Contacts of the helix formed by residues 1413 - 1431 (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 ASP1413 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1412D MET* 1.3 70.7 - - - +
1414D ALA* 1.3 72.1 + - - +
1415D LEU* 3.7 12.2 + - - +
1416D THR* 3.5 26.4 + - - -
1417D ALA* 2.9 25.5 + - - +
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Residues in contact with ALA1414 (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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1409D PHE* 3.8 33.6 + - + +
1412D MET 3.3 4.2 + - - -
1413D ASP* 1.3 76.0 + - - +
1415D LEU* 1.3 53.5 + - - +
1417D ALA* 3.6 1.2 + - - +
1418D THR* 2.6 38.7 + - - +
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Residues in contact with LEU1415 (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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1413D ASP* 3.3 12.8 + - - +
1414D ALA* 1.3 78.8 - - - +
1416D THR* 1.3 62.8 + - - +
1418D THR* 3.2 16.3 + - - +
1419D ARG* 3.2 13.5 + - - +
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Residues in contact with THR1416 (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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1413D ASP* 3.4 23.5 + - - -
1415D LEU* 1.3 74.5 - - - +
1417D ALA* 1.3 66.4 + - - +
1418D THR 3.2 0.2 + - - -
1419D ARG* 3.3 6.4 + - - +
1420D THR* 3.1 27.3 + - - -
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Residues in contact with ALA1417 (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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1409D PHE* 3.2 32.1 - - + -
1412D MET* 3.6 25.1 - - + +
1413D ASP 2.9 12.6 + - - +
1416D THR* 1.3 79.2 - - - +
1418D THR* 1.3 61.2 + - - +
1420D THR* 4.4 4.7 - - - -
1421D TYR* 2.9 38.1 + - + -
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Residues in contact with THR1418 (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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1401D TRP* 3.8 32.6 + - + +
1409D PHE* 4.4 2.9 - - - -
1414D ALA* 2.6 24.5 + - - +
1415D LEU* 3.3 9.4 - - - -
1416D THR 3.1 0.2 - - - -
1417D ALA* 1.3 74.6 - - - +
1419D ARG* 1.3 65.9 + - - +
1421D TYR* 4.1 0.2 - - - -
1422D GLN* 3.0 40.5 + - - +
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Residues in contact with ARG1419 (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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1345D HIS* 5.1 0.2 + - - -
1415D LEU 3.2 9.8 + - - +
1416D THR* 3.3 7.8 + - - +
1418D THR* 1.3 79.3 - - - +
1420D THR* 1.3 61.9 + - - +
1422D GLN* 3.9 8.1 - - - +
1423D THR* 2.9 32.8 + - - +
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Residues in contact with THR1420 (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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1342D VAL* 4.1 27.6 - - + -
1345D HIS* 4.0 24.5 + - + -
1416D THR* 3.1 17.6 + - - -
1417D ALA* 3.8 6.5 - - - -
1418D THR 3.1 0.2 - - - -
1419D ARG* 1.3 76.4 - - - +
1421D TYR* 1.3 69.3 + - + +
1423D THR* 3.9 1.6 - - - -
1424D ILE* 3.1 44.4 + - + +
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Residues in contact with TYR1421 (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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1338D GLN* 3.5 28.9 + - + +
1341D LEU* 6.4 0.4 - - + -
1342D VAL* 3.8 30.5 - - + +
1401D TRP* 3.6 27.8 - + + -
1405D MET* 3.5 21.1 - - + -
1407D PRO* 3.5 32.7 - - + +
1412D MET* 3.6 30.0 - - - +
1417D ALA* 2.9 30.0 + - + +
1420D THR* 1.3 77.1 - - + +
1422D GLN* 1.3 63.9 + - - +
1424D ILE* 3.2 8.5 + - + +
1425D ILE* 3.1 26.9 + - - +
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Residues in contact with GLN1422 (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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1394D GLU* 3.6 32.9 + - - +
1397D SER* 3.3 21.5 + - - +
1398D ILE* 3.7 24.4 - - + +
1401D TRP* 3.4 22.3 + - + +
1418D THR* 3.0 31.7 + - - +
1419D ARG* 3.9 7.8 - - - +
1421D TYR* 1.3 77.0 - - - +
1423D THR* 1.3 61.8 + - - +
1426D GLU* 2.9 29.4 + - - +
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Residues in contact with THR1423 (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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1345D HIS* 3.6 28.5 + - + -
1350D ARG* 6.1 3.1 - - - +
1353D LYS* 5.5 0.7 - - - +
