Contacts of the strand formed by residues 269 - 276 (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 ALA 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262C ALA* 4.4 14.4 - - + -
267C ALA* 3.2 12.1 - - + -
268C HIS* 1.3 78.5 - - - +
270C GLU* 1.3 63.1 + - - +
271C LEU* 3.5 13.1 + - + +
289C ILE* 4.3 1.3 - - - -
290C ILE* 2.8 29.9 + - - +
186D ASP* 3.6 19.5 - - - +
188D ARG* 4.7 2.9 - - - +
189D SER* 3.6 7.2 - - - +
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Residues in contact with GLU 270 (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* 2.5 36.7 + - + -
258C ARG* 5.0 4.2 + - - -
268C HIS 3.9 1.4 + - - -
269C ALA* 1.3 73.0 - - - +
271C LEU* 1.3 69.0 + - - +
287C PRO* 4.1 9.2 - - + -
288C ALA 3.4 5.2 - - - +
289C ILE* 3.8 10.2 - - + +
299C THR* 4.0 22.0 - - + -
185D LEU* 5.2 0.9 - - + +
189D SER* 2.9 31.8 + - - +
212D MET* 3.6 28.8 + - - -
213D GLY 4.0 3.0 + - - -
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C LEU* 4.7 11.4 - - + -
193C TYR* 5.8 1.1 - - - -
258C ARG* 3.4 44.4 - - + +
259C ILE* 4.1 23.3 - - + +
262C ALA* 4.0 24.2 - - + -
269C ALA* 3.5 10.0 + - + +
270C GLU* 1.3 81.4 - - - +
272C VAL* 1.3 61.0 + - - +
273C VAL* 3.4 16.8 + - + +
287C PRO* 4.0 4.3 - - - -
288C ALA* 3.0 27.7 + - - +
290C ILE* 3.9 21.5 - - + -
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Residues in contact with VAL 272 (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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166C THR 3.8 0.2 - - - +
168C THR* 3.3 22.9 - - - +
169C LEU* 3.5 42.5 + - + +
172C THR* 3.6 24.7 - - + +
193C TYR* 4.0 24.7 - - + -
194C ASN 3.8 9.4 - - - +
195C LEU* 4.5 1.6 - - + -
271C LEU* 1.3 71.1 - - - +
273C VAL* 1.3 58.4 + - - +
285C SER* 4.0 0.4 - - - -
286C TYR* 3.9 22.0 - - - +
287C PRO* 3.8 12.1 - - + +
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ILE* 4.5 9.0 - - + -
165C GLY 3.5 8.5 - - - +
166C THR 4.0 4.9 - - - +
169C LEU* 5.0 0.7 - - + -
259C ILE* 3.8 34.8 - - + -
271C LEU* 3.4 18.6 + - + +
272C VAL* 1.3 76.7 - - - +
274C SER* 1.3 63.1 + - - +
275C ASN* 2.8 39.3 + - + +
285C SER* 3.9 6.7 - - - -
286C TYR 3.3 13.0 + - - -
288C ALA* 4.5 2.5 - - + -
290C ILE* 3.9 27.1 - - + -
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Residues in contact with SER 274 (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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145C VAL* 4.9 1.1 - - - -
146C ASP* 2.5 39.0 + - - -
149C THR* 4.6 2.6 + - - -
164C ILE* 3.4 11.4 - - - +
165C GLY* 2.7 45.7 + - - -
167C GLY* 4.1 9.6 - - - +
273C VAL* 1.3 68.9 - - - +
275C ASN* 1.3 60.8 + - - +
283C TYR* 3.8 10.6 - - - +
284C LEU 3.5 12.6 + - - -
285C SER* 3.9 2.3 + - - -
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Residues in contact with ASN 275 (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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160C ALA 6.0 0.7 - - - +
164C ILE* 4.6 1.6 - - + -
273C VAL* 2.8 31.2 + - + +
274C SER* 1.3 75.2 + - - +
276C ARG* 1.3 63.0 + - - +
277C ARG* 3.6 21.4 + - - +
282C MET 3.9 0.7 - - - +
283C TYR* 3.4 11.2 - - - -
284C LEU* 3.1 29.6 + - - +
286C TYR* 2.9 21.6 + - - +
287C PRO 4.9 1.0 - - - +
288C ALA* 3.8 17.3 - - - +
295C VAL* 3.9 28.5 - - + +
298C GLU* 4.8 5.7 - - - +
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Residues in contact with ARG 276 (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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153C GLN* 3.7 23.9 + - - +
160C ALA* 3.3 34.2 + - + +
275C ASN* 1.3 75.3 - - - +
277C ARG* 1.3 66.0 + - - +
278C ASP* 3.8 2.1 + - - +
281C GLY* 3.4 27.9 + - - -
282C MET* 3.3 19.3 - - - +
283C TYR* 3.7 32.2 - - + +
298C GLU* 4.4 3.5 - - - +
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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