Contacts of the helix formed by residues 192 - 204 (chain C) in PDB entry 3C6Q
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 TYR 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C SER* 3.0 25.3 + - - -
11C VAL 3.2 15.9 + - - -
12C HIS* 3.2 30.7 - + + -
39C GLN 5.4 1.9 + - - -
162C ASP* 4.7 6.7 - - - +
164C GLU* 3.3 51.0 + - + -
165C ASP 4.9 0.7 - - - +
166C GLY* 3.7 33.7 - - - -
169C ALA* 5.0 3.4 - - + -
190C TYR* 3.4 8.7 - + + -
191C ALA* 1.3 77.8 - - - +
193C ASN* 1.3 65.1 + - - +
195C PRO* 2.9 18.6 - - - +
196C ALA* 3.3 15.3 + - - +
500C XYP 5.3 2.9 - - - -
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Residues in contact with ASN 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C GLY* 2.7 45.7 - - - +
130C THR* 3.5 8.3 - - - -
131C GLY* 3.8 0.3 + - - -
162C ASP* 3.1 23.6 + - - +
169C ALA* 4.6 4.0 - - - +
188C GLY* 3.5 15.0 - - - -
190C TYR* 3.2 27.2 + - - +
191C ALA 3.2 1.2 - - - -
192C TYR* 1.3 76.2 - - - +
194C GLY* 1.3 69.8 + - - +
196C ALA* 3.9 4.7 - - - +
197C GLN* 3.1 32.7 + - - +
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Residues in contact with GLY 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C TYR 3.7 7.3 + - - -
192C TYR 3.3 0.2 - - - -
193C ASN* 1.3 82.5 - - - +
195C PRO* 1.3 67.2 - - - +
197C GLN* 3.6 5.0 - - - +
198C ALA* 3.2 17.5 + - - +
212C ILE* 4.4 1.3 - - - +
214C CYS* 3.6 35.4 - - - +
221C ILE* 4.6 2.7 - - - -
230C ILE* 4.0 8.9 - - - +
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Residues in contact with PRO 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C HIS* 5.9 0.9 - - - +
191C ALA 3.1 15.3 - - - +
192C TYR* 2.9 18.4 - - - +
194C GLY* 1.3 80.9 - - - +
196C ALA* 1.3 63.4 + - - +
198C ALA* 3.1 11.2 + - + +
199C LEU* 2.9 23.3 + - - +
218C THR* 4.9 0.4 - - - +
220C ASP* 3.2 28.7 - - - +
221C ILE* 3.3 22.4 - - + +
224C TYR* 3.8 21.5 - - + -
230C ILE* 4.6 1.1 - - + -
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Residues in contact with ALA 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLY* 4.8 1.3 - - - +
169C ALA* 3.9 26.7 - - + -
170C VAL* 4.2 21.9 - - + +
173C ALA* 5.2 1.1 - - + -
192C TYR* 3.3 16.7 + - + +
193C ASN* 3.9 4.5 - - - +
195C PRO* 1.3 75.8 - - - +
197C GLN* 1.3 66.0 + - + +
199C LEU* 2.8 20.0 + - - +
200C VAL* 3.1 16.6 + - - +
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Residues in contact with GLN 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C GLY* 3.6 20.4 - - - +
173C ALA* 4.6 13.4 - - + +
186C PHE* 3.3 44.4 - - + +
187C PHE 3.5 21.8 + - - -
188C GLY* 3.4 16.5 + - - -
193C ASN* 3.1 22.8 + - - +
194C GLY* 3.6 2.1 - - - +
196C ALA* 1.3 77.8 - - + +
198C ALA* 1.3 63.3 + - - +
200C VAL* 3.3 1.7 + - - +
201C VAL* 2.9 28.6 + - - +
212C ILE* 3.5 23.4 - - + +
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLY 3.2 2.8 + - - +
195C PRO 3.1 10.0 + - - +
196C ALA 3.1 0.6 - - - -
197C GLN* 1.3 77.9 - - - +
199C LEU* 1.3 56.7 + - - +
201C VAL* 3.5 0.3 + - - +
202C LYS* 2.9 28.6 + - - +
212C ILE* 3.4 11.6 - - - +
224C TYR* 3.4 35.6 - - + -
229C VAL* 3.6 11.1 - - + +
230C ILE* 3.7 23.1 - - + -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL* 4.1 25.1 - - + -
195C PRO 2.9 10.7 + - - +
196C ALA* 2.8 18.1 + - - +
198C ALA* 1.3 67.3 - - - +
200C VAL* 1.3 58.4 + - - +
201C VAL 3.0 1.8 - - - -
202C LYS* 2.8 31.5 + - + +
203C ASN* 2.9 34.8 + - - +
224C TYR* 3.3 21.9 - - + +
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL* 3.2 36.3 - - + +
173C ALA* 3.5 37.5 - - + +
174C GLU* 3.6 19.7 - - + +
177C LEU* 3.7 22.3 - - + +
186C PHE* 5.0 3.8 - - + -
196C ALA 3.1 7.8 + - - +
197C GLN 3.8 6.1 - - - +
199C LEU* 1.3 78.9 - - - +
201C VAL* 1.3 59.7 + - - +
203C ASN* 3.7 11.6 + - - +
204C ALA* 3.5 15.4 + - - +
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LEU* 4.8 3.8 - - + -
186C PHE* 3.9 12.6 - - + -
197C GLN 2.9 22.4 + - - +
198C ALA 3.8 4.0 - - - +
200C VAL* 1.3 74.3 - - - +
202C LYS* 1.3 67.4 + - - +
203C ASN 3.3 0.2 + - - -
204C ALA 3.4 4.6 + - - +
206C LYS* 3.1 56.9 + - + +
207C VAL* 3.7 7.6 + - - +
208C GLY 5.1 0.2 - - - +
210C VAL* 3.9 31.2 - - + +
212C ILE* 3.7 17.5 - - + -
229C VAL* 4.6 6.1 - - + -
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Residues in contact with LYS 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ALA 2.9 14.4 + - - +
199C LEU* 2.8 15.5 + - + +
201C VAL* 1.3 77.8 - - - +
203C ASN* 1.3 63.9 + - - +
205C GLY* 3.3 11.1 + - - -
207C VAL* 4.2 19.9 - - + +
224C TYR* 4.0 21.9 - - + +
227C GLU* 3.4 28.3 + - - +
229C VAL* 4.9 3.4 - - + -
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Residues in contact with ASN 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL* 6.0 1.4 - - - +
174C GLU* 5.0 11.1 + - - +
199C LEU* 2.9 37.7 + - - +
200C VAL* 3.8 14.7 - - - +
202C LYS* 1.3 74.8 - - - +
204C ALA* 1.3 59.2 + - + +
205C GLY* 2.9 10.6 + - - -
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LEU* 3.6 31.0 - - + -
200C VAL 3.5 3.9 + - - +
201C VAL 3.4 3.7 + - - +
203C ASN* 1.3 76.8 - - - +
205C GLY* 1.3 63.3 + - - +
206C LYS* 3.6 26.8 + - + +
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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