Contacts of the helix formed by residues 1431 - 1437 (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 GLN1431 (chain D).
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Specific contacts
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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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Residues in contact with CYS1432 (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* 4.3 1.8 - - + -
1377D SER* 3.5 40.4 - - - -
1380D ASN* 3.8 12.8 - - + -
1428D PHE 3.1 13.0 + - - +
1429D ILE 3.4 16.2 - - - +
1430D GLN 3.2 0.4 - - - -
1431D GLN* 1.3 75.7 - - - +
1433D PRO* 1.3 66.2 - - + +
1435D PHE* 3.1 1.6 + - - -
1436D PHE* 2.8 53.1 + - - +
1437D TYR* 4.6 9.2 - - - -
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Residues in contact with PRO1433 (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 4.5 6.7 - - - -
1380D ASN* 4.6 7.2 - - - +
1430D GLN 4.1 9.0 - - - +
1431D GLN* 3.3 5.4 - - - +
1432D CYS* 1.3 96.3 - - + +
1434D PHE* 1.3 58.8 + - - +
1437D TYR* 3.0 71.2 + - + +
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Residues in contact with PHE1434 (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 4.2 14.6 - - - -
1351D GLU* 6.4 0.4 - - + -
1354D LEU* 3.5 46.0 - - + -
1355D HIS* 3.8 34.1 - + - -
1358D LYS* 2.8 48.8 + - + -
1431D GLN* 2.9 12.4 + - + +
1433D PRO* 1.3 80.1 - - - +
1435D PHE* 1.3 80.7 + + - +
1436D PHE 3.7 0.2 + - - -
1437D TYR 4.9 0.7 + - - +
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Residues in contact with PHE1435 (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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1354D LEU* 3.5 42.2 - - + -
1357D LEU* 3.8 12.6 - - + -
1358D LYS* 3.6 37.4 - - + +
1361D LEU* 3.6 13.9 - - + +
1369D HIS* 5.3 1.2 - - - -
1427D LEU* 3.4 21.3 - - + -
1428D PHE* 3.6 36.8 - + - -
1431D GLN* 3.0 35.5 + - + -
1432D CYS 3.8 1.3 - - - +
1434D PHE* 1.3 84.4 - + - +
1436D PHE* 1.3 84.3 + - + +
1437D TYR 4.0 0.2 - - - -
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Residues in contact with PHE1436 (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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1361D LEU* 3.5 26.2 - - + -
1369D HIS* 4.1 16.6 - + - -
1372D PHE* 3.9 23.8 - + - -
1373D LYS* 2.9 68.4 + - + +
1376D ILE* 3.9 24.0 - - + -
1377D SER* 5.5 0.9 - - - +
1428D PHE* 4.4 6.7 - + - -
1432D CYS* 2.8 42.8 + - - +
1435D PHE* 1.3 88.5 - - + +
1437D TYR* 1.3 70.7 + - + +
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Residues in contact with TYR1437 (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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1358D LYS* 5.7 2.4 + - - -
1377D SER* 5.7 4.2 - - - -
1380D ASN* 4.7 8.8 + - - -
1432D CYS* 4.6 11.8 - - - -
1433D PRO* 3.0 57.4 + - + +
1434D PHE 4.9 1.3 + - - +
1436D PHE* 1.3 89.1 - - + +
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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