Contacts of the helix formed by residues 1334 - 1345 (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 PRO1334 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1330D ASP* 6.2 1.1 - - + -
1331D PRO* 4.1 9.0 - - + +
1332D LEU 3.1 7.4 - - - +
1333D VAL* 1.3 88.0 - - + +
1335D TYR* 1.3 65.8 + - - +
1336D ASN* 3.3 20.2 - - - +
1337D MET* 3.1 19.5 + - + +
1338D GLN* 3.0 16.8 + - - +
1364D PHE* 4.5 8.5 - - + -
1365D PRO* 4.1 21.1 - - + -
1368D ASN* 3.7 21.1 - - + +
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Residues in contact with TYR1335 (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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1330D ASP* 5.7 2.5 - - + -
1331D PRO* 3.5 25.4 - - + -
1333D VAL 3.7 0.6 + - - -
1334D PRO* 1.3 72.2 - - - +
1336D ASN* 1.3 58.4 + - - +
1338D GLN* 2.9 41.1 + - - +
1339D ILE* 3.2 15.2 + - + +
1405D MET 3.3 9.2 - - - -
1406D ARG* 2.7 49.8 + - - +
1407D PRO* 4.7 3.4 - - + -
1408D ASP* 4.9 6.7 - - + +
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Residues in contact with ASN1336 (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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1334D PRO* 3.5 18.2 - - - +
1335D TYR* 1.3 74.4 + - - +
1337D MET* 1.3 90.9 + - + +
1339D ILE* 3.3 27.6 + - + +
1340D ASP* 3.6 14.7 + - - +
1365D PRO* 5.4 5.3 - - - +
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Residues in contact with MET1337 (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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1333D VAL* 4.6 1.1 - - + -
1334D PRO* 3.1 25.2 + - + +
1336D ASN* 1.3 100.1 - - + +
1338D GLN* 1.3 57.5 + - - +
1340D ASP* 3.3 21.0 + - - +
1341D LEU* 2.9 33.1 + - - +
1360D VAL* 3.7 7.9 - - - +
1363D LYS* 3.4 46.7 - - + +
1364D PHE* 3.7 39.3 - - + -
1365D PRO* 4.3 2.2 - - + -
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Residues in contact with GLN1338 (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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1331D PRO* 4.3 0.2 - - - +
1333D VAL* 3.0 30.2 + - + +
1334D PRO 3.0 14.7 + - - +
1335D TYR* 2.9 31.3 + - + +
1337D MET* 1.3 76.2 - - - +
1339D ILE* 1.3 62.1 + - + +
1341D LEU* 3.2 8.6 + - - +
1342D VAL* 2.9 31.1 + - - +
1405D MET* 2.6 47.2 + - + +
1407D PRO* 4.8 3.3 - - - +
1421D TYR* 3.5 29.7 + - + +
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Residues in contact with ILE1339 (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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1335D TYR* 3.3 11.4 - - + +
1336D ASN* 3.6 23.3 - - + +
1337D MET 3.2 0.4 - - - -
1338D GLN* 1.3 78.7 - - + +
1340D ASP* 1.3 67.1 + - - +
1342D VAL* 3.2 6.4 + - - +
1343D GLU* 3.0 33.9 + - + +
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Residues in contact with ASP1340 (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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1336D ASN 3.8 8.2 - - - +
1337D MET* 3.3 27.4 + - - +
1339D ILE* 1.3 80.7 - - - +
1341D LEU* 1.3 64.8 + - - +
1343D GLU* 3.1 10.3 + - - +
1344D ALA* 2.9 24.6 + - - +
1360D VAL* 3.4 25.0 - - + +
1363D LYS* 4.9 8.8 - - - +
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Residues in contact with LEU1341 (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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1333D VAL* 3.8 17.5 - - + -
1337D MET 2.9 16.7 + - - +
1338D GLN* 3.2 9.6 + - - +
1340D ASP* 1.3 75.5 - - - +
1342D VAL* 1.3 64.0 + - - +
1344D ALA* 3.4 2.6 + - - +
1345D HIS* 3.1 23.4 + - - +
1357D LEU* 3.6 26.3 - - + +
1360D VAL* 3.7 24.9 - - + +
1364D PHE* 4.3 10.3 - - + -
1372D PHE* 6.1 0.2 - - + -
1405D MET* 3.7 29.4 - - + -
1421D TYR* 6.4 0.2 - - + -
1424D ILE* 3.8 14.1 - - + +
1428D PHE* 3.7 24.9 - - + -
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Residues in contact with VAL1342 (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 2.9 21.4 + - - +
1339D ILE* 3.6 5.8 - - - +
1341D LEU* 1.3 76.7 - - - +
1343D GLU* 1.3 68.4 + - - +
1345D HIS* 3.4 15.4 - - + +
1346D LYS* 3.6 10.6 + - + +
1420D THR* 4.1 21.8 - - + +
1421D TYR* 3.8 31.9 - - + +
1424D ILE* 4.0 8.7 - - + -
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Residues in contact with GLU1343 (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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1339D ILE* 3.0 26.6 + - + +
1340D ASP* 3.1 12.1 + - - +
1342D VAL* 1.3 78.4 - - - +
1344D ALA* 1.3 66.7 + - - +
1346D LYS* 2.9 32.3 + - - +
1347D ILE* 4.2 1.9 + - - +
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Residues in contact with ALA1344 (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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1340D ASP 2.9 15.4 + - - +
1341D LEU 3.8 3.8 - - - +
1343D GLU* 1.3 75.3 - - - +
1345D HIS* 1.3 58.5 + - - +
1347D ILE* 2.9 36.4 + - - +
1353D LYS* 4.1 5.6 - - - +
1356D ALA* 3.4 40.6 - - + +
1357D LEU* 3.9 11.2 - - + +
1360D VAL* 4.7 3.4 - - + -
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Residues in contact with HIS1345 (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 3.1 10.9 + - - +
1342D VAL* 3.4 13.2 - - + +
1343D GLU 3.1 0.6 - - - -
1344D ALA* 1.3 77.8 - - - +
1346D LYS* 1.3 60.3 + - - +
1347D ILE 3.2 0.4 - - - -
1348D ASN* 5.4 0.3 - - - +
1353D LYS* 2.9 61.1 + - - +
1357D LEU* 4.7 3.9 - - + +
1419D ARG 5.6 0.2 - - - -
1420D THR* 4.0 30.1 + - + -
1423D THR* 3.6 36.2 + - + +
1424D ILE* 4.1 17.9 - - + +
1427D LEU* 4.6 4.0 - - - +
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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