Contacts of the helix formed by residues 201 - 216 (chain C) in PDB entry 6CXI
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 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ARG* 6.0 0.7 - - - +
62C GLY 6.0 1.1 - - - +
189C MET* 5.5 1.2 - - - +
199C PHE 3.6 1.1 - - - -
200C THR* 1.3 86.4 + - - +
202C THR* 1.3 61.9 + - - +
203C ALA* 3.6 22.7 - - + +
204C GLU* 3.1 28.9 + - - +
205C ARG* 2.9 28.3 + - - +
269D GLU* 3.7 25.4 + - - +
285E ASP* 6.1 4.3 - - - +
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Residues in contact with THR 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.8 40.8 + - + +
68C TYR* 4.2 23.7 + - + +
200C THR 4.2 0.8 + - - -
201C THR* 1.3 74.0 - - - +
203C ALA* 1.3 63.8 + - - +
205C ARG* 3.1 29.9 + - - +
206C GLU* 3.6 9.4 + - - +
269D GLU* 3.7 14.9 + - - -
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Residues in contact with ALA 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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61C ARG* 3.2 65.8 + - + +
62C GLY* 4.8 5.6 - - - +
64C LEU 5.7 0.4 - - - +
66C LEU* 4.6 6.6 - - + +
201C THR* 3.2 14.3 - - + +
202C THR* 1.3 80.6 - - - +
204C GLU* 1.3 60.7 + - - +
205C ARG 3.5 0.3 + - - -
206C GLU* 3.7 9.1 + - - +
207C ILE* 4.2 0.9 - - - +
269D GLU* 5.5 0.8 + - - +
286E VAL* 6.4 1.8 - - + -
287E ASP* 5.1 5.8 - - + -
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C SER 4.1 2.9 - - - +
199C PHE* 3.3 51.4 - - + -
200C THR* 3.3 7.6 + - - -
201C THR* 3.1 39.6 + - - +
203C ALA* 1.3 75.2 - - - +
205C ARG* 1.3 64.1 + - - +
206C GLU 3.2 1.3 - - - -
207C ILE* 3.2 28.0 + - + +
208C VAL* 3.6 10.4 + - - +
241C LEU* 5.4 1.3 - - + -
286E VAL* 3.4 33.7 - - + +
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Residues in contact with ARG 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.9 21.8 + - - -
182C ARG* 3.2 60.3 + - - +
185C THR* 3.7 18.6 - - + +
186C ASP* 2.9 30.5 + - - -
189C MET* 4.3 22.7 - - + -
199C PHE* 5.6 2.7 - - - -
201C THR 2.9 13.8 + - - +
202C THR* 3.1 27.6 + - - +
204C GLU* 1.3 78.2 - - - +
206C GLU* 1.3 58.8 + - + +
208C VAL* 2.9 29.5 - - - +
209C ARG* 3.5 3.6 + - - +
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Residues in contact with GLU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PRO* 5.3 1.0 - - - +
33C ILE* 4.1 11.8 - - - +
58C GLN* 3.0 39.5 + - - +
61C ARG* 3.5 17.5 + - - +
66C LEU* 4.2 8.7 - - - +
68C TYR* 3.6 23.3 + - - +
202C THR 3.6 8.0 + - - +
203C ALA 3.9 7.9 - - - +
204C GLU 3.2 0.2 - - - -
205C ARG* 1.3 78.2 - - + +
207C ILE* 1.3 58.7 + - + +
209C ARG* 3.1 36.4 + - - +
210C ASP* 2.8 27.6 + - - +
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Residues in contact with ILE 207 (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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61C ARG* 3.7 21.8 - - - +
199C PHE* 5.8 1.8 - - + -
203C ALA 4.2 3.4 - - - +
204C GLU* 3.2 23.9 + - + +
206C GLU* 1.3 77.3 - - + +
208C VAL* 1.3 64.0 + - + +
210C ASP* 3.1 8.4 + - + +
211C ILE* 2.9 23.2 + - + +
239C TYR* 3.7 17.9 - - + +
241C LEU* 3.4 45.1 - - + -
242C PRO* 3.9 22.9 - - + -
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C THR* 3.7 24.5 - - + +
188C LEU* 3.4 22.6 - - + +
189C MET* 4.5 12.1 - - + -
192C LEU* 3.9 28.5 - - + -
199C PHE* 4.3 18.6 - - + -
204C GLU 3.6 8.0 + - - +
205C ARG* 2.9 27.1 + - - +
207C ILE* 1.3 77.4 - - + +
209C ARG* 1.3 58.1 + - - +
211C ILE* 3.2 16.6 + - + +
212C LYS 2.9 23.2 + - - -
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Residues in contact with ARG 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLY* 6.2 4.2 - - - -
15C MET* 5.2 17.8 - - - +
58C GLN* 5.3 3.6 + - - -
