Contacts of the helix formed by residues 181 - 195 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 1.3 76.8 - - - +
182A ALA* 1.3 64.7 + - - +
183A LYS* 3.7 5.5 + - - +
184A ASN* 3.3 27.0 + - - -
185A TYR* 3.0 22.9 + - - +
211A PHE 3.7 9.4 - - - -
212A MET* 3.9 1.3 - - - -
156D GLN* 3.6 34.9 - - - -
160D ASP* 4.6 2.1 + - - -
109V GLN* 2.9 20.2 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A SER* 1.3 74.2 - - - +
183A LYS* 1.3 62.1 + - - +
185A TYR* 3.4 3.6 + - - +
186A GLY 3.2 16.6 + - - -
211A PHE 4.5 0.4 + - - -
212A MET* 3.7 24.2 - - + +
216A ASP* 3.6 31.4 - - + -
217A ARG* 3.8 11.9 - - - +
220A PHE* 3.6 23.4 - - + +
156D GLN* 4.9 1.6 + - - -
157D VAL* 5.8 4.9 - - + -
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 3.3 3.7 + - - +
182A ALA* 1.3 75.2 - - - +
184A ASN* 1.3 61.6 + - - +
187A ARG* 3.0 31.8 + - - +
220A PHE* 3.9 13.0 - - + -
160D ASP* 3.5 41.2 + - + +
163D ASN* 3.4 19.4 + - - -
165D TYR* 2.7 31.0 + - - +
65V ARG* 5.1 8.8 + - - +
66V TYR* 2.7 44.6 + - + +
100V ARG* 5.6 2.8 - - - +
111V GLN* 3.6 20.2 + - - +
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Residues in contact with ASN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.0 17.9 - - + +
181A SER* 3.3 12.6 + - - +
183A LYS* 1.3 75.7 - - - +
185A TYR* 1.3 61.3 + - - +
187A ARG* 2.9 34.9 + - - +
188A ALA* 3.0 28.8 + - - +
104V PHE* 4.1 13.8 - - - -
109V GLN* 2.9 42.5 + - - +
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 3.6 37.9 + - + +
176A PRO 5.0 7.2 - - - -
177A LYS 4.9 0.6 + - - -
180A LEU* 4.0 23.7 - - + +
181A SER 3.0 14.3 + - - +
182A ALA 3.4 6.5 - - - +
184A ASN* 1.3 77.8 - - - +
186A GLY* 1.3 57.1 + - - +
188A ALA* 3.3 5.7 + - - +
189A VAL* 3.0 34.5 + - + +
202A ASP* 3.3 40.7 - - - -
203A ASP 3.4 9.0 + - - -
206A VAL* 3.9 10.8 - - + +
212A MET* 3.6 30.3 - - + -
217A ARG* 3.8 15.9 - - + -
221A CYS* 4.0 12.3 - - - -
238A HIS* 4.1 4.0 - + - -
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ALA 3.2 8.8 + - - -
183A LYS 3.3 0.4 + - - -
185A TYR* 1.3 76.1 - - - +
187A ARG* 1.3 60.0 + - - +
189A VAL* 3.3 5.3 + - - -
190A TYR* 3.0 25.8 + - - +
220A PHE 4.2 9.6 - - - -
221A CYS* 4.5 3.5 - - - -
224A ALA* 3.1 18.6 - - - +
66V TYR* 3.1 21.7 - - - -
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS* 3.0 37.6 + - - +
184A ASN* 2.9 36.2 + - - +
185A TYR 3.2 0.2 - - - -
186A GLY* 1.3 77.8 - - - +
188A ALA* 1.3 63.7 + - - +
190A TYR* 3.5 4.8 + - - +
191A GLU* 3.3 28.8 + - + +
43V GLU* 3.0 31.7 + - - -
66V TYR* 3.4 17.9 + - + -
69V MET* 4.0 28.2 - - + +
100V ARG* 5.8 0.2 - - - +
102V ILE* 4.0 2.8 - - - +
104V PHE* 3.7 17.7 - - - -
111V GLN* 2.9 29.6 + - - -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 4.1 24.0 - - + -
180A LEU* 5.0 4.7 - - + -
184A ASN 3.0 16.1 + - - +
185A TYR 3.6 4.7 - - - +
187A ARG* 1.3 79.4 - - - +
189A VAL* 1.3 62.5 + - - +
191A GLU* 3.5 1.5 + - - -
192A CYS* 3.1 23.1 + - - -
407A LEU* 4.7 5.4 - - + -
