Contacts of the helix formed by residues 180 - 193 (chain A) in PDB entry 4OR9
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLU* 2.9 34.6 + - - -
175A CYS* 2.9 16.8 + - - +
176A LYS* 4.3 6.5 - - - +
179A TYR* 1.3 82.1 - - - +
181A GLU* 1.3 64.2 + - - +
182A ARG* 3.3 15.1 + - - +
183A VAL* 3.2 13.2 + - - +
184A TYR 3.2 8.7 + - - -
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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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172A LYS* 4.6 20.7 + - + -
176A LYS* 4.7 8.4 - - + +
180A SER* 1.3 73.7 - - - +
182A ARG* 1.3 60.5 + - - +
184A TYR* 3.2 19.5 + - + -
185A GLU* 2.8 34.2 + - + +
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Residues in contact with ARG 182 (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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67A GLU* 3.2 21.8 + - - +
68A GLU* 4.5 10.1 + - - -
71A LEU* 3.5 29.9 - - + +
180A SER* 3.1 10.2 + - - +
181A GLU* 1.3 79.3 - - - +
183A VAL* 1.3 56.5 - - - +
185A GLU* 3.4 5.7 + - - +
186A ALA* 2.9 29.1 + - - +
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Residues in contact with VAL 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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67A GLU* 4.1 14.6 - - + -
70A ALA* 4.1 13.9 - - + -
71A LEU* 3.9 19.3 - - + -
74A ILE* 3.8 17.5 - - + -
136A ILE* 4.1 19.3 - - + -
175A CYS* 4.4 5.6 - - - -
179A TYR* 3.7 30.5 - - + -
180A SER* 3.2 15.5 + - - +
182A ARG* 1.3 74.8 - - - +
184A TYR* 1.3 60.4 + - - +
186A ALA* 3.3 3.3 + - - +
187A CYS* 2.9 28.4 + - - -
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Residues in contact with TYR 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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163A ARG* 3.6 15.7 + - + +
166A THR* 2.7 32.3 + - - -
167A GLU* 3.9 5.4 + - - +
171A PHE* 4.1 2.7 - + - -
172A LYS* 3.6 59.0 - - + +
175A CYS* 3.6 28.2 - - + +
180A SER 3.2 5.0 + - - +
181A GLU* 3.2 19.9 + - + +
183A VAL* 1.3 80.2 - - - +
185A GLU* 1.3 68.6 + - + +
187A CYS* 3.0 6.5 + - - +
188A MET* 3.0 52.0 + - + +
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Residues in contact with GLU 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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163A ARG* 4.8 7.8 + - - -
181A GLU* 2.8 24.0 + - + +
182A ARG* 3.8 6.3 - - - +
184A TYR* 1.3 80.5 - - + +
186A ALA* 1.3 64.0 + - - +
188A MET* 3.1 22.0 + - - +
189A GLU* 3.2 35.5 + - - +
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Residues in contact with ALA 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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71A LEU* 3.7 19.1 - - + -
74A ILE* 3.5 18.7 - - + +
75A ASN* 3.8 21.5 - - - +
78A ALA* 5.5 0.5 - - - +
182A ARG 2.9 18.6 + - - +
183A VAL* 3.6 5.4 - - - +
184A TYR 3.3 0.2 - - - -
185A GLU* 1.3 76.8 - - - +
187A CYS* 1.3 60.0 + - - +
189A GLU* 3.4 9.4 + - - +
190A ALA* 3.0 18.0 + - - +
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Residues in contact with CYS 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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74A ILE* 3.6 26.5 - - - -
136A ILE* 4.0 10.8 - - - -
139A VAL* 4.3 13.0 - - - -
171A PHE* 3.8 36.8 - - + -
183A VAL* 2.9 23.6 + - - -
184A TYR 3.0 8.9 + - - +
186A ALA* 1.3 75.7 - - - +
188A MET* 1.3 60.5 + - + +
190A ALA* 3.3 1.5 + - - +
191A PHE* 2.8 41.5 + - + -
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Residues in contact with MET 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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162A CYS* 3.8 3.1 - - - -
163A ARG* 3.6 57.6 + - + +
166A THR* 3.7 7.6 - - + +
171A PHE* 4.1 6.3 - - + -
184A TYR* 3.0 61.0 + - + +
185A GLU* 3.1 16.8 + - - +
187A CYS* 1.3 78.5 - - - +
189A GLU* 1.3 60.3 + - - +
191A PHE* 3.4 32.5 + - + +
192A ASP* 3.1 27.7 + - - +
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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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75A ASN* 6.0 1.3 - - - +
78A ALA* 4.8 2.5 - - + -
82A ARG* 4.4 12.6 + - - +
163A ARG* 4.9 3.8 - - - +
185A GLU* 3.2 33.5 + - - +
186A ALA* 3.8 8.5 - - - +
188A MET* 1.3 73.6 - - - +
190A ALA* 1.3 66.5 + - - +
192A ASP* 3.3 20.2 + - - +
193A SER* 3.3 15.6 + - - -
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Residues in contact with ALA 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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74A ILE* 3.8 10.1 - - + -
78A ALA* 3.6 22.6 - - + +
81A LEU* 4.1 4.5 - - - +
143A TRP* 3.7 31.2 - - + +
186A ALA 3.0 17.2 + - - +
187A CYS* 3.3 5.6 + - - +
189A GLU* 1.3 76.4 - - - +
191A PHE* 1.3 59.9 + - + +
193A SER* 3.0 21.7 + - - -
194A LEU* 3.5 9.2 + - - +
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Residues in contact with PHE 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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128A TYR* 5.2 0.9 - + - -
129A VAL* 4.0 27.6 - - + -
139A VAL* 4.0 13.0 - - + -
143A TRP* 3.8 23.6 - + - -
157A ARG* 3.2 20.2 + - - +
161A GLU* 3.5 56.8 - - + +
162A CYS* 3.9 0.7 - - - -
166A THR* 4.7 0.4 - - + -
171A PHE* 4.1 6.7 - + - -
187A CYS* 2.8 32.2 + - + +
188A MET* 3.6 31.4 - - + +
189A GLU 3.2 0.2 - - - -
190A ALA* 1.3 72.9 - - + +
192A ASP* 1.3 62.4 + - - +
193A SER 3.0 6.6 + - - -
194A LEU* 3.1 25.3 + - + +
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Residues in contact with ASP 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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157A ARG* 2.9 27.1 + - - +
163A ARG* 2.7 37.2 + - - -
188A MET 3.1 14.4 + - - +
189A GLU* 3.4 12.8 - - - +
190A ALA 3.3 0.2 - - - -
191A PHE* 1.3 76.7 - - - +
193A SER* 1.3 59.7 + - - +
194A LEU 3.7 0.3 + - - +
226A ARG* 3.2 21.1 - - - +
227A PHE* 3.4 16.3 - - + -
228A LYS* 3.3 24.5 - - - +
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Residues in contact with SER 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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78A ALA 3.7 19.1 - - - -
81A LEU* 3.5 10.6 - - - +
82A ARG* 3.3 41.1 + - - +
189A GLU 3.3 6.6 + - - -
190A ALA 3.0 11.1 + - - -
191A PHE 3.0 1.2 - - - -
192A ASP* 1.3 78.7 - - - +
194A LEU* 1.3 60.1 + - - +
195A PRO* 3.4 0.7 - - - +
226A ARG* 2.9 27.3 + - - -
227A PHE* 4.0 9.7 - - - -
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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
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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