Contacts of the strand formed by residues 280 - 284 (chain A) in PDB entry 2XOA
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 LEU 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 4.4 9.2 - - + -
263A GLU 3.4 21.3 - - - +
264A PRO* 3.9 6.1 - - + -
265A LEU* 4.3 6.7 - - - +
274A LEU* 3.3 36.6 - - + -
275A ARG 6.0 0.9 - - - +
278A GLN* 4.1 11.4 - - + +
279A PRO* 1.3 76.2 - - - +
281A ARG* 1.3 66.3 + - - +
282A ILE* 3.4 32.5 - - + -
312A THR 3.8 0.2 - - - +
313A SER* 3.5 2.4 - - - +
314A PHE* 2.9 40.1 + - - +
315A CYS* 5.1 0.7 - - - -
316A PHE* 3.9 17.9 - - + -
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Residues in contact with ARG 281 (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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55A ALA* 2.7 37.5 + - - +
56A GLN* 3.7 4.4 + - - +
59A PRO* 3.5 22.6 - - - +
60A PRO* 5.3 0.6 - - - +
261A ARG 3.8 0.2 - - - +
262A LEU 3.8 0.3 - - - -
263A GLU* 2.8 42.5 + - + +
264A PRO 5.9 0.4 + - - -
265A LEU* 4.2 26.9 - - + +
280A LEU* 1.3 80.1 - - - +
282A ILE* 1.3 63.5 + - - +
283A ARG 4.0 0.7 - - - -
290A TYR* 3.9 26.7 - - + -
307A ALA* 2.7 29.4 + - - -
309A THR* 3.6 18.7 + - - +
312A THR* 2.6 42.0 - - + +
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Residues in contact with ILE 282 (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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222A LEU* 5.2 11.7 - - + -
231A LEU* 5.8 2.5 - - + -
260A TRP* 3.5 37.7 - - + -
261A ARG 3.6 2.9 - - - -
262A LEU* 4.2 13.7 - - + -
280A LEU* 3.4 26.7 - - + -
281A ARG* 1.3 72.9 - - - +
283A ARG* 1.3 61.0 + - - +
284A HIS 3.9 0.2 + - - -
290A TYR* 3.6 2.6 - - - -
291A LEU* 2.9 60.1 + - + +
312A THR 4.5 3.2 + - - -
314A PHE* 4.1 17.9 - - + -
316A PHE* 5.0 9.2 - - + -
348A VAL* 4.6 10.1 - - + -
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Residues in contact with ARG 283 (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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59A PRO 5.4 1.0 + - - -
60A PRO 4.7 1.0 + - - -
61A ASP* 3.6 35.4 + - - +
63A ALA* 6.2 1.6 - - - +
260A TRP* 3.3 5.8 - - - -
261A ARG* 2.8 54.7 + - + +
263A GLU* 3.5 21.0 + - - -
281A ARG 4.0 0.4 - - - -
282A ILE* 1.3 73.5 - - - +
284A HIS* 1.3 71.8 + - - +
285A VAL* 3.4 7.3 + - - +
288A GLY* 3.7 24.0 + - - +
289A ARG 3.5 5.2 - - - +
290A TYR* 2.6 60.9 + - + -
304A ALA* 5.4 2.6 - - - +
402A ARG* 3.8 12.7 - - - +
405A HIS* 3.9 11.5 + - - -
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Residues in contact with HIS 284 (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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233A ILE* 3.3 36.2 - - + +
256A ALA 4.7 0.4 + - - -
257A ARG* 2.7 36.3 - - - -
259A LEU 3.9 10.1 + - - -
260A TRP* 3.7 26.3 - - + -
282A ILE 3.9 0.2 + - - -
283A ARG* 1.3 73.0 - - - +
285A VAL* 1.3 57.5 + - - +
286A THR* 3.3 19.2 + - - -
287A THR* 2.8 42.2 - - - +
288A GLY* 2.7 32.2 + - - -
289A ARG* 2.6 19.6 + - - +
301A VAL* 4.9 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