Contacts of the strand formed by residues 289 - 294 (chain l) in PDB entry 6QX2
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 ILE 289 (chain l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277l ILE* 4.5 4.0 - - + -
281l VAL* 3.8 46.8 - - + +
286l ILE* 4.1 18.7 + - + +
287l ASP 3.8 0.6 - - - +
288l GLY* 1.3 75.9 - - - +
290l THR* 1.3 59.2 + - - +
291l ASP 3.5 25.6 - - - +
292l LEU* 4.9 5.2 - - + -
306l ILE* 3.6 25.4 - - + -
307l ASP 3.5 3.8 - - - +
308l VAL* 5.5 0.9 - - + -
317l ILE* 3.7 27.8 - - + -
321l LEU* 4.2 17.5 - - + -
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Residues in contact with THR 290 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252l ARG* 4.1 7.3 + - - +
288l GLY 4.7 0.4 - - - -
289l ILE* 1.3 74.1 - - - +
291l ASP* 1.3 64.3 + - - +
307l ASP* 2.9 26.1 + - - +
308l VAL 4.1 0.3 + - - -
309l ARG* 3.3 43.1 - - + +
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Residues in contact with ASP 291 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289l ILE* 3.5 14.3 - - - +
290l THR* 1.3 82.0 + - - +
292l LEU* 1.3 76.9 + - - +
293l ARG* 2.7 36.1 + - - +
305l VAL 4.6 0.2 - - - -
306l ILE* 3.5 1.6 - - - -
307l ASP* 3.0 40.5 + - + +
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Residues in contact with LEU 292 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274l ILE* 3.5 40.2 - - + +
277l ILE* 3.7 18.8 - - + -
278l ALA* 3.6 28.0 - - + +
281l VAL* 6.0 1.3 - - + -
289l ILE* 4.9 5.6 - - + -
291l ASP* 1.3 85.3 + - - +
293l ARG* 1.3 61.4 + - - +
304l VAL* 4.3 14.4 - - + -
305l VAL 3.4 5.4 - - - +
306l ILE* 3.7 28.0 - - + -
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Residues in contact with ARG 293 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422k SER* 4.7 20.4 - - - -
252l ARG* 6.0 0.2 - - - +
258l ARG* 4.7 9.5 - - - +
274l ILE* 5.5 1.8 - - - -
291l ASP* 2.7 41.0 + - - +
292l LEU* 1.3 76.0 - - - +
294l ASP* 1.3 58.6 + - - +
295l GLU* 2.8 38.9 + - + -
304l VAL* 3.6 7.0 - - - +
305l VAL* 2.8 59.8 + - + +
307l ASP* 3.0 25.9 + - - -
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Residues in contact with ASP 294 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449k SER* 3.8 13.5 + - - -
114l ASP* 4.0 5.0 - - - +
270l LYS* 2.6 27.0 + - - -
271l ALA* 5.8 0.2 - - - -
274l ILE* 3.6 29.6 - - + +
293l ARG* 1.3 71.1 - - - +
295l GLU* 1.3 59.0 + - - +
296l THR* 2.5 33.6 + - - +
303l ARG 3.6 3.8 - - - +
304l VAL* 3.9 5.6 - - - +
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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