Contacts of the helix formed by residues 181 - 193 (chain D) in PDB entry 1RHQ
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 GLY 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D LYS* 3.9 10.6 - - - +
179D ARG 2.9 2.0 + - - -
180D SER* 1.3 74.8 - - - +
182D THR* 1.3 67.5 + - - +
183D ASP* 3.0 5.2 - - - -
184D VAL* 2.9 36.5 + - - +
185D ASP* 3.4 7.7 + - - +
341E ARG* 5.1 1.8 - - - -
342E ASN 4.3 4.3 - - - -
343E SER 4.7 3.1 - - - -
346E GLY* 4.0 4.0 - - - -
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Residues in contact with THR 182 (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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169D ASN* 2.7 30.2 - - - +
170D ASN 3.9 1.6 - - - +
171D LYS* 3.6 7.3 - - - +
179D ARG* 2.9 65.2 + - - +
180D SER 3.8 0.2 - - - -
181D GLY* 1.3 74.6 - - - +
183D ASP* 1.3 56.0 + - - +
185D ASP* 2.9 14.4 - - - +
186D ALA* 2.6 34.3 + - - +
235D LEU* 3.5 15.0 - - + -
341E ARG* 4.8 2.0 - - - +
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Residues in contact with ASP 183 (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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169D ASN* 3.3 21.0 + - - -
171D LYS* 3.6 31.5 + - - +
181D GLY* 4.6 2.5 - - - -
182D THR* 1.3 74.1 - - - +
184D VAL* 1.3 58.0 + - + +
186D ALA* 3.8 7.1 - - - +
187D ALA* 2.6 38.7 + - + +
204D ASN* 5.4 1.0 - - - +
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Residues in contact with VAL 184 (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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181D GLY* 3.0 21.1 - - - +
183D ASP* 1.3 74.9 - - + +
185D ASP* 1.3 68.3 - - - +
187D ALA* 3.3 5.5 - - - +
188D ASN* 2.7 25.5 + - + +
344E LYS 3.2 23.6 - - - +
345E ASP* 2.6 28.9 - - - +
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Residues in contact with ASP 185 (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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179D ARG* 4.1 4.3 + - - -
181D GLY 3.6 4.8 - - - +
182D THR* 2.9 23.2 + - - +
184D VAL* 1.3 75.3 - - - +
186D ALA* 1.3 55.0 + - - +
187D ALA 2.4 1.9 + - - -
188D ASN* 2.3 37.7 + - - -
189D LEU* 2.9 12.0 + - - -
235D LEU* 4.1 9.8 - - + +
341E ARG* 4.5 0.9 - - - +
345E ASP 4.3 0.3 - - - +
346E GLY* 3.1 8.5 - - - -
347E SER* 2.8 45.6 + - - +
350E ILE* 3.6 28.4 - - + +
351E GLN* 4.8 2.3 + - - +
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Residues in contact with ALA 186 (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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167D ILE* 4.2 3.9 - - + +
169D ASN* 3.2 38.4 - - + +
182D THR 2.6 10.1 + - - +
183D ASP* 3.8 5.6 - - - +
185D ASP* 1.3 71.3 - - - +
187D ALA* 1.3 56.1 + - - +
189D LEU* 4.2 7.6 - - - -
190D ARG* 2.8 30.5 + - - +
202D ASN* 3.3 14.8 + - + +
235D LEU* 3.9 10.3 - - + +
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Residues in contact with ALA 187 (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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183D ASP 2.6 22.0 + - - +
184D VAL* 3.3 6.5 - - - +
185D ASP 2.4 10.0 + - - -
186D ALA* 1.3 68.7 - - - +
188D ASN* 1.3 61.3 + - - +
190D ARG* 3.5 9.1 - - - +
191D GLU* 3.1 22.0 + - - +
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Residues in contact with ASN 188 (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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184D VAL* 2.7 15.7 + - + +
185D ASP* 2.3 25.8 + - - +
187D ALA* 1.3 65.1 - - - +
189D LEU* 1.3 55.2 + - - +
191D GLU* 3.0 7.8 + - - +
192D THR* 2.7 38.1 + - - -
350E ILE* 5.6 0.4 - - + -
351E GLN* 4.7 12.3 + - - +
354E CYS* 3.3 33.0 - - - +
355E ALA 5.1 0.4 - - - +
358E LYS* 4.2 13.7 + - - +
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Residues in contact with LEU 189 (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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167D ILE* 3.9 21.5 - - + -
185D ASP 2.9 9.9 + - - +
186D ALA 4.2 3.8 - - - +
188D ASN* 1.3 74.8 - - - +
190D ARG* 1.3 65.8 + - - +
192D THR* 2.8 20.3 + - - -
193D PHE* 2.9 27.6 + - + +
233D VAL* 3.2 37.9 - - + -
235D LEU* 4.0 15.0 - - + -
350E ILE* 3.3 41.1 - - + +
353E LEU* 4.7 10.5 - - + -
354E CYS* 3.6 12.8 - - - -
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Residues in contact with ARG 190 (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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167D ILE* 3.6 10.5 - - - +
186D ALA 2.8 22.2 + - - +
187D ALA* 3.5 9.4 - - - +
188D ASN 3.2 0.2 - - - -
189D LEU* 1.3 76.7 - - - +
191D GLU* 1.3 58.4 + - - +
194D ARG* 3.1 26.0 + - + +
200D VAL* 3.8 32.1 + - + +
201D ARG* 4.7 0.6 - - - +
202D ASN* 2.5 53.4 + - - +
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Residues in contact with GLU 191 (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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187D ALA 3.1 12.8 + - - +
188D ASN* 3.0 10.2 + - - +
189D LEU 2.9 0.6 - - - -
190D ARG* 1.3 77.7 - - - +
192D THR* 1.3 63.2 + - - +
193D PHE 3.3 0.4 - - - -
194D ARG* 2.5 43.4 + - - +
195D ASN* 3.1 41.3 + - - +
358E LYS* 5.7 5.4 - - - +
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Residues in contact with THR 192 (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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188D ASN 2.7 26.3 + - - -
189D LEU* 2.8 8.9 + - - -
191D GLU* 1.3 73.3 - - - +
193D PHE* 1.3 60.5 + - + -
195D ASN* 3.8 6.7 + - - +
196D LEU* 3.4 23.0 - - + +
354E CYS* 3.0 33.0 - - - +
357E LEU* 3.8 39.7 - - + +
358E LYS* 3.6 15.9 + - + +
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Residues in contact with PHE 193 (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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165D CYS* 3.6 32.1 - - + -
189D LEU* 2.9 31.6 + - + +
192D THR* 1.3 75.6 - - + +
194D ARG* 1.3 63.1 + - - +
195D ASN 3.2 1.6 - - - -
196D LEU* 3.6 12.8 + - + +
198D TYR* 3.0 41.0 + + - +
200D VAL* 3.8 8.3 - - + -
231D VAL* 3.7 35.4 - - + -
233D VAL* 4.2 8.1 - - + -
279D LEU* 5.9 0.4 - - + -
281D ILE* 3.7 22.4 - - + -
353E LEU* 5.4 2.9 - - + -
357E LEU* 4.0 25.6 - - + -
366E PHE* 6.2 2.0 - + - -
400E PHE* 4.9 12.1 - + - -
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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