Contacts of the helix formed by residues 191 - 199 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 3.1 11.7 + - + +
189B PRO 2.9 1.0 - - - -
190B GLN* 1.3 79.6 - - - +
192B SER* 1.3 61.8 + - - +
194B LEU* 3.6 7.7 - - + +
195B LEU* 3.1 24.6 + - + +
245B LEU* 6.5 0.7 - - + -
274B LEU* 3.8 23.1 - - + +
277B LEU* 5.4 3.4 - - + -
278B GLU* 2.8 37.5 - - + +
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Residues in contact with SER 192 (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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188B LEU 3.4 3.7 + - - -
189B PRO* 2.8 34.3 + - - +
190B GLN 3.7 0.2 - - - -
191B ALA* 1.3 77.8 - - - +
193B GLY* 1.3 53.9 + - - +
195B LEU* 4.1 6.5 - - - -
196B HIS* 2.5 55.0 + - - +
201B TYR* 3.6 14.2 - - - -
278B GLU* 4.3 0.4 - - - -
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Residues in contact with GLY 193 (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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191B ALA 3.1 1.4 - - - -
192B SER* 1.3 80.7 - - - +
194B LEU* 1.3 60.6 + - - +
196B HIS* 3.3 10.4 + - - +
197B HIS* 3.3 13.7 + - - +
278B GLU* 3.3 15.4 + - - -
281B PHE* 3.5 14.5 - - - -
282B GLU* 5.7 0.7 - - - -
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Residues in contact with LEU 194 (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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191B ALA* 3.6 5.8 - - + +
193B GLY* 1.3 70.9 - - - -
195B LEU* 1.3 61.8 + - + +
197B HIS* 2.8 29.1 + - - +
198B CYS* 3.1 21.8 + - + +
245B LEU* 6.1 0.2 - - + -
266B TYR* 4.0 16.6 - - + +
277B LEU* 3.7 42.2 - - + -
278B GLU* 2.8 22.3 + - - +
281B PHE* 3.5 29.6 - - + -
286B VAL* 5.1 0.9 - - + -
288B VAL* 3.6 29.6 - - + -
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Residues in contact with LEU 195 (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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188B LEU* 3.3 44.2 - - + +
191B ALA* 3.1 16.8 + - + +
192B SER 3.6 2.5 - - - +
194B LEU* 1.3 80.2 - - + +
196B HIS* 1.3 61.5 + - - +
197B HIS 2.8 5.9 + - - -
198B CYS* 4.0 16.2 - - - -
199B CYS* 3.3 14.6 + - + -
200B PHE 3.1 21.8 + - - -
201B TYR* 3.1 40.5 + - + -
208B LEU* 5.1 9.4 - - + -
229B LEU* 6.0 0.4 - - + -
243B VAL* 6.2 0.9 - - + -
245B LEU* 4.8 18.2 - - + -
266B TYR* 6.1 2.2 - - + -
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Residues in contact with HIS 196 (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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192B SER* 2.5 42.9 + - - +
193B GLY* 3.5 9.9 - - - +
195B LEU* 1.3 72.7 - - - +
197B HIS* 1.3 61.6 + - - +
200B PHE* 4.4 7.0 - - - -
201B TYR* 3.0 30.4 + + + +
202B LYS* 4.3 12.7 - - + +
203B HIS* 4.3 14.6 + + + +
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Residues in contact with HIS 197 (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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193B GLY 3.3 3.0 + - - +
194B LEU 2.8 11.8 + - - +
196B HIS* 1.3 85.9 - - - +
198B CYS* 1.3 71.6 + - - +
199B CYS 3.4 1.3 + - - -
200B PHE* 3.7 15.6 - - - -
281B PHE* 3.7 32.8 - + + -
288B VAL* 4.7 11.0 - - + -
290B LEU* 4.1 24.3 - - + +
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Residues in contact with CYS 198 (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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194B LEU* 3.1 22.8 + - + +
195B LEU* 4.0 9.0 - - - -
197B HIS* 1.3 80.3 - - - +
199B CYS* 1.3 104.9 + - - +
200B PHE* 3.8 10.2 - - - -
231B TYR* 3.4 10.2 + - - -
266B TYR* 3.6 14.1 - - - +
267B GLN* 4.7 2.2 - - - +
288B VAL* 3.3 25.1 - - + -
289B VAL 4.9 2.2 - - - +
290B LEU* 3.6 14.5 - - - +
291B ILE 3.8 14.5 + - - +
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Residues in contact with CYS 199 (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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195B LEU* 3.3 18.8 + - + +
198B CYS* 1.3 121.0 - - - +
200B PHE* 1.3 73.5 + - - +
201B TYR* 3.1 3.4 + - - +
207B ASN* 3.5 14.7 + - - +
208B LEU* 4.5 8.6 - - + +
231B TYR* 3.4 21.1 - - + +
243B VAL* 4.0 35.2 - - + -
266B TYR* 4.6 2.2 - - - -
291B ILE* 5.4 2.5 - - - -
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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