Contacts of the strand formed by residues 203 - 211 (chain D) 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 PHE 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D ASN* 3.2 6.8 - - - -
195D LEU* 2.8 65.7 + - + -
196D GLY* 4.5 1.1 - - - -
201D SER 4.1 7.6 - - - +
202D GLN* 1.3 78.4 - - - +
204D VAL* 1.3 73.0 + - - +
205D ALA* 3.4 12.2 + - + -
231D GLU* 4.2 8.5 - - - +
303D LEU* 5.2 0.2 - - + -
307D GLU* 3.3 45.8 - - + -
310D LYS* 3.9 38.6 - - + +
311D LEU* 3.7 27.4 - - + -
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D MET* 3.9 21.5 - - + -
193D TYR 3.9 6.3 - - - +
194D ASN* 3.7 22.0 - - - +
203D PHE* 1.3 81.0 - - - +
205D ALA* 1.3 61.5 + - - +
206D TRP* 2.9 60.5 + - + +
209D VAL* 4.0 8.1 - - + -
231D GLU* 3.4 32.5 + - + +
234D ALA* 6.2 1.6 - - + -
307D GLU* 4.6 1.4 - - - +
310D LYS* 5.7 1.2 + - - -
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Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 2.8 18.7 + - + +
195D LEU* 3.8 16.6 - - + -
203D PHE* 3.4 9.3 + - + -
204D VAL* 1.3 71.9 - - - +
206D TRP* 1.3 52.1 + - - +
207D SER 3.1 2.5 - - - -
208D THR* 2.6 44.7 + - + +
209D VAL* 3.8 2.9 + - - +
303D LEU* 3.7 30.1 - - + -
307D GLU* 3.5 8.1 - - - +
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Residues in contact with TRP 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D MET* 4.5 3.4 - - + -
179D VAL* 4.2 17.5 - - + -
204D VAL* 2.9 44.3 + - + +
205D ALA* 1.3 67.6 - - - +
207D SER* 1.3 62.3 + - - +
208D THR 2.8 2.6 + - - -
209D VAL* 3.0 28.3 + - + +
216D ILE* 3.8 23.8 - - + +
217D VAL* 4.3 13.6 + - + +
227D LEU* 3.5 59.5 + - + +
230D ILE* 3.6 26.0 - - + -
231D GLU* 3.1 33.5 + - + -
307D GLU* 3.5 3.7 + - - +
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Residues in contact with SER 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D ALA 3.0 0.8 + - - -
206D TRP* 1.3 76.2 - - - +
208D THR* 1.3 62.5 + - - +
209D VAL 5.2 0.7 - - - -
210D ARG* 6.1 0.5 - - - +
215D PRO* 5.9 3.6 - - - +
217D VAL* 4.7 13.1 - - - +
302D ASP 4.0 13.0 + - - -
304D THR* 4.0 16.4 - - - -
307D GLU* 2.7 34.9 + - - -
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Residues in contact with THR 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ARG* 6.0 4.7 - - - +
191D SER* 3.6 4.3 + - - -
192D GLY* 3.3 16.4 + - - -
193D TYR* 3.1 29.9 + - + -
205D ALA* 2.6 33.1 + - + +
207D SER* 1.3 79.8 - - - +
209D VAL* 1.3 61.8 + - - +
210D ARG* 3.5 9.9 + - - +
301D LEU* 4.0 31.0 - - + -
302D ASP 5.8 2.5 - - - +
303D LEU* 4.3 4.3 - - + -
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D MET* 3.8 28.7 - - + -
179D VAL* 4.7 1.3 - - + -
190D VAL* 3.8 17.0 - - + -
191D SER 3.2 16.6 - - - +
192D GLY* 3.9 3.1 - - - -
193D TYR 4.4 0.4 - - - +
204D VAL* 4.0 4.0 - - + -
205D ALA 3.9 13.0 - - - +
206D TRP* 3.0 31.1 + - + +
207D SER 5.2 0.5 - - - -
208D THR* 1.3 76.7 - - - +
210D ARG* 1.3 64.7 + - - +
215D PRO* 3.8 2.6 - - - +
216D ILE* 2.9 45.8 + - + +
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Residues in contact with ARG 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C THR* 6.1 4.2 - - - +
210C ARG* 4.5 30.0 - - - +
302C ASP* 5.4 4.0 + - - +
189D SER 4.0 3.1 - - - +
190D VAL* 3.8 2.4 - - - +
191D SER* 3.1 39.1 + - - +
207D SER 6.1 0.2 - - - +
208D THR 4.0 7.6 - - - +
209D VAL* 1.3 79.8 - - - +
211D VAL* 1.3 66.9 + - - +
213D GLY* 3.0 31.7 + - - +
214D GLN 3.5 7.6 - - - +
215D PRO* 3.9 29.3 - - + +
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Residues in contact with VAL 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D VAL* 3.4 32.5 - - + -
183D PHE* 4.0 17.0 - - + -
185D LEU* 3.9 20.9 - - + -
189D SER 5.0 2.0 - - - -
190D VAL* 4.1 7.4 - - + -
209D VAL* 5.1 0.4 - - + -
210D ARG* 1.3 77.9 - - - +
212D MET* 1.3 72.9 + - + +
213D GLY 3.3 2.2 - - - -
214D GLN* 3.0 21.3 + - - +
216D ILE* 4.1 13.7 - - + -
219D LEU* 3.5 28.1 - - + +
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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