Contacts of the helix formed by residues 172 - 194 (chain A) in PDB entry 1R42
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 VAL 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.5 21.3 - - + +
127A TYR* 6.0 0.2 - - + -
130A GLY* 3.9 23.3 - - - -
131A LYS 4.2 4.5 - - - +
168A TRP* 3.0 69.3 + - + +
171A GLU* 1.3 82.4 - - + +
173A GLY* 1.3 75.4 + - - +
174A LYS 3.2 2.0 - - - -
175A GLN* 2.8 25.2 + - - +
176A LEU* 3.2 11.0 + - + +
502A SER* 5.1 1.3 - - - -
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TRP 3.3 5.0 + - - -
169A ARG* 3.4 14.5 + - - -
172A VAL* 1.3 85.0 - - - +
174A LYS* 1.3 57.5 + - - +
176A LEU* 2.9 32.9 + - - +
177A ARG 3.1 5.4 + - - -
498A CYS* 3.6 24.3 - - - +
502A SER* 4.7 5.8 - - - -
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG 3.3 7.7 + - - +
170A SER* 3.3 33.8 + - - +
171A GLU 4.9 0.7 - - - +
172A VAL 3.2 0.6 - - - -
173A GLY* 1.3 74.8 - - - +
175A GLN* 1.3 62.3 + - + +
177A ARG* 3.4 4.1 + - - +
178A PRO* 3.2 19.2 - - - +
496A THR* 3.1 50.2 - - + +
497A TYR* 3.6 35.1 + - + +
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Residues in contact with GLN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 4.3 28.1 - - + +
130A GLY* 5.6 3.8 - - - -
171A GLU* 3.1 25.5 + - - +
172A VAL* 2.8 20.7 + - - +
174A LYS* 1.3 77.3 - - + +
176A LEU* 1.3 63.2 + - - +
178A PRO* 3.3 11.6 - - - +
179A LEU* 3.7 16.0 - - + +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A MET* 3.9 28.0 - - + +
126A ILE* 3.1 43.5 - - + -
127A TYR* 5.2 4.3 - - + -
172A VAL* 3.2 8.9 + - + +
173A GLY* 2.9 15.4 + - - +
175A GLN* 1.3 82.5 - - - +
177A ARG* 1.3 56.8 + - - +
178A PRO 3.4 0.2 - - - -
179A LEU* 3.2 7.5 + - + +
180A TYR* 2.8 32.1 + - - +
498A CYS* 4.4 0.7 - - - -
501A ALA* 3.5 41.3 - - + +
502A SER* 4.7 2.9 - - - +
507A SER* 4.3 11.2 - - - +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLY 3.1 6.0 + - - +
174A LYS 3.6 7.6 - - - +
176A LEU* 1.3 77.7 - - - +
178A PRO* 1.3 71.9 - - + +
180A TYR* 3.3 1.4 + - - +
181A GLU* 2.6 55.2 + - - +
470A LYS* 2.6 33.7 + - - +
473A TRP* 3.5 25.5 - - - +
474A MET* 4.0 3.0 - - - +
495A GLU* 2.8 51.3 + - - +
496A THR* 3.7 13.5 - - - +
497A TYR 3.1 18.8 + - - +
498A CYS* 3.7 20.6 - - + -
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Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS 3.2 13.2 - - - +
175A GLN* 3.3 13.5 - - - +
177A ARG* 1.3 99.1 - - + +
179A LEU* 1.3 64.5 + - + +
181A GLU* 3.5 10.4 + - - +
182A GLU* 3.4 21.2 + - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 4.6 11.9 - - - +
119A ILE* 3.6 25.9 - - + +
122A THR* 3.8 32.1 - - + +
123A MET* 3.7 25.8 - - + +
126A ILE* 4.9 3.6 - - + -
175A GLN* 3.7 19.3 - - + +
176A LEU* 3.2 15.1 + - + +
178A PRO* 1.3 79.3 - - + +
180A TYR* 1.3 59.4 + - - +
182A GLU* 3.3 6.1 + - - +
183A TYR* 2.9 29.1 + - - +
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A MET* 3.8 16.1 - - - -
176A LEU 2.8 21.0 + - - +
177A ARG 3.7 3.6 - - - +
179A LEU* 1.3 74.2 - - - +
181A GLU* 1.3 62.1 + - - +
183A TYR* 3.2 38.1 + + - +
184A VAL* 3.0 35.8 + - + +
459A TRP* 4.2 20.1 - + - -
460A ARG* 4.1 18.9 + - - +
