Contacts of the helix formed by residues 218 - 227 (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 THR 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C HIS* 4.1 16.2 - - + -
13C PRO* 4.1 6.5 - - + -
14C TYR* 4.0 27.6 - - + +
17C GLN* 4.0 19.5 - - - +
191C ALA* 4.8 1.0 + - + -
216C ASP* 3.7 7.1 - - + -
217C THR* 1.3 82.4 - - - +
219C PRO* 1.3 70.6 - - - +
220C ASP* 3.2 11.1 + - - -
221C ILE* 3.2 26.8 + - - +
222C LEU* 2.8 26.0 + - - +
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Residues in contact with PRO 219 (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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13C PRO* 4.9 9.9 - - + -
17C GLN* 4.9 5.6 - - - +
218C THR* 1.3 93.1 - - + +
220C ASP* 1.3 60.7 + - - +
222C LEU* 3.6 6.9 + - + +
223C GLN* 3.1 25.6 + - - +
304C LYS* 3.8 52.7 - - + +
305C PHE* 3.9 26.7 - - + +
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Residues in contact with ASP 220 (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* 5.5 4.6 + - - -
13C PRO* 5.3 5.3 - - - +
195C PRO* 3.2 29.5 - - + +
218C THR* 3.5 16.0 + - - -
219C PRO* 1.3 78.7 - - - +
221C ILE* 1.3 68.1 + - - +
223C GLN* 2.9 17.0 + - - +
224C TYR* 2.9 26.6 + - + -
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Residues in contact with ILE 221 (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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191C ALA 3.7 17.9 - - - +
194C GLY* 4.6 3.8 - - - -
195C PRO* 3.3 27.8 - - + +
214C CYS* 4.0 12.3 - - - -
215C PHE 3.2 23.8 - - - +
216C ASP* 3.5 25.1 - - + +
217C THR* 4.7 1.1 - - - -
218C THR* 3.2 22.8 + - - +
220C ASP* 1.3 77.4 - - - +
222C LEU* 1.3 57.6 + - - +
223C GLN 3.1 0.3 + - - -
224C TYR* 3.2 2.1 + - - +
225C VAL* 3.0 36.7 + - + +
230C ILE* 4.3 10.3 - - + +
233C THR* 4.0 14.8 - - + +
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Residues in contact with LEU 222 (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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217C THR* 3.0 54.3 - - + +
218C THR 2.8 15.7 + - - +
219C PRO* 3.6 6.3 - - + +
221C ILE* 1.3 76.1 - - + +
223C GLN* 1.3 59.9 + - - +
225C VAL* 3.8 7.6 - - + +
226C LYS* 3.3 20.4 + - - +
233C THR* 5.1 2.5 - - + -
284C VAL* 5.1 4.0 - - + -
289C LEU* 4.2 27.5 - - + +
292C TYR* 5.0 4.3 - - + -
293C LEU* 4.3 11.4 - - + -
303C ILE* 4.2 24.2 - - + -
304C LYS 4.5 6.3 - - - +
305C PHE* 4.4 16.5 - - + -
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Residues in contact with GLN 223 (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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219C PRO 3.1 12.7 + - - +
220C ASP* 2.9 12.8 + - - +
222C LEU* 1.3 74.7 - - - +
224C TYR* 1.3 70.0 + - + +
225C VAL 3.0 1.1 - - - -
226C LYS* 2.9 20.6 + - - +
227C GLU* 2.9 49.7 + - - +
305C PHE* 4.8 18.2 - - + +
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Residues in contact with TYR 224 (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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195C PRO* 3.8 30.5 - - + -
198C ALA* 3.4 29.4 - - + -
199C LEU* 3.3 28.4 - - - +
202C LYS* 4.0 24.7 + - + +
220C ASP* 2.9 30.1 + - + +
223C GLN* 1.3 78.0 - - + +
225C VAL* 1.3 56.7 + - - +
227C GLU* 3.8 12.6 - - - -
228C GLY 3.1 2.9 + - - -
229C VAL* 2.7 50.6 + - + +
230C ILE* 3.1 21.6 + - + -
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Residues in contact with VAL 225 (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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221C ILE* 3.0 28.6 + - + +
222C LEU* 3.8 7.6 - - + +
223C GLN 3.0 0.2 - - - -
224C TYR* 1.3 74.4 - - - +
226C LYS* 1.3 59.4 - - - +
228C GLY* 2.7 26.7 + - - -
230C ILE* 3.4 33.7 - - + +
232C ALA 5.2 2.0 - - - +
233C THR* 4.4 12.8 - - + +
284C VAL* 5.1 2.7 - - + +
285C THR* 4.3 4.0 - - - -
286C PRO* 3.6 38.3 - - + +
289C LEU* 4.3 17.7 - - + -
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Residues in contact with LYS 226 (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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222C LEU 3.3 12.1 + - - +
223C GLN* 2.9 20.9 + - - +
225C VAL* 1.3 82.5 - - - +
227C GLU* 1.3 62.8 + - + +
228C GLY* 3.4 0.5 + - - -
286C PRO* 5.2 6.4 - - - +
289C LEU* 4.1 20.3 - - + +
290C ASP* 5.6 5.4 + - - -
305C PHE* 4.7 21.5 - - + -
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Residues in contact with GLU 227 (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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202C LYS* 3.4 32.6 + - - -
207C VAL* 5.5 2.6 - - - +
223C GLN* 2.9 49.0 + - - +
224C TYR* 3.8 8.5 - - - +
226C LYS* 1.3 76.8 - - + +
228C GLY* 1.3 61.3 + - - +
229C VAL* 3.7 20.7 - - + +
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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