Contacts of the strand formed by residues 191 - 200 (chain D) in PDB entry 5H2U
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 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D ARG* 3.7 14.1 - - + -
187D PRO 3.5 21.1 - - - -
188D ARG 3.2 14.2 + - - +
189D GLU* 3.0 6.2 - - - +
190D GLU* 1.3 81.5 - - + +
192D THR* 1.3 62.4 + - - +
193D LEU* 4.2 6.7 + - - +
209D LEU 3.3 5.4 - - - +
210D TRP* 3.6 38.4 - + + -
216D VAL* 4.5 9.0 - - + -
218D ILE* 4.5 9.0 - - + -
251D TYR* 4.5 2.5 - + - -
252D ALA* 3.6 18.2 - - + -
254D VAL* 3.7 25.4 - - + -
261D TYR* 4.5 12.5 - + + -
263D ILE* 3.6 35.4 - - + -
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Residues in contact with THR 192 (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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189D GLU 5.5 0.7 + - - -
190D GLU 5.2 1.4 + - - -
191D PHE* 1.3 73.0 - - - +
193D LEU* 1.3 73.1 - - - +
194D CYS* 4.5 9.6 - - - -
208D GLY* 3.2 6.1 - - - -
209D LEU* 2.9 43.4 + - + +
211D LYS* 5.7 0.3 + - - -
212D ASP* 3.9 20.1 + - - +
218D ILE* 3.7 4.2 - - - +
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Residues in contact with LEU 193 (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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191D PHE 4.3 6.7 - - - +
192D THR* 1.3 83.2 - - - +
194D CYS* 1.3 66.2 + - - +
206D PHE* 3.7 41.5 - - + -
207D GLU 4.1 2.5 - - - -
218D ILE* 4.0 17.5 - - + -
220D VAL* 3.8 16.4 - - + -
261D TYR* 3.3 37.2 - - + +
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Residues in contact with CYS 194 (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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192D THR* 4.4 12.6 - - - -
193D LEU* 1.3 80.9 - - - +
195D ARG* 1.3 73.5 + - - +
196D LYS 3.8 0.2 + - - -
206D PHE* 3.7 12.0 - - - +
207D GLU* 2.8 26.0 + - + +
208D GLY* 4.3 11.2 - - - -
209D LEU* 4.5 20.9 - - - -
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Residues in contact with ARG 195 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D CYS* 1.3 85.3 + - - +
196D LYS* 1.3 104.9 + - - +
197D LEU* 4.2 1.1 - - + +
206D PHE* 3.6 10.1 - - - -
207D GLU* 2.8 43.1 + - - +
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Residues in contact with LYS 196 (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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194D CYS 3.8 0.6 + - - -
195D ARG* 1.3 106.1 + - - +
197D LEU* 1.3 62.7 + - - +
198D GLY* 3.6 22.7 - - - +
199D SER* 3.5 16.8 + - - -
204D GLU* 2.7 30.9 + - + +
205D VAL 3.3 14.6 - - - +
206D PHE* 3.5 28.0 - - + -
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Residues in contact with LEU 197 (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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195D ARG* 4.5 1.8 - - + +
196D LYS* 1.3 78.3 - - - +
198D GLY* 1.3 56.5 + - - +
205D VAL* 2.7 18.7 + - + +
206D PHE 4.2 4.3 - - - +
207D GLU* 3.7 40.8 - - + +
217D ALA* 4.8 0.4 - - + -
266D LEU* 3.8 21.8 - - + -
504D 1N1 3.5 81.1 + - + +
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Residues in contact with GLY 198 (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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196D LYS* 3.6 15.4 - - - +
197D LEU* 1.3 80.2 - - - +
199D SER* 1.3 62.0 + - - -
204D GLU* 3.6 3.5 - - - -
205D VAL* 2.9 34.8 + - - +
504D 1N1 4.9 2.9 - - - -
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Residues in contact with SER 199 (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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196D LYS* 3.5 24.1 + - - -
198D GLY* 1.3 71.2 + - - -
200D GLY* 1.3 59.7 + - - +
202D PHE* 4.2 6.7 - - - -
203D GLY 3.4 11.2 + - - -
204D GLU* 4.2 4.0 + - - +
205D VAL* 5.4 0.3 - - - +
316D ARG* 6.0 0.2 + - - -
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Residues in contact with GLY 200 (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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199D SER* 1.3 77.6 - - - +
201D TYR* 1.3 58.9 + - - -
202D PHE* 3.0 23.6 - - - -
203D GLY* 2.8 25.2 + - - +
345D HIS* 5.9 0.7 - - - -
346D ASP* 5.7 3.1 - - - -
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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