Contacts of the helix formed by residues 200 - 210 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D GLY* 3.8 20.0 - - - -
16D PHE 4.2 1.3 - - - +
198D LEU* 3.1 20.8 + - + -
199D ASP* 1.3 84.4 + - - +
201D ASP* 1.3 66.6 + - - +
202D MET 3.4 6.8 + - - -
203D GLN* 3.3 2.7 + - - +
204D GLN* 3.0 22.7 + - - +
231D CYS* 3.9 10.1 - - - -
301D NDP 2.7 49.4 + - - +
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Residues in contact with ASP 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 3.1 39.8 + - - +
200D THR* 1.3 76.5 - - - +
202D MET* 1.3 57.2 + - - +
204D GLN* 3.5 18.4 + - - +
205D LEU* 2.9 27.2 + - - +
301D NDP 3.7 10.6 + - - +
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Residues in contact with MET 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLY 3.4 33.7 - - - +
100D SER* 3.8 11.0 - - - -
101D LEU* 3.9 19.1 - - + +
167D TYR* 4.0 15.7 - - - -
200D THR* 3.1 5.6 + - - +
201D ASP* 1.3 75.0 - - - +
203D GLN* 1.3 67.7 + - - +
205D LEU* 3.1 10.0 + - + +
206D ALA* 3.0 22.7 + - - +
301D NDP 3.5 71.4 + - - +
302D 43O 3.9 17.5 - - - +
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Residues in contact with GLN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D TRP* 5.7 0.2 - - - -
197D PRO* 4.0 11.1 - - - +
198D LEU 2.9 32.0 + - - +
200D THR* 3.3 11.9 + - - +
202D MET* 1.3 79.2 - - - +
204D GLN* 1.3 56.5 + - - +
206D ALA* 3.2 4.5 + - - +
207D ARG* 2.9 44.2 + - - +
219D LEU* 3.4 35.0 - - - +
228D LEU* 4.2 18.6 - - + +
301D NDP 2.9 28.4 + - - +
302D 43O 3.9 18.5 - - - +
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Residues in contact with GLN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ASP* 6.0 0.2 - - - +
200D THR 3.0 16.1 + - - +
201D ASP* 3.6 18.3 - - - +
203D GLN* 1.3 76.3 - - - +
205D LEU* 1.3 59.0 + - - +
207D ARG* 3.4 26.4 - - - +
208D GLU* 2.8 63.5 + - - +
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.1 28.9 - - + +
102D GLY 4.2 9.4 - - - +
104D VAL* 5.3 0.4 - - + -
201D ASP 2.9 18.4 + - - +
202D MET* 3.1 9.6 + - + +
204D GLN* 1.3 77.2 - - - +
206D ALA* 1.3 56.3 + - - +
208D GLU* 5.0 1.6 - - - -
209D THR* 2.5 67.5 + - + +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 3.9 13.4 - - + +
104D VAL* 4.7 0.7 - - - -
164D TRP* 3.5 31.9 - - + -
202D MET 3.0 13.0 + - - +
203D GLN* 3.5 8.3 - - - +
205D LEU* 1.3 73.5 - - - +
207D ARG* 1.3 66.0 + - - +
210D SER* 2.8 34.4 + - - -
216D ARG* 4.4 0.2 - - - +
219D LEU* 3.5 10.3 - - + +
302D 43O 4.1 7.0 - - - -
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Residues in contact with ARG 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ASP* 4.8 6.9 + - - -
203D GLN* 2.9 40.7 + - - +
204D GLN* 3.4 37.8 + - - +
206D ALA* 1.3 75.5 - - - +
208D GLU* 1.3 66.6 + - + +
216D ARG* 3.1 27.6 - - - +
219D LEU* 3.3 22.0 + - + +
220D GLN* 3.7 50.8 + - + +
223D LYS* 3.7 45.0 - - - +
228D LEU* 4.3 3.4 - - - +
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Residues in contact with GLU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D GLN* 2.8 50.7 + - + +
205D LEU* 4.4 1.1 - - - +
207D ARG* 1.3 92.1 + - + +
209D THR* 1.3 67.1 + - + +
210D SER 3.7 0.7 - - - -
216D ARG* 3.4 16.9 + - - +
220D GLN* 5.5 2.2 - - - +
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Residues in contact with THR 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASP* 5.9 0.2 - - - -
104D VAL* 3.3 20.8 + - - +
105D SER* 3.5 20.7 + - - -
205D LEU* 2.5 47.7 + - + +
208D GLU* 1.3 85.8 - - + +
210D SER* 1.3 67.7 + - - +
211D VAL* 3.3 2.6 + - - -
216D ARG* 5.5 0.7 - - - -
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Residues in contact with SER 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 3.7 11.9 - - - +
164D TRP* 3.0 29.3 + - - -
206D ALA 2.8 23.0 + - - -
208D GLU 3.7 0.6 - - - -
209D THR* 1.3 76.7 + - - +
211D VAL* 1.3 64.8 + - - +
212D ASP 4.6 0.4 - - - -
215D MET* 3.5 26.3 - - - +
216D ARG* 3.3 30.0 + - - +
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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