Contacts of the strand formed by residues 290 - 300 (chain C) in PDB entry 1XKH
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 290 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C ALA* 2.9 4.7 - - - +
286C GLY* 2.5 45.0 + - - +
287C SER 2.9 22.0 + - - +
288C TRP* 6.0 1.4 - - - -
289C ASP* 1.3 73.3 - - - +
291C TYR* 1.3 64.7 + - - +
292C ARG* 5.0 0.3 + - - +
316C GLN* 3.2 24.7 + - - +
318C LYS* 3.1 39.7 - - + +
319C HIS 5.2 0.4 + - - -
808C MSE 4.4 10.9 - - - +
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Residues in contact with TYR 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C GLY 3.6 3.6 - - - +
285C ALA* 3.1 28.3 - - + -
286C GLY 5.4 0.9 - - - -
289C ASP* 4.5 21.6 + - + +
290C ASN* 1.3 81.1 + - - +
292C ARG* 1.3 61.6 + - - +
316C GLN* 3.2 3.3 - - - +
317C ASP* 2.8 43.3 + - + +
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Residues in contact with ARG 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ASN* 3.0 37.0 + - - +
239C ASP* 2.4 43.2 + - - -
241C ALA* 3.2 7.7 - - - +
282C GLU* 3.7 18.0 + - - -
283C LEU* 3.7 3.5 - - - +
284C GLY* 2.8 30.1 + - - +
290C ASN* 5.0 0.4 - - - +
291C TYR* 1.3 77.5 - - - +
293C SER* 1.3 78.9 + - - +
294C GLU* 3.2 25.8 + - - +
314C ALA* 4.2 7.7 - - - +
315C TYR 3.1 14.4 - - - +
316C GLN* 3.0 38.3 + - + +
808C MSE 5.5 5.5 - - + +
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Residues in contact with SER 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C VAL* 5.9 1.1 - - - -
282C GLU* 3.0 15.9 - - - -
283C LEU* 3.8 20.9 - - - -
292C ARG* 1.3 84.4 - - - +
294C GLU* 1.3 60.4 + - - +
314C ALA* 3.1 2.6 - - - -
315C TYR* 2.7 56.2 + - - +
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ARG* 5.3 6.4 + - - -
241C ALA* 3.2 23.8 - - + +
271C LYS* 4.6 6.4 + - - -
280C HIS* 3.6 23.1 + - - +
281C VAL* 3.1 25.5 - - - +
282C GLU* 2.9 36.0 + - + +
292C ARG* 3.2 27.9 + - - +
293C SER* 1.3 72.8 - - - +
295C LEU* 1.3 63.4 + - - +
296C ASP* 4.7 4.2 - - - +
312C VAL* 4.8 1.9 - - + +
313C ALA 3.3 7.6 - - - +
314C ALA* 3.3 19.1 - - + -
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C HIS 3.0 28.0 - - - +
281C VAL* 3.4 22.7 - - + -
294C GLU* 1.3 80.5 - - - +
296C ASP* 1.3 60.5 + - - +
297C VAL* 4.0 22.2 - - + -
311C ALA 3.7 1.8 - - - +
312C VAL* 3.0 27.2 - - - +
313C ALA* 2.9 13.9 + - + +
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Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C GLU* 3.6 4.2 - - - +
271C LYS* 4.1 6.0 - - - +
278C LYS* 5.2 1.4 - - - +
279C GLY* 2.8 7.2 - - - -
280C HIS* 2.6 72.5 + - + +
294C GLU* 4.7 1.6 - - - +
295C LEU* 1.3 72.3 - - - +
297C VAL* 1.3 72.5 + - - +
298C SER* 5.3 0.4 - - - -
310C ARG* 2.4 53.0 + - - +
311C ALA 3.9 0.2 - - - -
312C VAL* 3.9 16.6 - - + +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C PHE* 4.1 22.4 - - + -
278C LYS 3.9 3.4 - - - -
279C GLY* 5.0 1.3 - - - -
280C HIS 5.0 0.9 - - - +
295C LEU* 4.0 26.9 - - + -
296C ASP* 1.3 83.4 + - - +
298C SER* 1.3 63.5 + - - +
309C GLY 4.2 0.3 - - - +
310C ARG* 3.3 2.8 - - - +
311C ALA* 2.8 43.9 + - + +
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Residues in contact with SER 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C PRO* 3.1 8.5 - - - +
274C THR* 2.6 46.1 + - - +
277C PHE* 3.0 18.2 - - - -
278C LYS 2.8 25.0 + - - +
279C GLY* 4.7 0.2 - - - -
296C ASP* 5.5 0.7 - - - -
297C VAL* 1.3 76.3 - - - +
299C GLY* 1.3 60.9 + - - +
309C GLY 3.4 6.1 - - - -
310C ARG* 3.4 26.4 - - - +
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Residues in contact with GLY 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C THR 3.2 17.0 - - - -
276C GLU 4.0 2.7 - - - -
277C PHE* 4.2 3.8 - - - -
298C SER* 1.3 83.1 + - - +
300C PRO* 1.3 73.2 - - - +
301C LEU* 4.5 2.1 - - - +
308C ARG* 3.4 5.0 - - - +
309C GLY 2.9 30.6 + - - +
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Residues in contact with PRO 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C HIS 2.7 24.7 - - - +
276C GLU* 4.6 2.5 - - - -
277C PHE* 4.3 15.5 - - + +
299C GLY* 1.3 84.9 - - - +
301C LEU* 1.3 72.0 + - - +
302C THR 4.4 13.2 - - - +
303C GLU 5.5 1.6 - - - +
305C GLY* 4.5 9.9 - - - -
307C VAL 3.8 8.3 - - - +
308C ARG* 4.3 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