463A VAL* 5.2 1.3 - - + -
464A PHE* 4.2 8.4 - + - -
473A TRP* 3.8 19.3 - + + -
498A CYS* 4.1 18.4 - - - -
501A ALA* 4.4 5.6 - - + -
506A VAL* 3.6 41.2 + - + +
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Residues in contact with GLU 181 (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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177A ARG* 2.6 49.9 + - - +
178A PRO* 3.8 9.9 - - - +
179A LEU 3.3 0.2 - - - -
180A TYR* 1.3 72.8 - - - +
182A GLU* 1.3 68.7 + - - +
184A VAL* 3.1 20.1 - - - +
185A VAL* 3.4 9.4 + - - +
470A LYS* 3.2 34.3 + - + +
473A TRP* 3.4 29.6 - - + -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 2.7 50.5 + - - +
119A ILE* 3.3 21.2 - - + +
178A PRO 3.4 10.0 + - - +
179A LEU* 3.3 7.0 + - - +
181A GLU* 1.3 77.7 - - - +
183A TYR* 1.3 62.7 + - - +
185A VAL* 3.2 12.2 + - + +
186A LEU* 3.1 30.3 + - + +
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.4 5.6 - - + -
119A ILE* 4.0 15.8 - - + +
120A LEU* 3.8 17.7 - - + -
123A MET* 3.6 17.9 - - + -
179A LEU 2.9 14.4 + - - +
180A TYR* 3.3 49.5 + + - +
181A GLU 3.1 0.2 - - - -
182A GLU* 1.3 74.0 - - - +
184A VAL* 1.3 76.8 + - + +
186A LEU* 3.5 5.1 + - - +
187A LYS* 2.9 43.3 + - + +
199A TYR* 3.4 15.0 - + - -
203A TRP* 4.3 6.1 - - - -
460A ARG* 4.9 0.5 + - - -
464A PHE* 4.3 8.9 - + - -
506A VAL 4.6 1.6 + - - -
509A ASP* 2.6 37.6 + - + +
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Residues in contact with VAL 184 (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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180A TYR* 3.0 30.3 + - + +
181A GLU* 3.1 17.9 - - - +
183A TYR* 1.3 85.2 - - + +
185A VAL* 1.3 61.6 + - + +
187A LYS* 3.7 3.8 - - - +
188A ASN* 2.7 44.7 + - - +
463A VAL* 4.0 14.1 - - + +
464A PHE* 3.6 31.4 - - + -
470A LYS* 4.8 3.4 - - - +
473A TRP* 4.3 12.3 - - + -
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Residues in contact with VAL 185 (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 GLU 3.5 14.4 - - - +
182A GLU* 3.3 12.1 - - + +
184A VAL* 1.3 85.5 - - + +
186A LEU* 1.3 71.7 + - + +
188A ASN* 3.8 5.2 - - - +
189A GLU* 3.0 34.2 + - - +
192A ARG* 5.1 2.2 + - - +
470A LYS* 4.3 14.6 - - - +
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Residues in contact with LEU 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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108A LEU* 4.3 8.6 - - + +
112A LYS* 4.0 33.0 - - + +
115A ARG* 4.1 11.9 - - + -
116A LEU* 4.1 37.5 - - + +
119A ILE* 4.1 22.4 - - + -
182A GLU* 3.1 21.9 + - + +
183A TYR 3.9 3.4 - - - +
185A VAL* 1.3 91.5 - - + +
187A LYS* 1.3 58.2 + - - +
189A GLU* 3.4 13.6 - - + +
190A MET* 3.0 25.5 + - - +
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Residues in contact with LYS 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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105A SER* 5.2 5.1 + - - -
116A LEU* 3.9 35.0 - - + +
120A LEU* 4.5 6.2 - - - +
183A TYR* 2.9 36.6 + - + +
184A VAL* 3.7 6.1 - - - +
186A LEU* 1.3 75.2 - - - +
188A ASN* 1.3 60.0 + - - +
189A GLU 3.1 1.3 - - - -
190A MET* 3.2 10.7 + - + +
191A ALA* 2.9 28.9 + - - +
