Contacts of the strand formed by residues 269 - 276 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 6.3 0.4 - - - +
262A ALA* 4.3 15.3 - - + -
267A ALA* 3.3 10.5 - - + -
268A HIS* 1.3 76.3 - - - +
270A GLU* 1.3 64.0 + - - +
271A LEU* 3.5 12.4 + - + +
288A ALA 3.5 0.9 - - - +
289A ILE* 4.3 1.3 - - - -
290A ILE* 2.9 29.2 + - - +
186B ASP* 3.6 20.4 - - - +
188B ARG* 4.9 2.9 - - - +
189B SER* 3.6 7.2 - - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 3.1 30.5 + - + -
258A ARG* 5.2 2.6 + - - -
268A HIS 3.9 1.0 + - - -
269A ALA* 1.3 73.0 - - - +
271A LEU* 1.3 68.3 + - - +
287A PRO* 4.2 8.6 - - + +
288A ALA 3.1 11.9 - - - +
289A ILE* 3.7 11.4 - - + +
299A THR* 3.5 29.1 - - + +
301A LEU* 5.7 0.2 - - - +
189B SER* 3.0 32.0 + - - +
212B MET* 3.8 7.1 + - - -
213B GLY* 3.7 16.6 + - - -
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Residues in contact with LEU 271 (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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169A LEU* 4.5 11.0 - - + -
193A TYR* 5.7 1.1 - - - -
258A ARG* 3.7 42.2 - - + +
259A ILE* 4.0 33.4 - - + +
262A ALA* 4.2 15.9 - - + -
269A ALA* 3.5 10.5 + - + +
270A GLU* 1.3 83.0 - - - +
272A VAL* 1.4 63.3 + - - +
273A VAL* 3.4 18.6 + - + +
287A PRO* 4.0 4.7 - - - -
288A ALA* 3.0 26.6 + - - +
290A ILE* 4.1 17.9 - - + +
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Residues in contact with VAL 272 (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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168A THR* 3.5 20.2 - - - +
169A LEU* 3.3 41.9 - - + +
172A THR* 3.7 23.1 - - + +
193A TYR* 3.9 23.0 - - + -
194A ASN 3.8 8.7 - - - +
195A LEU* 4.3 2.9 - - + -
271A LEU* 1.4 71.8 - - - +
273A VAL* 1.3 65.7 + - - +
286A TYR* 4.0 9.2 - - - +
287A PRO* 3.8 26.4 - - + +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 4.5 11.9 - - + -
165A GLY 3.4 9.4 - - - +
166A THR 4.1 4.3 - - - +
169A LEU* 4.8 0.2 - - + -
259A ILE* 3.6 35.4 - - + -
271A LEU* 3.4 20.1 + - + +
272A VAL* 1.3 79.8 - - - +
274A SER* 1.3 65.5 + - - +
275A ASN* 2.8 36.1 + - + +
285A SER* 3.3 17.2 - - - -
286A TYR 3.3 1.7 + - - -
288A ALA* 4.5 2.2 - - + -
290A ILE* 4.2 22.2 - - + -
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Residues in contact with SER 274 (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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145A VAL* 5.3 0.4 - - - -
146A ASP* 2.7 35.1 + - - -
149A THR* 4.6 3.7 + - - -
164A ILE* 3.4 11.8 - - - +
165A GLY* 2.8 44.3 + - - -
167A GLY* 4.1 5.3 - - - +
273A VAL* 1.3 70.7 - - - +
275A ASN* 1.3 56.4 + - - +
283A TYR* 3.8 14.7 - - - +
284A LEU 3.6 13.0 + - - -
285A SER* 3.7 7.9 + - - -
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Residues in contact with ASN 275 (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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164A ILE* 4.4 1.3 - - + -
273A VAL* 2.8 24.0 + - + +
274A SER* 1.3 74.8 + - - +
276A ARG* 1.3 61.4 + - - +
277A ARG* 3.3 28.4 + - - +
282A MET 4.0 0.7 - - - +
283A TYR* 3.7 10.4 - - - -
284A LEU* 3.1 22.2 + - - +
286A TYR* 2.8 34.6 + - - +
287A PRO 5.0 1.0 - - - +
288A ALA* 3.9 16.4 - - - +
295A VAL* 4.0 28.1 - - + +
298A GLU* 4.9 4.9 - - - +
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Residues in contact with ARG 276 (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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153A GLN* 3.5 23.6 + - - +
160A ALA* 3.6 30.1 + - + +
275A ASN* 1.3 75.0 - - - +
277A ARG* 1.3 64.3 + - - +
278A ASP* 3.8 5.1 + - - +
281A GLY* 4.1 16.3 - - - -
282A MET* 3.8 26.2 - - - +
283A TYR* 3.6 33.4 - - + +
298A GLU* 4.3 2.9 - - - +
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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