Contacts of the strand formed by residues 269 - 275 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ASP* 3.5 20.6 - - - +
188A ARG* 4.9 2.7 - - - +
189A SER* 3.6 7.2 - - - +
262B ALA* 4.3 14.8 - - + -
267B ALA* 3.2 9.2 - - + -
268B HIS* 1.3 77.5 - - - +
270B GLU* 1.3 63.4 + - - +
271B LEU* 3.3 14.7 + - + +
289B ILE* 3.5 1.5 - - - -
290B ILE* 2.9 28.4 + - - +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 6.0 0.2 - - - +
189A SER* 2.9 31.0 + - - +
212A MET* 3.4 29.6 + - - -
213A GLY 3.8 4.5 + - - -
193B TYR* 2.6 38.0 + - - -
258B ARG* 5.4 2.3 + - - -
268B HIS 3.9 0.6 + - - -
269B ALA* 1.3 71.1 - - - +
271B LEU* 1.3 65.6 + - - +
287B PRO* 4.1 8.3 - - + -
288B ALA 3.3 5.8 - - - +
289B ILE* 3.8 19.0 - - + +
299B THR* 3.9 13.9 - - + -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 4.7 8.5 - - + -
193B TYR* 6.0 0.9 - - - -
258B ARG* 3.5 45.5 - - + +
259B ILE* 4.0 35.7 - - + +
262B ALA* 4.2 19.1 - - + -
269B ALA* 3.3 12.3 + - + +
270B GLU* 1.3 79.2 - - - +
272B VAL* 1.3 62.8 + - - +
273B VAL* 3.3 13.3 + - + +
287B PRO* 4.1 4.7 - - - -
288B ALA* 3.0 28.3 + - - +
290B ILE* 4.2 18.6 - - + +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B THR 3.8 0.7 - - - +
168B THR* 3.5 21.1 - - - +
169B LEU* 3.3 42.6 + - + +
172B THR* 3.6 25.1 - - + +
193B TYR* 4.1 20.9 - - + -
194B ASN 4.0 8.1 - - - +
195B LEU* 4.5 2.0 - - + -
271B LEU* 1.3 71.4 - - - +
273B VAL* 1.3 62.1 + - - +
285B SER* 4.1 1.3 - - - -
286B TYR* 3.8 24.5 - - - +
287B PRO* 3.8 13.6 - - + +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE* 4.5 12.3 - - + -
165B GLY 3.4 9.6 - - - +
166B THR 4.0 4.5 - - - +
169B LEU* 4.8 0.2 - - + -
259B ILE* 3.5 36.1 - - + -
271B LEU* 3.3 17.6 + - + +
272B VAL* 1.3 78.4 - - - +
274B SER* 1.3 61.5 + - - +
275B ASN* 2.9 38.4 + - + +
285B SER* 3.3 14.1 - - - -
286B TYR 3.3 5.7 + - - +
288B ALA* 4.4 2.0 - - + -
290B ILE* 4.0 24.2 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 5.4 0.9 - - - -
146B ASP* 2.7 37.6 + - - -
149B THR* 4.6 3.0 - - - -
164B ILE* 3.4 9.9 - - - +
165B GLY* 2.8 43.9 + - - -
167B GLY* 4.2 4.9 - - - -
273B VAL* 1.3 68.7 - - - +
275B ASN* 1.3 59.0 + - - +
283B TYR* 3.6 12.0 - - - +
284B LEU 3.4 13.8 + - - -
285B SER* 3.7 6.5 + - - -
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Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ALA 5.8 0.2 - - - -
164B ILE* 4.4 1.6 - - + -
273B VAL* 2.9 31.3 + - + +
274B SER* 1.3 75.0 - - - +
276B ARG* 1.3 59.9 + - - +
277B ARG* 3.5 28.4 + - - +
282B MET 4.1 0.5 - - - +
283B TYR* 3.5 9.6 - - - -
284B LEU* 3.0 30.4 + - - +
286B TYR* 3.0 20.8 + - - +
287B PRO 5.1 1.2 - - - +
288B ALA* 4.0 16.3 - - - +
295B VAL* 4.0 29.4 - - + +
298B GLU* 5.1 4.0 - - - +
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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