Contacts of the helix formed by residues 402 - 411 (chain B) 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 ASN 402 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B GLU* 5.5 0.2 - - - -
384B LEU* 6.0 0.2 - - + -
388B GLN* 3.3 32.4 - - + +
389B MET* 3.0 34.8 + - - +
401B LYS* 1.3 75.0 - - + +
403B TYR* 1.3 103.8 + - + +
405B ILE* 3.3 5.6 + - - +
406B LYS* 2.9 47.8 + - - +
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B GLU* 2.8 34.4 + - - -
303B GLN* 4.0 5.2 + - - +
305B ALA* 3.7 39.2 - - + +
306B LEU* 3.4 23.9 - - + +
309B TYR* 3.6 36.3 - + + +
312B ILE* 3.7 16.7 - - + +
388B GLN* 5.5 4.0 + - - +
401B LYS* 3.5 0.6 - - - +
402B ASN* 1.3 103.2 + - + +
404B GLN* 1.3 61.4 + - - +
406B LYS* 3.9 7.0 - - + +
407B GLN* 2.9 33.4 + - - +
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Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TYR* 5.3 1.3 + - - -
399B ILE 3.8 6.2 - - - +
400B LEU* 3.6 13.5 - - + +
401B LYS* 2.7 46.4 + - + +
403B TYR* 1.3 74.5 - - - +
405B ILE* 1.3 63.2 + - - +
407B GLN* 4.1 6.4 - - - +
408B GLN* 3.4 34.1 + - - +
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 3.7 25.1 - - + -
293B MET* 5.1 1.6 - - - -
389B MET* 3.4 33.2 - - + -
390B ILE* 3.8 15.3 - - - +
391B ALA* 3.7 20.2 - - + +
400B LEU* 3.4 44.0 - - + +
401B LYS 3.0 13.2 + - - +
402B ASN 3.5 5.6 - - - +
404B GLN* 1.3 77.9 - - - +
406B LYS* 1.3 61.9 - - - +
408B GLN* 3.4 7.3 + - - +
409B ALA* 3.3 18.5 + - - +
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B MET* 3.8 29.2 - - + +
298B GLU* 2.9 33.5 + - - +
312B ILE* 3.8 19.7 - - + -
316B HIS* 5.4 1.3 - - - +
387B GLY 2.6 30.5 + - - -
389B MET* 3.5 31.9 - - + -
402B ASN* 2.9 36.0 + - - +
403B TYR* 3.9 9.0 - - + -
404B GLN 3.4 0.2 - - - -
405B ILE* 1.3 76.6 - - - +
407B GLN* 1.3 60.2 + - - +
409B ALA* 3.3 3.5 + - - +
410B ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ASP 4.9 3.6 + - - -
309B TYR* 3.5 36.8 - - + +
311B GLU* 5.4 11.3 + - + +
312B ILE* 3.7 11.1 - - + +
403B TYR 2.9 20.2 + - - +
404B GLN* 4.1 7.1 - - - +
406B LYS* 1.3 76.2 - - - +
408B GLN* 1.3 60.3 + - - +
410B ALA* 3.2 1.6 + - - +
411B GLN* 2.9 51.5 + - + +
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Residues in contact with GLN 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B LEU* 5.3 16.6 - - - +
404B GLN* 3.4 18.5 + - - +
405B ILE* 3.5 11.1 - - - +
406B LYS 3.2 0.4 - - - -
407B GLN* 1.3 83.1 - - + +
409B ALA* 1.3 61.7 + - - +
411B GLN* 3.5 29.3 + - - +
412B LYS* 3.7 12.0 - - - +
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B GLU* 3.9 28.5 - - + +
293B MET* 3.8 25.1 - - + -
315B PHE* 4.4 8.1 - - + -
405B ILE* 3.3 6.4 + - + +
406B LYS 3.3 8.5 + - - +
408B GLN* 1.3 78.9 - - - +
410B ALA* 1.3 63.1 + - - +
412B LYS* 3.3 29.1 + - - +
415B TYR* 4.4 2.8 + - - -
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Residues in contact with ALA 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B MET* 5.2 0.4 - - + -
311B GLU* 3.3 39.9 - - + +
312B ILE* 3.8 7.9 - - + +
315B PHE* 3.8 21.3 - - + -
406B LYS 2.9 17.6 + - - +
407B GLN 3.2 4.5 + - - +
409B ALA* 1.3 76.4 - - - +
411B GLN* 1.3 59.4 + - - +
412B LYS 3.2 1.5 + - - -
413B TYR 3.4 14.9 - - - +
415B TYR* 3.6 9.4 - - - -
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Residues in contact with GLN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B GLU* 3.2 29.3 - - - +
407B GLN* 2.9 38.3 + - - +
408B GLN* 3.5 27.5 + - - +
410B ALA* 1.3 75.4 - - - +
412B LYS* 1.3 60.8 + - - +
413B TYR* 3.3 5.4 + - - +
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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