Contacts of the helix formed by residues 181 - 195 (chain B) in PDB entry 1IR1
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 SER 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLN* 3.7 35.4 - - - -
160A ASP* 4.6 2.2 + - - -
180B LEU* 1.3 75.4 - - - +
182B ALA* 1.3 63.8 + - - +
183B LYS* 3.7 6.2 + - - +
184B ASN* 3.3 27.6 + - - +
185B TYR* 3.0 21.8 + - - +
211B PHE 3.7 9.6 - - - -
212B MET* 3.9 1.6 - - - -
109S GLN* 2.9 19.1 + - - +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLN* 5.1 1.8 + - - -
157A VAL* 5.8 5.6 - - + -
181B SER* 1.3 72.7 - - - +
183B LYS* 1.3 63.8 + - - +
185B TYR* 3.2 4.9 + - - +
186B GLY 3.2 17.0 + - - -
211B PHE 4.5 0.8 + - - -
212B MET* 3.7 24.1 - - + +
216B ASP* 3.7 30.1 - - + +
217B ARG* 3.8 5.8 - - - +
220B PHE* 3.6 29.1 - - + +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 3.3 52.1 + - + +
163A ASN* 3.4 20.4 + - - -
165A TYR* 2.6 26.1 + - - +
181B SER* 3.3 4.4 + - - +
182B ALA* 1.3 79.3 - - - +
184B ASN* 1.3 59.3 + - - +
187B ARG* 3.0 30.0 + - - +
220B PHE* 3.8 11.7 - - + -
65S ARG* 5.2 8.7 + - - +
66S TYR* 2.7 46.5 + - + +
100S ARG* 5.7 2.4 - - - +
111S GLN* 3.8 14.6 + - - +
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Residues in contact with ASN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 4.3 16.7 - - + +
181B SER* 3.3 14.3 + - - +
183B LYS* 1.3 76.3 - - - +
185B TYR* 1.3 60.7 + - - +
187B ARG* 2.9 35.9 + - - +
188B ALA* 3.0 28.6 + - - +
104S PHE* 4.1 13.5 - - - -
109S GLN* 2.9 42.2 + - - +
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.6 44.4 + - + +
176B PRO 5.0 6.1 - - - -
177B LYS 4.8 0.8 + - - -
180B LEU* 4.0 18.8 - - + +
181B SER 3.0 9.9 + - - +
182B ALA 3.4 9.6 - - - +
184B ASN* 1.3 77.6 - - - +
186B GLY* 1.3 57.6 + - - +
188B ALA* 3.3 6.7 + - - +
189B VAL* 2.9 34.6 + - + +
202B ASP* 3.3 23.1 - - - -
203B ASP* 3.3 25.8 + - - +
206B VAL* 3.8 11.3 - - + +
212B MET* 3.7 33.0 - - + -
217B ARG* 3.8 13.9 - - + -
221B CYS* 3.9 15.3 - - - -
238B HIS* 4.1 4.7 - + - -
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA 3.2 9.8 + - - -
183B LYS 3.3 0.2 + - - -
185B TYR* 1.3 79.3 - - - +
187B ARG* 1.3 56.6 + - - +
189B VAL* 3.3 5.8 + - - -
190B TYR* 2.9 26.5 + - - +
220B PHE 4.0 16.2 - - - -
221B CYS* 4.5 2.8 - - - -
224B ALA* 3.1 12.3 - - - +
66S TYR* 3.3 20.0 - - - -
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LYS* 3.0 38.2 + - - +
184B ASN* 2.9 36.7 + - - +
185B TYR 3.2 0.2 - - - -
186B GLY* 1.3 76.1 - - - +
188B ALA* 1.3 62.6 + - - +
190B TYR* 3.5 4.6 + - - +
191B GLU* 3.3 28.7 + - + +
43S GLU* 2.9 31.5 + - - -
66S TYR* 3.5 19.8 + - + -
69S MET* 4.1 26.2 - - + +
100S ARG* 5.8 0.4 - - - +
102S ILE* 4.0 2.8 - - - +
104S PHE* 3.8 16.7 - - - -
111S GLN* 3.0 28.6 + - - -
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.2 23.1 - - + -
180B LEU* 5.3 3.6 - - + -
184B ASN 3.0 16.3 + - - +
185B TYR 3.7 4.0 - - - +
187B ARG* 1.3 78.0 - - - +
189B VAL* 1.3 62.6 + - - +
191B GLU* 3.5 1.0 + - - -
192B CYS* 3.0 24.3 + - - -