199A TYR* 2.8 72.1 + - + +
509A ASP* 3.0 18.5 + - - -
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Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 2.7 29.2 + - - +
185A VAL* 3.8 5.1 - - - +
187A LYS* 1.3 72.7 - - - +
189A GLU* 1.3 57.0 + - - +
191A ALA* 3.4 1.0 + - - +
192A ARG* 2.9 52.1 + - - +
198A ASP* 3.0 11.5 - - - +
199A TYR* 2.7 35.3 + - - +
463A VAL 4.7 2.0 + - - -
464A PHE* 2.9 32.4 + - - +
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Residues in contact with GLU 189 (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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108A LEU* 4.1 17.3 - - + +
112A LYS* 2.6 34.1 + - - +
185A VAL* 3.0 24.9 + - - +
186A LEU* 3.4 16.5 - - - +
188A ASN* 1.3 76.9 - - - +
190A MET* 1.3 68.3 + - - +
192A ARG* 3.9 22.1 + - - +
193A ALA* 3.1 25.3 + - + +
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Residues in contact with MET 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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104A GLY* 3.1 30.3 - - - +
105A SER* 3.8 10.1 - - - +
107A VAL* 4.0 9.0 - - - -
108A LEU* 4.2 14.5 - - + +
116A LEU* 5.5 0.9 - - + -
186A LEU 3.0 14.4 + - - +
187A LYS* 3.2 18.6 + - + +
189A GLU* 1.3 76.9 - - - +
191A ALA* 1.3 84.2 + - - +
193A ALA* 3.3 2.1 + - - +
194A ASN* 2.7 52.1 + - - +
199A TYR* 4.7 7.9 - - - -
202A TYR* 3.2 48.0 - - + +
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Residues in contact with ALA 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 LYS 2.9 17.3 + - - +
188A ASN 3.6 2.2 - - - +
190A MET* 1.3 91.9 - - + +
192A ARG* 1.3 62.5 + - - +
194A ASN* 3.0 9.8 + - - +
195A HIS 3.3 0.5 + - - -
196A TYR* 3.0 25.1 + - + +
198A ASP* 3.5 10.3 - - - +
199A TYR* 3.5 30.1 - - - +
202A TYR* 4.2 6.7 - - + -
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Residues in contact with ARG 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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185A VAL* 5.1 2.2 + - - +
188A ASN* 2.9 49.7 + - - +
189A GLU* 3.9 29.2 + - - +
191A ALA* 1.3 72.4 - - - +
193A ALA* 1.3 56.2 + - - +
195A HIS* 2.7 28.2 + - - -
196A TYR 3.1 10.4 + - - +
197A GLU 3.5 22.1 + - - +
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Residues in contact with ALA 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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107A VAL* 3.8 33.4 - - + +
108A LEU* 6.2 0.9 - - + -
189A GLU* 3.1 17.5 + - + +
190A MET 3.7 3.6 - - - +
192A ARG* 1.3 79.0 - - - +
194A ASN* 1.3 58.2 + - - +
195A HIS* 3.2 18.0 + - - -
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Residues in contact with ASN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 5.4 2.4 - - - +
103A ASN* 3.8 14.4 + - - +
104A GLY 2.9 38.7 + - - -
107A VAL* 3.4 7.7 - - - +
190A MET* 2.7 46.6 + - + +
191A ALA 3.0 10.0 + - - +
192A ARG 3.0 1.0 - - - -
193A ALA* 1.3 76.0 - - - +
195A HIS* 1.3 77.4 + - - +
196A TYR* 3.4 20.5 - - + -
202A TYR* 4.9 2.0 - - - -
801A NAG 4.9 6.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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