156C ASP* 4.8 14.5 + - - -
182C ARG* 6.3 1.6 - - - +
185C THR* 3.8 27.6 - - + +
188C LEU* 5.2 0.2 - - - -
205C ARG* 4.0 6.1 - - - +
206C GLU* 3.1 45.3 + - - +
208C VAL* 1.3 83.1 - - - +
210C ASP* 1.3 57.8 + - - +
212C LYS* 3.2 18.5 + - - +
213C GLU* 2.9 62.8 + - + +
335C LYS* 5.7 0.2 - - - +
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Residues in contact with ASP 210 (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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206C GLU 2.8 12.5 + - - +
207C ILE* 3.1 15.2 + - + +
209C ARG* 1.3 76.3 - - - +
211C ILE* 1.3 65.7 + - - +
213C GLU* 3.2 24.3 + - - +
214C LYS* 2.8 43.0 + - - +
239C TYR* 2.8 18.2 + - - +
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Residues in contact with ILE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 5.4 4.7 - - + -
192C LEU* 5.6 3.4 - - + -
207C ILE* 2.9 24.8 + - + +
208C VAL* 3.3 21.5 - - + +
210C ASP* 1.3 75.2 - - - +
212C LYS* 1.3 59.4 + - - +
215C LEU* 2.8 42.1 + - + +
216C CYS* 3.6 2.8 + - - -
239C TYR* 3.6 44.0 - - + -
247C ILE* 4.5 22.2 - - + -
249C ILE* 3.6 32.3 - - + -
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Residues in contact with LYS 212 (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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181C GLY* 2.7 36.8 + - - -
184C LEU* 4.1 3.3 - - + +
185C THR* 2.9 20.3 + - - +
188C LEU* 4.2 8.3 - - + -
208C VAL 2.9 12.0 + - - +
209C ARG* 3.2 20.7 - - - +
211C ILE* 1.3 79.0 - - - +
213C GLU* 1.3 63.5 + - - +
216C CYS* 2.9 44.0 + - + +
256C CYS* 3.9 26.0 - - - -
257C PRO* 5.4 0.7 - - + -
302C THR* 5.4 0.2 - - - -
305C TYR* 3.0 38.4 + - + +
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Residues in contact with GLU 213 (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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15C MET* 5.9 0.2 - - - +
209C ARG* 2.9 51.7 + - + +
210C ASP* 3.2 18.2 + - - +
212C LYS* 1.3 79.3 - - - +
214C LYS* 1.3 59.9 + - + +
216C CYS 4.5 2.1 - - - +
301C GLY 5.8 2.2 - - - +
304C MET* 5.9 3.4 - - + +
305C TYR* 3.9 26.4 - - + +
335C LYS* 4.2 16.3 + - - -
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Residues in contact with LYS 214 (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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210C ASP* 2.8 39.5 + - - +
213C GLU* 1.3 78.1 - - + +
215C LEU* 1.3 80.8 + - + +
216C CYS 3.3 5.4 - - - +
237C LYS* 5.2 4.2 + - - -
239C TYR* 3.2 21.7 + - - -
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Residues in contact with LEU 215 (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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211C ILE* 2.8 32.0 + - + +
214C LYS* 1.3 91.7 - - + +
216C CYS* 1.3 60.8 + - - +
217C TYR* 4.0 4.0 + - - -
237C LYS* 3.9 35.7 + - + +
238C SER 5.3 2.7 - - - +
239C TYR* 3.5 45.3 - - + +
249C ILE* 4.2 13.9 - - + -
253C ARG* 3.0 31.9 + - - +
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Residues in contact with CYS 216 (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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188C LEU* 5.4 4.0 - - - -
211C ILE* 4.1 5.6 - - - -
212C LYS* 2.9 50.9 + - + +
213C GLU 4.5 3.1 - - - +
214C LYS 3.3 4.6 - - - +
215C LEU* 1.3 80.3 - - - +
217C TYR* 1.3 62.1 + - - +
253C ARG* 3.2 45.3 - - - +
256C CYS* 5.4 1.8 - - - -
257C PRO* 4.6 8.3 - - + -
305C TYR* 4.1 16.9 - - + +
306C PRO* 4.7 3.6 - - - +
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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
------------------------------------------------------------
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