Contacts of the strand formed by residues 283 - 291 (chain C) in PDB entry 1HYH
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 TYR 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ASP* 3.7 20.2 - - - +
149C THR* 3.5 21.5 - - + -
150C ALA* 3.6 28.5 - - + -
153C GLN* 3.5 19.2 - - + +
160C ALA* 2.9 31.6 + - - -
163C VAL 2.9 19.8 + - - -
274C SER* 3.8 8.1 - - - +
275C ASN* 3.4 22.9 - - - -
276C ARG* 3.8 41.1 - - + -
282C MET* 1.3 81.0 - - + +
284C LEU* 1.3 62.4 + - - +
318C ILE* 3.4 23.6 - - - +
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Residues in contact with LEU 284 (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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146C ASP* 3.4 13.7 - - - -
196C GLY* 3.9 5.4 - - - +
273C VAL 3.5 0.7 - - - +
274C SER* 3.8 3.9 + - - -
275C ASN* 3.1 28.5 + - - +
277C ARG* 4.4 6.3 - - + -
280C MET* 4.1 25.1 - - + -
282C MET 4.8 1.6 - - - +
283C TYR* 1.3 76.1 - - - +
285C SER* 1.3 77.7 + - - +
286C TYR* 3.6 12.2 + - + -
311C LEU* 3.8 26.9 - - + +
314C SER* 4.5 4.5 - - - -
315C ARG* 3.8 38.4 - - + +
318C ILE* 3.9 10.3 - - + -
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Residues in contact with SER 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASP* 3.8 1.5 + - - -
167C GLY* 3.2 12.6 - - - -
168C THR* 2.9 47.1 + - - +
195C LEU* 3.8 7.4 - - - +
196C GLY 3.1 32.9 + - - -
198C HIS* 5.3 0.3 - - - +
272C VAL* 4.0 4.7 - - - -
273C VAL 3.3 8.1 - - - -
274C SER* 3.9 5.4 + - - -
284C LEU* 1.3 78.6 - - - +
286C TYR* 1.3 66.1 + - - +
311C LEU* 4.5 0.2 - - - +
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C LEU* 4.0 6.1 - - + -
272C VAL* 3.9 5.9 - - - +
273C VAL 3.3 8.7 + - - +
275C ASN* 2.9 21.0 + - - +
277C ARG* 3.2 55.2 + - - +
284C LEU* 3.6 6.0 + - + -
285C SER* 1.3 76.6 - - - +
287C PRO* 1.3 82.6 - - + +
288C ALA 3.5 0.7 + - - -
299C THR* 3.3 19.5 + - - -
300C THR* 3.9 2.4 - - - +
301C LEU* 2.9 47.4 + - + +
303C LEU* 4.3 8.7 - - + +
311C LEU* 3.8 32.8 - - + -
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Residues in contact with PRO 287 (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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193C TYR* 3.9 28.9 - - + -
195C LEU* 3.7 17.0 - - + -
270C GLU* 4.1 19.3 - - + +
271C LEU 3.4 9.9 - - - +
272C VAL* 3.8 9.4 - - + -
275C ASN* 4.9 0.5 - - - +
277C ARG* 4.2 2.3 + - - -
286C TYR* 1.3 101.5 - - + +
288C ALA* 1.3 59.6 + - - +
299C THR* 2.8 38.4 + - + +
301C LEU* 3.9 14.6 - - + -
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Residues in contact with ALA 288 (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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269C ALA 3.6 0.2 - - - +
270C GLU* 3.4 2.3 - - - -
271C LEU 3.0 29.6 + - - +
273C VAL* 4.5 1.8 - - + -
275C ASN* 3.8 25.1 - - - +
286C TYR 4.2 0.9 - - - +
287C PRO* 1.3 76.2 - - - +
289C ILE* 1.3 66.9 + - - +
290C ILE* 3.7 12.9 + - + +
295C VAL* 3.9 13.7 - - + -
297C ALA 3.5 12.3 - - - +
298C GLU* 4.8 1.3 - - - -
299C THR* 4.2 4.7 - - - +
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Residues in contact with ILE 289 (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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268C HIS* 3.4 38.1 - - + +
269C ALA 3.5 1.3 - - - -
270C GLU* 3.8 15.5 - - + -
288C ALA* 1.3 74.9 - - - +
290C ILE* 1.3 56.0 + - - +
295C VAL 3.6 0.9 - - - -
296C LEU* 2.7 40.9 + - + +
297C ALA* 2.8 30.7 + - + +
298C GLU 4.9 0.2 - - - +
299C THR* 3.8 19.7 - - + -
184D ASP 4.9 2.0 - - - +
185D LEU* 3.6 22.7 - - + -
212D MET* 3.8 24.9 - - + -
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Residues in contact with ILE 290 (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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164C ILE* 4.5 10.5 - - + -
259C ILE* 4.6 8.7 - - + -
262C ALA* 4.2 14.8 - - + +
263C VAL* 3.8 26.9 - - + -
267C ALA 4.4 0.9 + - - -
268C HIS* 2.8 25.3 + - - -
269C ALA 2.8 19.6 + - - +
271C LEU* 3.9 26.7 - - + -
273C VAL* 3.9 27.4 - - + -
288C ALA* 4.1 10.1 - - + +
289C ILE* 1.3 76.2 - - - +
291C GLY* 1.3 61.2 + - - +
294C GLY 3.7 4.5 - - - +
295C VAL* 4.0 21.5 - - + -
296C LEU* 4.5 0.4 - - - -
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Residues in contact with GLY 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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262C ALA 4.0 7.0 - - - -
263C VAL* 3.4 22.9 - - - +
266C ASP* 3.5 11.4 - - - -
268C HIS 4.1 3.1 - - - -
290C ILE* 1.3 74.2 - - - +
292C ARG* 1.3 60.0 + - - -
293C ASP 3.2 3.1 - - - -
294C GLY 3.0 22.7 + - - +
296C LEU* 3.8 12.9 - - - +
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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