Contacts of the helix formed by residues 173 - 188 (chain A) in PDB entry 1ORN
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ILE* 3.7 9.7 - - + +
170A PRO* 2.6 44.7 + - + +
172A GLU* 1.3 79.2 - - + +
174A TRP* 1.3 61.5 + - - -
175A SER 3.4 2.2 - - - -
176A ILE* 3.5 14.8 - - + +
177A THR* 2.7 37.5 + - - +
180A ARG* 5.5 3.5 + - - -
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Residues in contact with TRP 174 (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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134A PRO* 3.6 31.6 - - + -
135A ALA* 3.7 16.3 - - - +
136A ILE* 3.8 23.4 - - + +
166A MET* 3.4 58.1 + - + +
169A ILE* 2.7 34.8 + - + -
170A PRO 3.3 11.2 - - - -
171A LYS* 3.3 38.9 + - + +
172A GLU 3.6 0.2 - - - -
173A GLU* 1.3 77.8 - - - +
175A SER* 1.3 64.0 + - - +
177A THR* 3.8 2.1 - - - -
178A HIS* 3.1 23.6 + - - +
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 2.7 33.0 + - - -
132A GLY 5.3 1.6 + - - -
133A VAL 4.0 1.7 + - - -
134A PRO* 3.9 16.8 - - - +
135A ALA 4.0 5.6 + - - -
171A LYS 4.9 0.4 + - - -
172A GLU 5.3 1.7 + - - -
173A GLU 3.4 0.4 - - - -
174A TRP* 1.3 77.5 - - - +
176A ILE* 1.3 62.8 + - - +
178A HIS* 3.4 6.2 - - - +
179A HIS* 3.1 32.3 + - - -
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Residues in contact with ILE 176 (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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19A PRO 5.4 5.2 - - - +
21A ALA* 3.6 24.9 - - + +
172A GLU 5.4 1.1 + - - +
173A GLU* 3.5 23.0 + - + +
175A SER* 1.3 76.5 - - - +
177A THR* 1.3 64.5 + - - +
179A HIS* 3.3 8.3 + - + +
180A ARG* 2.9 70.1 + - + +
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Residues in contact with THR 177 (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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11A LEU* 3.7 29.6 - - + +
136A ILE* 6.1 0.4 - - - -
169A ILE* 3.3 37.5 - - + +
173A GLU* 2.7 29.4 + - - +
174A TRP 3.8 2.5 - - - -
176A ILE* 1.3 81.6 - - - +
178A HIS* 1.3 57.7 + - - +
180A ARG* 3.2 16.0 + - + +
181A MET* 2.9 33.9 + - + +
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 6.4 0.7 - - - -
125A VAL* 4.5 10.8 - - + +
128A SER* 5.6 4.5 - - - -
135A ALA 4.5 1.8 - - - +
136A ILE* 4.5 18.6 - - + +
137A ALA* 2.8 52.3 + - + +
139A ASP* 5.1 1.6 - - + -
142A VAL* 4.0 5.4 - - - +
174A TRP 3.1 13.9 + - - +
175A SER* 3.4 12.6 - - - +
177A THR* 1.3 77.5 - - - +
179A HIS* 1.3 88.5 + + - +
181A MET* 3.2 9.2 + - - +
182A ILE* 3.0 53.7 + - + +
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Residues in contact with HIS 179 (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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21A ALA* 3.5 29.2 + - - +
22A HIS* 3.7 11.5 - - - +
23A CYS* 3.7 34.2 + - + +
125A VAL* 6.1 0.4 - - - +
128A SER* 4.9 4.9 - - - -
129A VAL* 3.9 22.1 - - + +
175A SER* 3.1 23.5 + - - -
176A ILE* 3.3 10.8 + - - +
178A HIS* 1.3 98.5 + + - +
180A ARG* 1.3 63.3 + - - +
182A ILE* 3.3 9.7 + - + +
183A PHE* 3.0 22.7 + - - -
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 5.0 3.9 + - - +
14A MET* 4.5 17.2 - - + +
15A ALA* 3.4 40.0 + - - +
18A PHE* 3.8 22.2 + - - +
19A PRO* 5.3 8.5 + - - +
21A ALA* 3.7 11.2 - - + -
173A GLU* 5.5 5.1 + - - +
176A ILE* 2.9 55.6 + - + +
177A THR* 3.6 15.1 + - + +
179A HIS* 1.3 77.3 - - - +
181A MET* 1.3 58.2 + - + +
183A PHE* 3.4 2.5 + - - +
184A PHE* 2.9 29.3 + - - +
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.0 17.5 - - + -
14A MET* 3.9 22.2 - - - -
136A ILE* 5.9 0.7 - - - -
141A HIS* 4.7 1.2 - - - +
142A VAL* 3.9 27.6 - - + +
145A VAL* 4.0 21.4 - - + +
