Contacts of the helix formed by residues 191 - 199 (chain D) in PDB entry 2C11
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 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D LEU* 3.1 10.3 + - + +
189D PRO 2.9 0.8 - - - -
190D GLN* 1.3 78.0 - - - +
192D SER* 1.3 61.2 + - - +
194D LEU* 3.1 8.1 + - + +
195D LEU* 3.0 25.7 + - + +
274D LEU* 3.8 23.6 - - + +
277D LEU* 5.5 2.9 - - + -
278D GLU* 2.6 38.4 - - + +
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Residues in contact with SER 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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188D LEU 3.4 0.8 + - - -
189D PRO* 2.5 35.6 + - - +
190D GLN 3.6 0.2 - - - -
191D ALA* 1.3 77.7 - - - +
193D GLY* 1.3 53.2 + - - +
195D LEU* 4.0 0.9 - - - -
196D HIS* 2.5 57.6 + - - -
201D TYR* 3.5 23.8 - - - -
278D GLU* 4.4 0.2 - - - -
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Residues in contact with GLY 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 ALA 3.0 2.0 + - - -
192D SER* 1.3 80.8 - - - +
194D LEU* 1.3 62.9 + - - +
196D HIS* 3.4 10.6 + - - +
197D HIS* 3.3 12.5 + - - +
278D GLU* 3.1 13.9 + - - +
281D PHE* 3.7 15.3 - - - -
282D GLU* 5.5 2.2 - - - -
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Residues in contact with LEU 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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191D ALA* 3.6 5.4 - - + +
193D GLY* 1.3 70.8 - - - -
195D LEU* 1.3 64.0 + - + +
197D HIS* 2.9 24.3 + - - +
198D CYS* 3.1 16.3 + - + +
266D TYR* 3.9 22.7 - - + +
277D LEU* 3.7 41.5 - - + -
278D GLU* 2.7 21.5 + - - +
281D PHE* 3.7 31.8 - - + -
286D VAL* 4.8 1.1 - - + -
288D VAL* 3.4 31.4 - - + -
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Residues in contact with LEU 195 (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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188D LEU* 3.2 45.5 - - + +
191D ALA* 3.0 17.6 + - + +
192D SER 3.5 4.5 - - - +
194D LEU* 1.3 76.7 - - + +
196D HIS* 1.3 54.7 + - - +
197D HIS 2.7 15.2 + - - -
198D CYS* 3.8 15.3 - - - -
199D CYS* 3.2 17.3 + - + -
200D PHE 3.1 21.3 + - - -
201D TYR* 3.1 38.5 + - + -
208D LEU* 4.9 9.2 - - + -
229D LEU* 6.2 0.2 - - + -
243D VAL* 6.3 1.1 - - + -
245D LEU* 4.8 17.7 - - + -
266D TYR* 6.2 1.8 - - + -
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Residues in contact with HIS 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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192D SER* 2.5 46.9 + - - +
193D GLY* 3.5 9.0 - - - +
195D LEU* 1.3 70.6 - - - +
197D HIS* 1.3 61.2 + - - +
200D PHE* 4.5 7.1 - - - -
201D TYR* 2.9 37.1 + + + +
202D LYS* 4.1 10.1 - - + -
203D HIS* 4.4 10.0 - - + +
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Residues in contact with HIS 197 (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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193D GLY 3.3 8.2 + - - +
194D LEU* 2.9 9.8 + - + +
195D LEU 2.7 1.8 + - - -
196D HIS* 1.3 83.9 - - - +
198D CYS* 1.3 71.8 + - - +
199D CYS 3.4 0.7 + - - -
200D PHE* 3.6 15.8 - - - -
281D PHE* 3.8 28.1 - + + -
288D VAL* 4.6 10.7 + - + -
290D LEU* 3.9 28.8 - - + +
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Residues in contact with CYS 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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194D LEU* 3.1 21.9 + - + +
195D LEU* 3.8 9.2 - - - -
197D HIS* 1.3 80.5 - - - +
199D CYS* 1.3 103.9 + - - +
200D PHE* 3.6 10.2 - - - -
231D TYR* 3.5 10.6 + - - -
266D TYR* 3.5 13.0 - - - +
267D GLN* 4.8 2.0 - - - +
288D VAL* 3.4 25.1 - - + -
289D VAL 4.9 2.0 - - - +
290D LEU* 3.5 16.1 - - - +
291D ILE* 3.8 14.5 + - + +
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Residues in contact with CYS 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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195D LEU* 3.2 18.6 + - + +
198D CYS* 1.3 119.0 - - - +
200D PHE* 1.3 74.9 + - - +
201D TYR* 3.3 2.2 + - - +
207D ASN* 3.6 8.7 + - - +
208D LEU* 4.5 14.1 - - + +
231D TYR* 3.6 24.0 - - + +
243D VAL* 4.1 34.1 - - + -
266D TYR* 4.7 3.4 - - - -
291D ILE* 5.7 1.8 - - - -
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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