1419D ARG* 2.9 19.4 + - - +
1420D THR 3.9 0.4 - - - -
1422D GLN* 1.3 79.3 - - - +
1424D ILE* 1.3 66.3 + - - +
1426D GLU* 3.2 14.4 + - + +
1427D LEU* 2.9 36.3 + - + +
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Residues in contact with ILE1424 (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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1341D LEU* 3.8 42.6 - - + +
1342D VAL* 4.0 8.1 - - + +
1345D HIS* 4.1 17.9 - - + +
1357D LEU* 4.4 11.2 - - + -
1405D MET* 4.4 7.6 - - + -
1420D THR* 3.1 35.6 + - + +
1421D TYR* 3.2 10.7 + - + +
1423D THR* 1.3 73.8 - - - +
1425D ILE* 1.3 64.6 + - + +
1427D LEU* 3.0 21.8 + - + +
1428D PHE* 3.1 40.3 + - + -
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Residues in contact with ILE1425 (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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1372D PHE* 3.9 28.9 - - + -
1376D ILE* 4.6 7.0 - - + -
1397D SER* 3.6 26.5 - - - -
1400D PHE* 4.8 6.5 - - + -
1401D TRP* 3.6 29.2 - - + +
1404D LEU* 4.7 7.6 - - + -
1405D MET* 3.6 31.2 - - + -
1421D TYR 3.1 8.8 + - - +
1424D ILE* 1.3 72.0 - - - +
1426D GLU* 1.3 67.1 + - - +
1428D PHE* 3.2 6.2 + - + +
1429D ILE* 2.9 33.3 + - + +
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Residues in contact with GLU1426 (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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1393D SER* 4.2 9.0 + - - -
1394D GLU* 3.5 47.9 + - - +
1397D SER* 3.5 14.1 + - - +
1422D GLN* 2.9 21.9 + - - +
1423D THR* 3.2 18.1 + - - +
1425D ILE* 1.3 76.0 - - - +
1427D LEU* 1.3 59.7 + - + +
1429D ILE* 3.3 3.1 + - - +
1430D GLN* 2.8 42.5 + - - +
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Residues in contact with LEU1427 (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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1345D HIS* 4.6 2.9 - - - +
1350D ARG* 3.5 31.6 - - - +
1353D LYS* 4.3 16.6 - - + -
1354D LEU* 4.4 20.2 - - + -
1357D LEU* 4.0 24.0 - - + -
1423D THR* 2.9 37.1 + - + +
1424D ILE* 3.4 9.4 - - - +
1426D GLU* 1.3 75.5 - - + +
1428D PHE* 1.3 59.8 + - + +
1430D GLN* 4.4 5.8 - - - +
1431D GLN* 2.7 46.9 + - + +
1435D PHE* 3.4 4.4 - - + -
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Residues in contact with PHE1428 (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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1341D LEU* 3.7 29.8 - - + -
1357D LEU* 4.4 15.7 - - + -
1361D LEU* 4.1 21.1 - - + -
1364D PHE* 5.5 0.2 - + - -
1372D PHE* 4.0 31.0 - + + -
1376D ILE* 3.1 23.7 - - + +
1424D ILE* 3.1 47.7 + - + -
1425D ILE* 3.2 9.8 + - + +
1427D LEU* 1.3 78.6 - - + +
1429D ILE* 1.3 58.4 + - - +
1431D GLN 3.8 0.2 - - - -
1432D CYS* 3.1 22.5 + - - -
1435D PHE* 3.6 41.0 - + + -
1436D PHE* 4.4 4.6 - + - -
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Residues in contact with ILE1429 (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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1376D ILE* 3.8 22.2 - - + -
1379D LEU* 3.6 33.4 - - + +
1380D ASN* 2.8 47.6 + - - +
1383D SER* 4.7 1.8 - - - +
1393D SER* 3.4 25.1 - - - +
1396D LEU* 3.9 7.2 - - + -
1397D SER* 3.9 23.3 - - - +
1425D ILE* 2.9 27.6 + - + +
1426D GLU 3.6 3.6 - - - +
1428D PHE* 1.3 78.8 - - - +
1430D GLN* 1.3 61.1 + - - +
1432D CYS* 3.4 7.6 - - - +
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Residues in contact with GLN1430 (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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1350D ARG* 5.9 0.7 + - - -
1380D ASN* 4.2 7.1 + - - +
1383D SER* 6.1 0.2 - - - -
1393D SER* 3.9 22.9 + - - +
1426D GLU* 2.8 35.1 + - - +
1427D LEU* 4.3 6.1 - - + +
1429D ILE* 1.3 75.4 - - - +
1431D GLN* 1.3 79.6 + - + +
1432D CYS 3.2 1.8 + - - -
1433D PRO* 4.1 7.4 - - - +
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Residues in contact with GLN1431 (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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8D UNX 3.4 21.4 - - - -
1350D ARG* 5.3 4.0 + - - -
1354D LEU* 4.0 29.0 - - + +
1427D LEU* 2.7 30.8 + - + +
1430D GLN* 1.3 99.7 + - + +
1432D CYS* 1.3 65.7 + - - +
1433D PRO* 3.2 4.5 - - - -
1434D PHE* 2.9 21.4 + - + +
1435D PHE* 3.0 26.6 + - + -
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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