Contacts of the helix formed by residues 1431 - 1437 (chain A) 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 GLN1431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A UNX 2.6 31.3 - - - -
1350A ARG* 5.2 4.6 + - - -
1354A LEU* 4.1 29.4 - - + +
1427A LEU* 2.7 31.8 + - + +
1430A GLN* 1.3 97.5 + - + +
1432A CYS* 1.3 64.6 + - - +
1433A PRO* 3.2 4.7 - - - -
1434A PHE* 2.9 20.7 + - + +
1435A PHE* 3.0 26.9 + - + -
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Residues in contact with CYS1432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376A ILE* 4.2 2.0 - - - -
1377A SER* 3.5 41.7 - - - -
1380A ASN* 3.8 13.5 - - + -
1428A PHE 3.1 15.3 + - - +
1429A ILE 3.4 15.7 - - - +
1430A GLN 3.2 0.4 - - - -
1431A GLN* 1.3 74.9 - - - +
1433A PRO* 1.4 65.5 - - + +
1435A PHE* 3.1 1.7 + - - -
1436A PHE* 2.8 52.4 + - - +
1437A TYR* 4.7 9.2 - - - -
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Residues in contact with PRO1433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1380A ASN* 4.6 6.5 - - - +
1430A GLN 4.1 6.1 - - - +
1431A GLN* 3.3 8.3 - - - +
1432A CYS* 1.4 95.9 - - + +
1434A PHE* 1.3 57.9 + - - +
1437A TYR* 3.0 73.0 + - + +
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Residues in contact with PHE1434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A UNX 4.4 10.1 - - - -
1351A GLU* 6.4 0.4 - - + -
1354A LEU* 3.5 44.9 - - + -
1355A HIS* 3.9 34.5 - + - -
1358A LYS* 2.8 47.6 + - + -
1431A GLN* 2.9 14.4 + - + +
1433A PRO* 1.3 80.2 - - - +
1435A PHE* 1.3 82.0 + + - +
1436A PHE 3.7 0.2 + - - -
1437A TYR 4.9 0.7 + - - +
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Residues in contact with PHE1435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354A LEU* 3.5 31.0 - - + -
1357A LEU* 3.8 12.6 - - + -
1358A LYS* 3.6 50.2 - - + +
1361A LEU* 3.6 16.3 - - + +
1369A HIS* 5.3 1.4 - - - -
1427A LEU* 3.5 20.0 - - + -
1428A PHE* 3.6 36.1 - + - -
1431A GLN* 3.0 36.0 + - + -
1432A CYS 3.8 1.1 - - - +
1434A PHE* 1.3 84.0 - + - +
1436A PHE* 1.3 84.1 + - + +
1437A TYR 4.0 0.2 - - - -
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Residues in contact with PHE1436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361A LEU* 3.6 26.0 - - + -
1369A HIS* 4.0 16.6 - + - -
1372A PHE* 3.9 24.0 - + - -
1373A LYS* 2.9 70.3 + - + +
1376A ILE* 3.9 23.6 - - + -
1377A SER* 5.5 1.1 - - - +
1428A PHE* 4.3 7.0 - + - -
1432A CYS* 2.8 41.7 + - - +
1435A PHE* 1.3 89.8 - - + +
1437A TYR* 1.3 69.5 + - + +
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Residues in contact with TYR1437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358A LYS* 5.7 2.4 + - - -
1377A SER* 5.7 4.1 - - - -
1380A ASN* 4.7 9.0 + - - -
1432A CYS* 4.4 12.4 - - - -
1433A PRO* 3.0 58.0 + - + +
1434A PHE 4.9 1.1 + - - +
1435A PHE 4.0 0.2 - - - -
1436A PHE* 1.3 87.4 - - + +
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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