contact with GLN1430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350B ARG* 5.9 1.0 + - - -
1380B ASN* 4.3 6.6 + - - +
1393B SER* 4.1 18.0 + - - +
1426B GLU* 2.8 32.5 + - - +
1427B LEU* 4.3 6.1 - - + +
1429B ILE* 1.3 78.9 - - - +
1431B GLN* 1.3 81.5 + - + +
1432B CYS 3.2 2.5 + - - -
1433B PRO* 4.1 6.6 - - - +
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Residues in contact with GLN1431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B UNX 3.1 22.6 - - - -
1350B ARG* 5.3 3.7 + - - +
1354B LEU* 4.1 29.0 - - + +
1427B LEU* 2.7 31.7 + - + +
1430B GLN* 1.3 98.9 + - + +
1432B CYS* 1.3 66.0 + - - +
1433B PRO* 3.2 4.5 - - - -
1434B PHE* 2.9 21.4 + - + +
1435B PHE* 3.0 26.3 + - + -
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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