407B LEU* 4.8 5.2 - - + -
413B ASN* 3.1 27.7 + - - +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.1 15.0 - - + -
185B TYR* 2.9 22.4 + - + +
186B GLY* 3.3 7.6 + - - +
188B ALA* 1.3 74.1 - - - +
190B TYR* 1.3 67.1 + - - +
192B CYS* 3.3 1.9 + - - +
193B LEU* 3.0 38.0 + - + +
200B THR* 3.4 21.3 - - - +
221B CYS* 4.0 18.4 - - - +
224B ALA* 4.2 9.2 - - + -
238B HIS* 3.6 33.9 - - + +
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY 2.9 16.6 + - - +
187B ARG* 3.9 5.8 - - - +
189B VAL* 1.3 77.9 - - - +
191B GLU* 1.3 88.1 + - + +
193B LEU* 4.0 0.7 - - - +
194B ARG* 3.0 44.5 + - + +
224B ALA* 3.6 28.5 - - + +
227B LYS* 3.4 37.4 - - + -
228B ALA* 4.0 10.3 - - + -
231B GLU* 2.5 29.4 + - - -
66S TYR* 5.1 6.7 - + + -
67S TRP 3.7 20.0 - - - -
68S THR* 2.9 19.9 + - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ARG* 3.3 21.7 + - + +
188B ALA* 4.0 1.6 - - - +
190B TYR* 1.3 95.0 - - + +
192B CYS* 1.3 61.1 + - - +
194B ARG* 3.0 37.8 + - - +
195B GLY 3.7 0.2 + - - -
413B ASN* 3.6 22.2 - - + +
414B ALA* 3.2 29.9 + - - +
67S TRP 4.4 0.9 - - - +
68S THR* 3.7 1.6 - - - +
69S MET* 3.1 47.3 + - + +
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Residues in contact with CYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B CYS* 3.9 23.6 - - - -
174B ILE* 4.3 6.5 - - - -
188B ALA 3.0 23.7 + - - +
189B VAL 3.7 0.2 - - - +
190B TYR 3.3 0.2 - - - -
191B GLU* 1.3 77.4 - - - +
193B LEU* 1.3 62.3 + - - +
195B GLY 3.3 1.4 + - - -
197B LEU* 3.7 13.0 - - + +
200B THR* 3.6 19.1 - - + -
406B THR* 4.0 8.3 - - - -
407B LEU* 4.0 5.4 - - - -
413B ASN* 3.4 30.1 - - - -
417B ALA* 3.1 25.4 - - - +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 3.0 37.2 + - + +
192B CYS* 1.3 74.0 - - - +
194B ARG* 1.3 61.6 + - - +
195B GLY 3.0 6.4 + - - -
196B GLY 3.2 4.3 + - - -
197B LEU* 3.6 12.7 - - + +
198B ASP 3.8 23.1 - - - +
199B PHE 3.8 20.9 - - - +
200B THR* 3.8 10.1 - - + +
225B LEU* 3.9 24.7 - - + -
228B ALA* 3.6 15.3 - - + -
236B LYS* 2.9 42.3 + - + -
237B GLY 3.8 8.1 - - - +
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B TYR* 3.0 46.4 + - + +
191B GLU* 3.0 33.7 + - - +
193B LEU* 1.3 76.6 - - - +
195B GLY* 1.3 60.4 + - - +
196B GLY 3.4 0.4 + - - -
228B ALA* 3.9 6.0 - - + +
231B GLU* 3.0 34.5 + - - +
232B THR* 3.5 23.5 - - + +
414B ALA* 3.9 10.9 - - + +
68S THR* 3.6 21.9 - - - +
69S MET 4.9 1.2 + - - -
3T VAL* 4.5 5.7 - - - +
4T TRP* 2.9 59.7 + - - +
5T PRO 3.4 8.5 + - - -
6T THR* 3.6 4.6 - - - +
17T TYR* 4.3 1.7 + - - -
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Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B GLU 3.7 1.2 + - - -
192B CYS 3.3 3.6 + - - -
193B LEU 3.0 1.8 - - - -
194B ARG* 1.3 83.1 - - - +
196B GLY* 1.3 57.0 + - - +
414B ALA* 3.7 15.3 - - - -
417B ALA* 3.6 19.1 - - - -
418B VAL* 3.2 36.0 + - - +
421B ARG* 4.5 0.2 - - - +
4T TRP* 4.5 3.8 - - - -
17T TYR* 3.6 8.9 - - - -
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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