Contacts of the helix formed by residues 200 - 210 (chain C) in PDB entry 4XWY
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 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C GLY* 4.0 15.7 - - - -
16C PHE 4.3 1.1 - - - +
198C LEU* 3.2 23.3 + - + -
199C ASP* 1.3 83.3 + - - +
201C ASP* 1.3 60.9 + - - +
202C MET 3.2 7.8 + - - -
203C GLN* 3.2 3.3 + - - +
204C GLN* 3.0 25.9 + - - +
207C ARG* 5.4 0.3 + - - -
231C CYS* 3.9 14.1 - - - -
301C NDP 2.6 47.1 + - - +
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Residues in contact with ASP 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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14C ARG* 3.1 44.9 + - - +
200C THR* 1.3 74.3 - - - +
202C MET* 1.3 56.9 + - - +
204C GLN* 3.2 21.9 + - - +
205C LEU* 2.9 30.8 + - - +
301C NDP 3.8 4.2 + - - +
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Residues in contact with MET 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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99C GLY 3.6 24.7 - - - +
100C SER* 3.7 16.4 - - - -
101C LEU* 3.9 19.8 - - + +
167C TYR* 4.0 11.7 - - - -
200C THR* 3.2 2.6 + - - -
201C ASP* 1.3 77.0 - - - +
203C GLN* 1.3 58.2 + - - +
205C LEU* 3.3 12.5 + - + +
206C ALA* 2.9 27.0 + - - +
301C NDP 3.6 73.0 + - - +
302C 43O 3.8 20.4 - - - +
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Residues in contact with GLN 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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197C PRO* 4.1 7.2 - - - +
198C LEU 3.0 26.7 + - - +
199C ASP* 5.4 0.2 - - - +
200C THR* 3.2 12.3 + - - +
202C MET* 1.3 77.6 - - - +
204C GLN* 1.3 64.8 + - - +
206C ALA* 3.1 2.3 + - - +
207C ARG* 2.9 41.9 + - - +
219C LEU* 3.7 43.0 + - - +
228C LEU* 4.0 22.9 - - + +
301C NDP 2.9 25.8 - - - +
302C 43O 3.6 19.9 - - - +
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Residues in contact with GLN 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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200C THR 3.0 13.2 + - - +
201C ASP* 3.2 25.2 + - - +
203C GLN* 1.3 75.2 - - - +
205C LEU* 1.3 62.8 + - - +
207C ARG* 3.3 24.8 + - - +
208C GLU* 2.9 61.1 + - - +
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Residues in contact with LEU 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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101C LEU* 4.1 22.4 - - + +
102C GLY 5.2 3.8 - - - +
104C VAL* 5.8 0.4 - - + -
201C ASP 2.9 12.8 + - - +
202C MET* 3.3 13.9 - - + +
204C GLN* 1.3 75.7 - - - +
206C ALA* 1.3 56.4 + - - +
208C GLU* 4.9 3.1 - - - -
209C THR* 2.4 67.2 + - + +
303C SO4 6.0 2.0 - - - +
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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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101C LEU* 3.9 10.2 - - + +
164C TRP* 3.6 23.1 - - + -
202C MET 2.9 13.5 + - - +
203C GLN* 3.5 7.2 - - - +
205C LEU* 1.3 77.1 - - - +
207C ARG* 1.3 63.4 + - - +
209C THR* 4.5 0.4 - - - -
210C SER* 2.8 34.3 + - - -
216C ARG* 4.6 0.5 - - - +
219C LEU* 3.6 20.4 - - + +
302C 43O 3.9 10.1 - - - -
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Residues in contact with ARG 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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199C ASP* 4.6 8.1 + - - -
200C THR 5.5 0.2 + - - -
203C GLN* 2.9 43.2 + - - +
204C GLN* 3.5 32.0 - - - +
206C ALA* 1.3 75.9 - - - +
208C GLU* 1.3 63.2 + - + +
216C ARG* 3.4 28.8 - - - +
219C LEU* 3.6 30.8 + - + +
220C GLN* 3.4 55.4 + - + +
223C LYS* 3.7 32.0 - - - +
228C LEU* 4.4 4.0 - - - +
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Residues in contact with GLU 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 GLN* 2.9 53.0 + - + +
205C LEU* 4.3 2.1 - - - +
207C ARG* 1.3 88.8 + - + +
209C THR* 1.3 66.3 + - + +
210C SER 3.8 0.2 - - - -
216C ARG* 4.0 11.4 - - - +
220C GLN* 5.6 2.2 - - - +
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Residues in contact with THR 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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103C ASP* 5.5 0.9 - - - -
104C VAL* 3.4 15.6 - - - +
105C SER* 3.4 31.4 - - - -
205C LEU* 2.4 55.9 + - + +
208C GLU* 1.3 81.8 - - + +
210C SER* 1.3 70.9 + - - +
211C VAL* 3.3 2.3 + - - +
216C ARG* 4.6 0.2 - - - -
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Residues in contact with SER 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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104C VAL* 3.7 11.6 - - - +
162C LYS 5.8 0.9 - - - -
164C TRP* 3.1 31.7 + - - -
206C ALA 2.8 23.5 + - - -
208C GLU 3.8 0.4 - - - -
209C THR* 1.3 80.9 + - - +
211C VAL* 1.3 54.7 + - - +
212C ASP 4.6 0.9 - - - -
215C MET* 3.9 22.2 - - - +
216C ARG* 2.8 40.4 + - - +
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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