413A ASN* 3.2 26.4 + - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 4.1 15.9 - - + -
185A TYR* 3.0 21.9 + - + +
186A GLY* 3.6 7.2 - - - +
187A ARG 3.3 0.2 - - - -
188A ALA* 1.3 74.3 - - - +
190A TYR* 1.3 67.6 + - - +
192A CYS* 3.2 1.6 + - - +
193A LEU* 3.0 39.3 + - + +
200A THR* 3.4 19.3 - - - +
221A CYS* 4.1 16.6 - - - +
224A ALA* 4.1 10.5 - - + -
238A HIS* 3.6 34.3 - - + +
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Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLY 3.0 16.9 + - - +
187A ARG* 3.9 4.7 - - - +
189A VAL* 1.3 76.3 - - - +
191A GLU* 1.3 89.0 + - + +
193A LEU* 3.4 0.9 + - - +
194A ARG* 3.0 42.9 + - + +
224A ALA* 3.7 20.4 - - + -
227A LYS* 3.6 34.7 - - + -
228A ALA* 3.9 20.9 - - + -
231A GLU* 2.5 29.7 + - - -
66V TYR* 5.1 7.4 - + + -
67V TRP 3.8 19.5 - - - -
68V THR* 2.8 22.0 + - - +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ARG* 3.3 22.9 + - + +
188A ALA* 3.8 2.0 - - - +
190A TYR* 1.3 96.1 - - + +
192A CYS* 1.3 63.0 + - - +
194A ARG* 3.0 37.2 + - - +
195A GLY 3.7 0.3 + - - -
413A ASN* 3.6 22.9 - - + +
414A ALA* 3.3 30.6 + - - +
67V TRP 4.4 0.7 - - - +
68V THR* 3.9 1.2 - - - +
69V MET* 3.0 48.8 + - + +
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Residues in contact with CYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A CYS* 3.9 24.0 - - - -
174A ILE* 4.2 9.4 - - - -
188A ALA 3.1 23.5 + - - +
189A VAL 3.2 0.6 + - - +
191A GLU* 1.3 77.2 - - - +
193A LEU* 1.3 63.5 + - - +
195A GLY 3.2 2.1 + - - -
197A LEU* 3.8 13.8 - - + +
200A THR* 3.5 20.2 - - + -
406A THR* 4.1 7.2 - - - -
407A LEU* 4.2 2.7 - - - -
413A ASN* 3.4 30.1 - - - -
417A ALA* 3.2 24.4 - - - +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.0 37.0 + - + +
192A CYS* 1.3 78.0 - - - +
194A ARG* 1.3 60.9 + - - +
195A GLY 3.1 1.4 + - - -
196A GLY 3.3 3.6 + - - -
197A LEU* 3.5 18.1 - - - +
198A ASP 3.8 9.9 - - - +
199A PHE* 3.7 28.7 - - - +
200A THR* 3.8 11.0 - - + +
225A LEU* 3.8 29.4 - - + -
228A ALA* 3.5 15.9 - - + -
236A LYS* 2.8 39.8 + - + -
237A GLY 3.9 5.4 - - - +
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Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A TYR* 3.0 46.2 + - + +
191A GLU* 3.0 31.8 + - - +
192A CYS 3.3 0.2 - - - -
193A LEU* 1.3 76.0 - - - +
195A GLY* 1.3 61.6 + - - +
196A GLY 3.4 0.6 + - - -
228A ALA* 3.9 5.5 - - + +
231A GLU* 2.9 31.2 + - - +
232A THR* 3.6 23.1 - - + +
414A ALA* 3.9 12.2 - - + +
3S VAL* 4.4 5.7 - - - +
4S TRP* 2.7 60.3 + - + +
5S PRO 3.4 10.5 + - - -
6S THR* 3.7 4.0 - - - +
17S TYR* 4.4 2.4 + - - -
68V THR* 3.6 23.4 - - - +
69V MET 4.9 1.4 + - - -
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU 3.7 0.8 + - - -
192A CYS 3.2 3.8 + - - -
193A LEU 3.1 1.8 - - - -
194A ARG* 1.3 82.1 - - - +
196A GLY* 1.3 56.0 + - - +
414A ALA* 3.7 16.6 - - - -
417A ALA* 3.5 20.0 - - - -
418A VAL* 3.2 36.7 + - - +
4S TRP* 4.6 2.2 - - - -
17S TYR* 3.7 8.6 - - - -
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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