Contacts of the helix formed by residues 401 - 411 (chain A) in PDB entry 1OFD
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 LYS 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A TYR* 3.5 20.7 + - - +
356A ILE* 4.3 7.0 - - - -
380A GLU* 3.1 32.7 + - - -
389A MET 4.6 0.9 - - - -
390A ILE* 3.8 24.5 - - + -
399A ILE* 4.0 9.6 + - + +
400A LEU* 1.3 74.1 - - - +
402A ASN* 1.3 67.4 + - - +
403A TYR 3.5 1.3 - - - +
404A GLN* 3.1 16.4 + - + +
405A ILE* 3.0 21.0 + - - +
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Residues in contact with ASN 402 (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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388A GLN* 3.2 33.3 - - + +
389A MET* 3.0 38.7 + - - +
401A LYS* 1.3 75.5 - - - +
403A TYR* 1.3 103.0 + - + +
405A ILE* 3.3 6.0 + - - +
406A LYS* 3.0 47.5 + - - +
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Residues in contact with TYR 403 (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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298A GLU* 3.0 33.2 + - - -
303A GLN* 4.1 10.7 + - - +
305A ALA* 3.7 32.3 - - + +
306A LEU* 3.4 25.2 - - + +
309A TYR* 3.6 35.7 - + + +
312A ILE* 3.7 16.0 - - + +
388A GLN* 5.3 5.9 + - - +
401A LYS* 3.5 1.0 - - - +
402A ASN* 1.3 101.6 + - + +
404A GLN* 1.3 60.2 + - - +
406A LYS* 3.9 7.4 - - + +
407A GLN* 2.9 34.4 + - - +
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Residues in contact with GLN 404 (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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309A TYR* 5.3 0.8 + - - -
398A LYS* 5.9 2.2 - - - +
399A ILE 4.2 3.5 - - - +
400A LEU* 3.5 37.3 - - + +
401A LYS* 3.1 15.4 + - + +
403A TYR* 1.3 77.1 - - - +
405A ILE* 1.3 61.7 + - - +
407A GLN* 4.1 8.0 - - - +
408A GLN* 3.1 55.4 + - + +
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Residues in contact with ILE 405 (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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289A LEU* 3.7 30.3 - - + -
293A MET* 5.1 1.8 - - - -
389A MET* 3.3 32.5 - - + +
390A ILE* 3.8 15.9 - - - +
391A ALA* 3.7 19.7 - - + +
400A LEU* 3.4 39.0 - - + +
401A LYS 3.0 11.9 + - - +
402A ASN 3.5 5.4 - - - +
404A GLN* 1.3 77.0 - - - +
406A LYS* 1.3 64.6 + - - +
408A GLN* 3.4 7.5 + - - +
409A ALA* 3.3 20.0 + - + +
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A MET* 3.7 31.3 - - + +
298A GLU* 2.8 34.6 + - - +
312A ILE* 3.6 21.1 - - + -
316A HIS* 5.5 1.8 - - - +
387A GLY 2.7 30.2 + - - -
388A GLN* 4.0 0.4 - - - +
389A MET* 3.4 27.4 - - + -
402A ASN* 3.0 37.5 + - - +
403A TYR* 3.4 8.7 + - + +
405A ILE* 1.3 76.8 - - - +
407A GLN* 1.3 60.5 + - - +
409A ALA 3.4 1.4 + - - -
410A ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 407 (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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308A ASP 5.1 4.2 + - - -
309A TYR* 3.8 32.8 - - + +
311A GLU* 5.4 11.8 + - + +
312A ILE* 3.7 10.0 - - + +
403A TYR 2.9 19.0 + - - +
404A GLN* 4.1 8.4 - - - +
406A LYS* 1.3 74.0 - - - +
408A GLN* 1.3 60.3 + - - +
410A ALA* 3.2 1.9 + - - +
411A GLN* 2.9 51.5 + - + +
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Residues in contact with GLN 408 (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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400A LEU* 4.9 8.9 - - - +
404A GLN* 3.1 53.3 + - + +
405A ILE* 3.7 6.5 - - - +
406A LYS 3.3 0.2 - - - -
407A GLN* 1.3 81.2 - - + +
409A ALA* 1.3 62.2 + - - +
411A GLN* 3.6 27.4 + - - +
412A LYS* 3.8 11.8 - - - +
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Residues in contact with ALA 409 (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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289A LEU* 6.5 0.2 - - + -
290A GLU* 3.9 26.3 - - + +
293A MET* 3.8 25.8 - - + -
315A PHE* 4.3 8.9 - - + -
405A ILE* 3.3 8.1 + - + +
406A LYS 3.8 6.7 - - - +
407A GLN 3.3 0.4 - - - -
408A GLN* 1.3 78.6 - - - +
410A ALA* 1.3 63.2 + - - +
412A LYS* 3.4 29.7 + - - +
415A TYR* 4.4 2.8 + - - -
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Residues in contact with ALA 410 (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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293A MET* 5.2 0.4 - - + -
311A GLU* 3.3 40.7 - - + +
312A ILE* 3.9 10.5 - - + +
315A PHE* 3.9 18.2 - - + -
406A LYS 2.9 18.0 + - - +
407A GLN 3.2 4.0 + - - +
409A ALA* 1.3 76.4 - - - +
411A GLN* 1.3 60.0 + - - +
412A LYS 3.2 1.7 + - - -
413A TYR 3.5 14.4 - - - +
415A TYR* 3.5 10.6 - - - -
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Residues in contact with GLN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLU* 3.3 27.8 + - - +
407A GLN* 2.9 36.5 + - - +
408A GLN* 3.6 25.2 + - - +
409A ALA 3.3 0.2 - - - -
410A ALA* 1.3 74.8 - - - +
412A LYS* 1.3 61.9 + - + +
413A TYR 3.3 4.9 + - - +
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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