Contacts of the helix formed by residues 200 - 211 (chain C) in PDB entry 7UUT
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 ARG 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C ILE 5.2 0.2 - - - -
176C GLY* 4.2 16.6 - - - +
177C PRO* 5.2 3.4 - - - +
199C SER* 1.3 83.7 + - - +
201C PRO* 1.3 65.9 - - + +
203C CYS* 3.0 37.5 + - - +
204C VAL* 2.8 27.2 + - - +
340C LYS* 4.5 26.2 - - - +
341C PRO 3.8 9.8 + - - -
342C LYS* 3.8 52.5 - - + +
344C LEU 2.7 27.3 + - - -
345C ILE* 5.6 0.4 - - - +
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Residues in contact with PRO 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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199C SER 3.3 7.8 - - - +
200C ARG* 1.3 84.7 - - + +
202C VAL* 1.3 57.7 + - - +
204C VAL* 3.7 8.8 - - + +
205C ASP* 2.9 31.2 + - - +
342C LYS* 4.8 11.0 - - + +
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Residues in contact with VAL 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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200C ARG* 4.6 1.1 - - + -
201C PRO* 1.3 79.9 - - - +
203C CYS* 1.3 69.3 + - - +
205C ASP* 3.8 8.2 + - + +
206C ALA* 3.3 15.2 + - - +
318C LYS* 5.5 0.3 + - - -
321C THR* 4.1 15.5 - - + -
342C LYS 3.3 24.2 + - - +
343C ASP* 3.8 29.8 - - + +
344C LEU 4.2 2.0 - - - +
345C ILE* 3.6 22.3 - - + +
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Residues in contact with CYS 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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175C ILE* 3.3 38.6 - - + +
176C GLY* 4.7 1.6 - - - -
180C LEU* 3.6 4.4 - - - +
200C ARG* 3.0 51.4 + - + +
202C VAL* 1.3 81.6 - - - +
204C VAL* 1.3 59.8 + - - +
206C ALA* 3.2 2.1 + - - -
207C ALA* 2.8 30.1 + - - +
345C ILE* 4.1 23.8 - - - -
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Residues in contact with VAL 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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175C ILE* 4.0 15.3 - - + -
198C GLY 4.2 7.2 - - - +
199C SER* 4.2 9.0 - - - +
200C ARG 2.8 22.8 + - - +
201C PRO* 3.7 7.6 - - + +
203C CYS* 1.3 75.1 - - - +
205C ASP* 1.3 63.7 + - - +
207C ALA* 3.3 3.6 + - - +
208C LYS* 3.1 39.3 + - - +
215C ILE* 3.8 41.5 - - + -
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Residues in contact with ASP 205 (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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201C PRO 2.9 17.3 + - - +
202C VAL* 3.9 7.6 - - - +
204C VAL* 1.3 79.0 - - - +
206C ALA* 1.3 60.5 + - - +
208C LYS* 3.4 11.4 + - - +
209C TYR* 3.1 19.4 + - - +
318C LYS* 2.5 31.8 + - - -
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Residues in contact with ALA 206 (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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180C LEU* 3.7 28.5 - - + -
202C VAL 3.3 13.8 + - - +
203C CYS 3.2 2.3 + - - +
205C ASP* 1.3 75.6 - - - +
207C ALA* 1.3 66.1 + - - +
209C TYR* 3.1 3.5 + - - +
210C TYR* 2.9 39.4 + - + -
318C LYS* 4.1 20.9 - - + +
345C ILE* 4.0 7.9 - - + -
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Residues in contact with ALA 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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175C ILE* 4.2 9.2 - - + -
180C LEU* 3.4 16.3 - - + +
183C VAL* 3.8 6.8 - - + +
196C ALA* 4.0 16.4 - - + -
203C CYS 2.8 16.7 + - - +
204C VAL 3.3 5.8 + - - +
206C ALA* 1.3 75.9 - - - +
208C LYS* 1.3 60.6 + - - +
210C TYR* 3.2 2.9 + - - +
211C GLY 3.1 6.8 + - - -
212C ALA* 2.8 37.7 + - + +
215C ILE* 4.2 3.4 - - + -
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Residues in contact with LYS 208 (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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204C VAL* 3.1 25.6 + - + +
205C ASP* 3.7 11.0 - - - +
207C ALA* 1.3 75.9 - - - +
209C TYR* 1.3 63.2 + - - +
211C GLY* 3.3 10.9 + - - -
212C ALA 3.9 16.4 + - - +
215C ILE* 3.8 29.8 - - + -
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Residues in contact with TYR 209 (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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187C LYS* 6.1 0.5 - - - -
205C ASP 3.1 12.4 + - - +
206C ALA 3.1 8.4 + - - +
208C LYS* 1.3 79.1 - - - +
210C TYR* 1.3 93.7 + + - +
211C GLY* 3.5 0.7 + - - -
315C ASP* 3.6 29.9 + - + +
318C LYS* 3.4 40.6 - - + -
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Residues in contact with TYR 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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180C LEU* 3.9 22.0 - - + +
181C MET* 3.6 14.6 - - + -
183C VAL* 3.5 22.6 - - + +
184C ALA* 3.7 24.4 - - + +
187C LYS* 3.6 17.9 - - - +
206C ALA* 2.9 31.8 + - + +
207C ALA* 3.2 1.1 + - - +
209C TYR* 1.3 99.2 - + - +
211C GLY* 1.3 57.5 + - - +
314C VAL* 4.3 5.6 - - + -
315C ASP 2.6 33.6 + - - -
316C PRO* 3.3 17.3 + - - +
318C LYS* 3.6 15.1 + - + +
319C LEU* 3.7 21.1 + - + +
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Residues in contact with GLY 211 (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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313B ARG* 2.8 41.6 + - - -
183C VAL* 3.9 4.7 - - - -
187C LYS* 4.3 6.7 - - - -
194C ILE* 3.7 6.2 - - - +
207C ALA 3.1 1.2 + - - -
208C LYS 3.3 4.8 + - - -
209C TYR 3.3 5.2 - - - -
210C TYR* 1.3 80.2 - - - +
212C ALA* 1.3 66.8 + - - +
213C THR* 3.3 0.9 + - - +
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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