Contacts of the helix formed by residues 199 - 210 (chain D) in PDB entry 1H5R
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 GLU 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D LEU* 5.3 2.2 + - - +
90D ALA* 4.0 2.6 - - - +
162D GLU* 4.0 18.8 - - + +
190D LEU* 3.7 10.5 - - - +
191D LYS 5.5 0.6 + - - -
193D SER* 2.6 32.6 + - - +
195D ARG* 3.0 41.1 + - - +
197D GLU* 3.3 19.3 + - - +
198D LEU* 1.3 72.4 - - - +
200D ILE* 1.3 65.0 + - - +
201D THR* 4.0 7.6 - - - +
202D ASP* 3.1 39.0 + - - +
203D ILE* 3.5 4.7 + - - +
1294D G1P 4.7 2.3 + - - -
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Residues in contact with ILE 200 (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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89D LEU* 3.9 25.4 - - + +
90D ALA* 4.3 2.3 - - - +
93D PHE* 4.5 2.0 - - + -
107D LEU* 3.2 35.0 - - + -
177D TYR* 3.3 46.9 - - + +
179D TYR* 3.4 24.7 - - + +
198D LEU 3.8 2.4 + - - -
199D GLU* 1.3 74.6 + - - +
201D THR* 1.3 68.6 + - - +
203D ILE* 3.1 22.4 + - + +
204D ASN* 2.9 25.1 + - - +
1294D G1P 4.3 11.6 + - - +
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Residues in contact with THR 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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147D GLY* 4.5 5.0 - - - -
160D LEU* 4.2 15.0 - - + +
161D GLU 4.0 5.6 - - - +
162D GLU* 2.4 52.7 + - - +
199D GLU* 4.3 6.3 - - - +
200D ILE* 1.3 82.0 + - - +
202D ASP* 1.3 58.6 + - - +
204D ASN* 3.3 8.7 + - - +
205D ARG* 3.0 48.3 + - - +
1294D G1P 3.9 2.9 + - - -
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Residues in contact with ASP 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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190D LEU* 3.6 22.3 - - + +
191D LYS 4.6 9.2 - - - +
193D SER* 4.8 5.9 - - - -
199D GLU* 3.1 30.4 + - - +
200D ILE 3.1 0.6 - - - -
201D THR* 1.3 78.2 - - - +
203D ILE* 1.3 65.3 + - - +
205D ARG* 3.3 26.8 + - - +
206D ILE* 3.0 28.8 + - - +
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Residues in contact with ILE 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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90D ALA* 3.0 40.4 - - + -
93D PHE* 4.3 11.9 - - + -
179D TYR* 3.8 21.1 - - + +
183D VAL* 3.7 24.7 - - + -
186D MET* 4.2 11.7 - - + -
187D ALA* 4.8 3.6 - - + -
190D LEU* 3.9 13.6 - - + +
199D GLU 3.5 6.9 + - - +
200D ILE* 3.1 17.6 + - + +
202D ASP* 1.3 76.3 - - - +
204D ASN* 1.3 64.3 + - - +
206D ILE* 3.2 13.7 + - - +
207D TYR* 3.1 28.4 + - + -
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Residues in contact with ASN 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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135D VAL* 3.8 17.2 - - + +
160D LEU* 3.6 19.1 - - + -
173D VAL* 4.6 7.3 - - - +
177D TYR* 3.7 21.2 - - - -
179D TYR* 2.5 39.0 + - - -
200D ILE* 2.9 23.7 + - - +
201D THR* 3.8 5.3 - - - +
202D ASP 3.2 0.4 - - - -
203D ILE* 1.3 75.8 - - - +
205D ARG* 1.3 57.0 + - - +
207D TYR* 3.3 7.8 + - - +
208D LEU* 2.8 27.9 + - - +
213D LEU* 3.7 12.0 - - + +
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Residues in contact with ARG 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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159D SER* 5.6 1.8 - - - -
160D LEU* 2.1 48.8 + - + +
161D GLU* 4.0 12.1 - - - +
162D GLU* 4.4 3.2 - - - +
201D THR* 3.0 31.4 + - - +
202D ASP* 3.7 25.7 + - - +
204D ASN* 1.3 73.3 - - - +
206D ILE* 1.3 61.0 + - - +
208D LEU* 3.4 10.2 - - + +
209D GLU* 2.7 37.3 + - + +
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Residues in contact with ILE 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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186D MET* 3.8 33.0 - - + +
190D LEU* 4.5 13.9 - - + -
202D ASP* 3.0 18.2 + - + +
203D ILE* 3.4 14.8 - - - +
205D ARG* 1.3 77.8 - - - +
207D TYR* 1.3 64.4 + - - +
209D GLU* 3.2 5.4 + - - +
210D GLN* 3.1 43.6 + - + +
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Residues in contact with TYR 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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132D GLY* 3.7 20.9 - - - -
133D ALA* 3.8 16.8 - - + -
179D TYR* 3.5 27.8 - + - -
180D ASP* 2.7 26.9 + - - -
182D ASP* 3.8 0.2 - - - +
183D VAL* 3.3 22.5 + - + +
186D MET* 3.4 23.6 - - + -
203D ILE* 3.1 29.3 + - + -
204D ASN* 3.7 6.5 - - - +
206D ILE* 1.3 78.6 - - - +
208D LEU* 1.3 64.3 + - - +
210D GLN* 3.2 7.6 + - - -
211D GLY 3.2 3.8 + - - -
212D ARG* 2.9 54.7 + - + -
213D LEU* 3.9 17.5 - - + +
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Residues in contact with LEU 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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157D ALA* 3.9 28.3 - - + +
158D ILE 3.8 23.6 - - - +
159D SER* 4.0 15.7 - - - +
160D LEU* 4.1 17.3 - - + +
204D ASN 2.8 18.6 + - - +
205D ARG* 3.0 15.5 + - + +
207D TYR* 1.3 73.2 - - - +
209D GLU* 1.3 63.7 + - - +
211D GLY* 2.9 15.5 + - - -
213D LEU* 3.7 30.2 - - + +
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Residues in contact with GLU 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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205D ARG* 2.7 23.5 + - + +
206D ILE* 3.8 4.9 - - - +
208D LEU* 1.3 74.3 - - - +
210D GLN* 1.3 58.8 + - + +
211D GLY 3.3 1.2 + - - -
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Residues in contact with GLN 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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186D MET* 4.0 9.3 - - - +
206D ILE* 3.1 35.5 + - + +
207D TYR* 3.2 9.1 + - - +
209D GLU* 1.3 75.5 - - + +
211D GLY* 1.3 60.8 + - - +
212D ARG* 2.8 48.3 + - + +
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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