146A SER* 3.4 26.0 - - - +
151A PHE* 4.0 15.9 - - + -
165A LEU* 4.0 23.3 - - + -
177A THR* 2.9 25.0 + - + +
178A HIS* 3.6 7.2 - - - +
180A ARG* 1.3 74.6 - - - +
182A ILE* 1.3 64.1 + - - +
184A PHE* 3.3 2.8 + - - +
185A GLY* 3.0 20.3 + - - -
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 6.5 0.7 - - - -
139A ASP* 3.9 14.6 - - - +
141A HIS* 4.1 14.3 - - + +
142A VAL* 3.8 15.3 - - + -
178A HIS* 3.0 50.4 + - + +
179A HIS* 3.3 14.3 + - + +
181A MET* 1.3 77.9 - - - +
183A PHE* 1.3 61.0 + - + +
185A GLY 3.3 0.9 + - - -
186A ARG* 2.8 64.7 + - - +
18C PED 5.0 3.6 - - + +
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Residues in contact with PHE 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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18A PHE* 3.8 30.4 - + + -
20A ASP 4.7 1.6 - - - -
21A ALA* 3.7 18.4 - - + -
22A HIS* 3.2 49.4 - + - -
24A GLU* 3.6 31.6 - - + -
179A HIS* 3.0 20.3 + - - +
180A ARG 3.8 4.3 - - - +
182A ILE* 1.3 76.9 - - + +
184A PHE* 1.3 60.6 + - - +
186A ARG* 4.3 7.6 - - - -
187A TYR* 2.8 59.7 + + - +
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Residues in contact with PHE 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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13A GLU* 6.5 0.2 - - + -
14A MET* 3.8 36.3 - - + -
17A MET* 3.7 28.0 - - + -
18A PHE* 3.4 10.5 - + + -
145A VAL* 3.8 21.3 - - + -
149A LEU* 4.4 0.2 - - + -
180A ARG 2.9 18.5 + - - +
181A MET 3.5 4.7 - - - +
182A ILE 3.3 0.2 - - - -
183A PHE* 1.3 76.3 - - - +
185A GLY* 1.3 49.9 + - - +
188A HIS* 2.9 38.5 + + - +
189A CYS* 2.7 50.1 + - + -
199A CYS* 4.0 3.6 - - - -
201A LEU* 4.0 15.7 - - + -
300A SF4 3.6 24.0 - - - -
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Residues in contact with GLY 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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141A HIS* 3.6 4.2 - - - -
144A ARG* 2.9 30.8 + - - -
145A VAL* 3.6 19.0 - - - +
181A MET 3.0 12.0 + - - -
182A ILE 3.8 1.8 - - - -
184A PHE* 1.3 76.1 - - - +
186A ARG* 1.3 62.8 + - - +
189A CYS 3.3 11.4 - - - +
190A LYS* 3.3 9.9 + - - -
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Residues in contact with ARG 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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22A HIS 5.3 0.2 + - - -
24A GLU* 2.9 25.8 + - - +
45A ASP* 3.2 24.7 + - - -
141A HIS* 3.6 14.5 + - + -
182A ILE* 2.8 50.5 + - - +
183A PHE* 3.9 7.1 - - - +
185A GLY* 1.3 74.3 - - - +
187A TYR* 1.3 91.8 + - + +
190A LYS* 3.4 17.7 - - - +
18C PED 3.1 50.4 + - - +
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Residues in contact with TYR 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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18A PHE* 4.0 16.9 - + + -
24A GLU* 2.7 35.7 + - - -
183A PHE* 2.8 52.9 + + - +
186A ARG* 1.3 99.5 - - + +
188A HIS* 1.3 57.5 + - - +
190A LYS* 4.1 11.8 - - - +
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Residues in contact with HIS 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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17A MET* 3.8 15.2 - - + -
18A PHE* 4.2 15.0 - - + -
184A PHE* 2.9 45.1 + + + +
186A ARG 3.7 0.6 - - - -
187A TYR* 1.3 80.4 + - - +
189A CYS* 1.3 57.6 + - - +
190A LYS* 2.9 14.0 + - - +
193A SER 4.0 0.5 - - - +
194A PRO* 3.5 1.0 - - - +
195A GLN* 3.0 54.3 + - + +
198A SER* 4.2 11.7 - - - -
199A CYS* 3.5 30.5 - - - +
200A PRO* 4.2 2.6 - - + +
300A SF4 4.1 4.3 - - - -
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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