Contacts of the strand formed by residues 285 - 292 (chain F) in PDB entry 4Q44
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 ARG 285 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F ILE* 3.6 9.0 - - - +
284F ALA* 1.3 88.1 - - + +
286F GLN* 1.3 64.6 + - - +
301F GLU* 3.7 40.7 + - + +
302F HIS 3.2 14.4 - - - +
303F VAL* 3.8 9.2 - - + +
304F TRP 4.0 1.6 - - - +
336F VAL* 3.5 2.6 - - - -
337F THR* 2.9 55.5 + - - +
865H C 3.8 15.0 + - - +
866H T 2.3 66.2 + - - +
867H A 5.2 1.6 + - - -
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Residues in contact with GLN 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F ILE* 3.7 9.6 - - + -
285F ARG* 1.3 75.4 - - - +
287F GLY* 1.3 59.2 + - - +
301F GLU* 4.2 4.7 - - - -
302F HIS* 2.9 35.9 + - - +
304F TRP* 3.6 27.9 - - + +
307F LEU* 3.6 15.2 - - - +
308F ASN 3.0 39.5 + - - +
311F ASP* 2.9 30.4 + - - +
312F LEU* 3.5 17.8 - - + +
335F HIS* 3.4 13.0 - - - +
336F VAL* 4.1 2.5 - - + +
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Residues in contact with GLY 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F GLN* 1.3 78.1 - - - +
288F VAL* 1.3 69.4 + - - +
300F GLN 3.0 13.7 - - - -
301F GLU* 4.0 6.4 - - - +
302F HIS* 5.2 0.9 - - - -
312F LEU* 3.5 13.2 - - - +
315F THR* 5.1 3.6 - - - -
334F LEU* 3.6 0.5 - - - -
335F HIS* 2.8 35.1 + - - +
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Residues in contact with VAL 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F ILE* 5.5 0.4 - - + -
287F GLY* 1.3 79.8 - - - +
289F LYS* 1.3 62.6 + - - +
290F LEU* 5.7 2.2 - - + -
299F THR* 3.2 6.2 - - - -
300F GLN* 2.9 31.5 + - + +
301F GLU* 4.6 1.7 - - - +
312F LEU* 3.6 23.6 - - + +
315F THR* 3.9 15.9 - - + -
316F ALA* 3.9 17.3 - - + -
319F THR* 3.9 25.1 - - + +
332F VAL* 6.0 2.0 - - + -
333F GLY 3.3 7.2 - - - +
334F LEU* 3.6 25.6 - - + +
335F HIS* 4.7 3.6 - - - +
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Residues in contact with LYS 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F GLU* 2.5 39.6 + - - -
288F VAL* 1.3 76.9 - - - +
290F LEU* 1.3 74.5 + - - +
297F GLN* 3.3 36.9 + - + +
298F THR 3.2 11.7 - - - +
299F THR* 3.9 10.3 - - + -
331F LEU* 4.0 22.3 - - + +
332F VAL* 3.6 5.7 - - - +
333F GLY* 2.8 35.5 + - - +
335F HIS* 6.2 2.9 - - + -
842G G 5.9 0.8 + - - -
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Residues in contact with LEU 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F CYS* 4.3 12.1 - - - -
288F VAL* 5.7 3.6 - - + -
289F LYS* 1.3 82.9 - - - +
291F LYS* 1.3 60.7 + - - +
292F PHE* 4.1 24.3 + - + -
297F GLN* 3.2 4.7 - - - +
298F THR* 2.9 40.8 + - + +
316F ALA* 4.4 4.9 - - + +
319F THR* 3.7 27.9 - - + +
320F TRP* 3.8 34.5 - - + +
324F ARG* 5.7 0.2 - - - -
329F VAL* 4.5 10.3 - - + -
331F LEU 3.9 3.8 - - - +
332F VAL* 3.9 24.5 - - + -
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Residues in contact with LYS 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F THR* 5.0 0.4 + - - -
289F LYS 4.3 0.2 - - - -
290F LEU* 1.3 75.7 - - - +
292F PHE* 1.3 64.8 + - - +
295F PHE* 3.6 45.3 - - - +
296F GLN 3.4 15.0 - - - +
297F GLN* 3.6 25.3 + - + +
329F VAL* 3.5 5.4 - - - +
330F ARG* 2.9 43.0 + - + +
331F LEU* 3.1 48.9 + - + +
840G A 4.4 8.5 + - - -
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Residues in contact with PHE 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F LEU* 4.1 18.8 - - + -
291F LYS* 1.3 73.8 - - - +
293F ASP* 1.3 66.0 + - - +
294F ASP* 3.3 13.2 - - - +
295F PHE* 3.2 9.6 + - - -
296F GLN* 3.1 27.2 + - - -
297F GLN* 4.7 0.4 - - - -
298F THR* 3.9 25.8 - - + -
323F ARG* 3.0 22.2 - - + -
324F ARG* 3.4 23.6 - - + -
327F ARG* 3.3 42.6 - - + -
328F GLY 3.3 9.0 - - - +
329F VAL* 3.6 21.8 - - + -
330F ARG* 3.2 22.3 - - - +
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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