Contacts of the helix formed by residues 1349 - 1363 (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 ASP1349 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1347C ILE* 3.5 2.9 - - + +
1348C ASN* 1.3 77.3 - - - +
1350C ARG* 1.3 60.8 + - - +
1351C GLU* 3.4 9.4 + - - +
1352C GLN* 3.0 44.5 + - + +
1353C LYS* 2.8 30.3 + - - +
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Residues in contact with ARG1350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348C ASN 3.4 5.9 + - - +
1349C ASP* 1.3 75.2 + - - +
1351C GLU* 1.3 64.1 + - - +
1353C LYS* 3.3 22.4 + - - +
1354C LEU* 3.0 45.0 + - + +
1423C THR* 6.1 3.0 - - - +
1427C LEU* 3.4 27.6 - - - +
1430C GLN* 5.9 0.8 + - - -
1431C GLN* 5.2 5.5 + - - -
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Residues in contact with GLU1351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349C ASP* 3.4 8.0 + - - +
1350C ARG* 1.3 78.0 - - - +
1352C GLN* 1.3 69.5 + - - +
1354C LEU* 3.1 10.3 + - - +
1355C HIS* 3.1 53.5 + - + +
1434C PHE* 6.4 0.4 - - + -
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Residues in contact with GLN1352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347C ILE* 3.5 26.9 - - + +
1349C ASP* 3.0 28.8 + - + +
1351C GLU* 1.3 79.7 - - - +
1353C LYS* 1.3 63.4 + - - +
1355C HIS* 3.2 15.8 + - - +
1356C ALA* 2.9 23.0 + - - +
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Residues in contact with LYS1353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1344C ALA* 4.1 7.8 - - - +
1345C HIS* 2.9 58.0 + - - +
1347C ILE* 3.3 24.9 + - - +
1348C ASN* 4.8 7.8 + - - +
1349C ASP 2.8 18.0 + - - +
1350C ARG* 3.4 23.8 - - - +
1352C GLN* 1.3 76.3 - - - +
1354C LEU* 1.3 58.5 + - + +
1356C ALA* 3.3 4.7 + - - +
1357C LEU* 2.9 43.8 + - + +
1423C THR* 5.6 1.2 - - - +
1427C LEU* 4.4 13.6 - - + +
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Residues in contact with LEU1354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350C ARG* 3.0 38.7 + - + +
1351C GLU* 3.1 8.0 + - + +
1353C LYS* 1.3 78.2 - - + +
1355C HIS* 1.3 57.6 + - - +
1357C LEU* 3.3 13.4 + - + +
1358C LYS 2.8 24.3 + - - -
1427C LEU* 4.4 14.4 - - + -
1431C GLN* 4.1 28.7 - - + +
1434C PHE* 3.5 29.7 - - + -
1435C PHE* 3.5 30.0 - - + -
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Residues in contact with HIS1355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351C GLU* 3.1 56.5 + - + +
1352C GLN* 3.2 15.8 + - - +
1354C LEU* 1.3 73.3 - - - +
1356C ALA* 1.3 67.8 + - - +
1358C LYS* 3.1 9.1 + - + +
1359C GLU* 2.9 27.6 + - + +
1434C PHE* 3.8 24.9 - + - -
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Residues in contact with ALA1356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1344C ALA* 3.4 24.6 - - + +
1347C ILE* 3.4 28.7 - - + -
1352C GLN 2.9 6.3 + - - +
1353C LYS 3.4 6.5 - - - +
1355C HIS* 1.3 75.0 - - - +
1357C LEU* 1.3 63.0 + - - +
1359C GLU* 3.2 22.3 + - - +
1360C VAL* 3.2 11.6 + - - +
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Residues in contact with LEU1357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341C LEU* 3.6 46.0 - - + +
1344C ALA* 4.2 9.0 - - + -
1345C HIS* 4.8 4.5 - - - +
1353C LYS* 2.9 32.9 + - + +
1354C LEU* 3.6 13.2 - - + +
1356C ALA* 1.3 74.2 - - - +
1358C LYS* 1.3 65.5 + - - +
1359C GLU 3.1 0.2 + - - -
1360C VAL* 3.1 7.6 + - - +
1361C LEU* 2.9 20.6 + - - +
1424C ILE* 4.3 16.6 - - + -
1427C LEU* 4.0 28.3 - - + -
1428C PHE* 4.4 6.1 - - + -
1435C PHE* 3.8 16.8 - - + -
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Residues in contact with LYS1358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354C LEU 2.8 17.3 + - - +
1355C HIS* 3.1 9.2 + - + +
1357C LEU* 1.3 76.0 - - - +
1359C GLU* 1.3 62.3 + - - +
1361C LEU* 3.1 12.7 + - + +
1362C LYS* 3.0 38.8 + - + +
1434C PHE* 2.8 46.7 + - + +
1435C PHE* 3.6 30.0 - - + +
1437C TYR 5.6 3.6 + - - -
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Residues in contact with GLU1359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1355C HIS* 2.9 15.7 + - + +
1356C ALA* 3.2 14.1 - - - +
1357C LEU 3.0 0.2 - - - -
1358C LYS* 1.3 73.9 - - - +
1360C VAL* 1.3 65.2 + - + +
1362C LYS* 2.8 54.9 + - - +
1363C LYS* 3.6 11.0 + - - +
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Residues in contact with VAL1360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337C MET* 3.7 24.9 - - - +
1340C ASP* 3.5 39.9 - - + +
1341C LEU* 3.7 25.1 - - + +
1344C ALA* 4.7 4.0 - - + -
1356C ALA 3.2 11.9 + - - +
1357C LEU 3.1 7.3 + - - +
1359C GLU* 1.3 76.4 - - + +
1361C LEU* 1.3 54.8 + - - +
1363C LYS* 2.7 33.1 + - + +
1364C PHE* 3.4 16.1 - - + -
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Residues in contact with LEU1361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341C LEU* 5.2 0.4 - - - +
1357C LEU 2.9 13.2 + - - +
1358C LYS* 3.2 16.2 - - + +
1360C VAL* 1.3 77.0 - - - +
1362C LYS* 1.3 59.0 + - - +
1363C LYS 3.4 0.5 + - - -
1364C PHE* 3.4 30.9 + - + +
1369C HIS* 3.3 41.0 + - + +
1372C PHE* 4.1 23.6 - - + -
1428C PHE* 4.1 11.0 - - + -
1435C PHE* 3.5 41.7 - - + +
1436C PHE* 3.6 19.3 - - + -
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Residues in contact with LYS1362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358C LYS* 3.0 32.3 + - + +
1359C GLU* 2.8 41.5 + - - +
1360C VAL 3.0 0.6 - - - -
1361C LEU* 1.3 78.3 - - - +
1363C LYS* 1.3 59.7 + - + +
1364C PHE 3.3 5.0 + - - +
1369C HIS* 5.4 1.8 - - - -
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Residues in contact with LYS1363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337C MET* 3.4 24.4 - - + +
1340C ASP* 4.9 11.2 - - - +
1359C GLU* 3.6 11.9 + - - +
1360C VAL* 2.7 18.2 + - - +
1362C LYS* 1.3 73.2 - - + +
1364C PHE* 1.3 66.5 + - - +
1365C PRO* 3.5 3.6 - - - +
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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