Contacts of the helix formed by residues 174 - 190 (chain A) in PDB entry 2ORY
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 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 3.3 13.5 - - - -
91A GLY* 6.1 0.7 - - - -
92A THR 5.0 3.0 + - - -
94A PRO* 3.5 8.2 - - - +
100A TRP* 3.2 18.9 - - - -
173A HIS* 1.3 79.3 - - - +
175A LYS* 1.3 69.9 + - - +
176A GLY 2.9 0.2 - - - -
177A GLY* 2.7 22.0 + - - -
178A ALA 3.5 3.3 + - - -
206A PHE 3.1 8.1 + - - -
207A ALA 3.5 15.6 + - - -
208A GLY* 3.5 9.0 - - - -
209A PRO* 3.8 4.6 - - - +
312A HIS* 2.9 27.0 + - - -
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Residues in contact with LYS 175 (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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68A PHE* 2.8 29.1 + - - +
69A ASN* 4.4 9.9 + - - +
70A ASP 5.5 0.9 - - - +
91A GLY* 4.1 15.5 - - - -
92A THR* 3.8 16.5 + - - +
100A TRP* 3.6 48.9 + - + +
104A ASP* 5.6 5.1 - - - -
128A SER* 5.6 4.2 + - - -
174A SER* 1.3 81.8 + - - +
176A GLY* 1.3 56.9 + - - +
178A ALA* 3.1 6.5 + - - +
179A LEU* 2.9 39.9 + - + +
209A PRO* 4.7 8.7 - - + -
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Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.6 32.0 - - - +
90A ARG* 4.7 2.0 - - - -
91A GLY 4.4 3.6 - - - +
172A GLY* 3.4 9.3 - - - -
173A HIS 2.9 13.2 + - - -
175A LYS* 1.3 80.4 - - - +
177A GLY* 1.3 56.0 + - - +
179A LEU* 3.9 1.1 - - - -
180A SER* 2.8 32.6 + - - -
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Residues in contact with GLY 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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172A GLY 3.3 16.2 - - - -
173A HIS 3.5 3.2 - - - -
174A SER 2.7 13.2 + - - -
176A GLY* 1.3 77.6 - - - +
178A ALA* 1.3 57.8 + - - -
180A SER* 3.3 4.2 + - - -
181A SER* 3.0 17.3 + - - -
205A PRO* 3.1 22.0 - - - +
206A PHE 3.6 12.1 - - - -
208A GLY* 4.3 5.6 - - - -
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Residues in contact with ALA 178 (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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129A THR* 5.0 7.6 - - + -
174A SER 3.5 3.2 + - - -
175A LYS* 3.1 8.8 + - - +
177A GLY* 1.3 77.2 - - - +
179A LEU* 1.3 55.8 + - + +
181A SER* 3.1 12.1 + - - -
182A THR* 2.6 30.7 + - - -
208A GLY* 4.1 2.2 - - - -
209A PRO* 3.6 39.3 - - + +
211A ALA* 4.2 14.7 - - + +
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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
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71A ALA* 5.5 5.2 - - + -
89A ILE* 3.9 27.1 - - + -
90A ARG 5.0 5.6 - - - +
91A GLY* 5.3 2.5 - - - -
129A THR* 4.1 17.9 - - + +
132A GLY* 3.8 36.1 - - - +
133A LEU* 3.8 10.7 - - + +
136A LEU* 4.1 14.4 - - + +
175A LYS* 2.9 30.5 + - + +
176A GLY* 4.8 0.2 - - - -
178A ALA* 1.3 77.2 - - + +
180A SER* 1.3 54.3 + - - +
182A THR* 3.2 4.7 + - - -
183A LEU* 2.6 38.1 + - - +
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Residues in contact with SER 180 (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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89A ILE* 3.8 8.9 - - - +
170A VAL* 3.5 22.3 - - - +
171A THR* 3.5 26.4 - - - -
172A GLY 3.6 8.0 + - - -
176A GLY 2.8 24.9 + - - -
177A GLY 3.3 5.9 + - - -
179A LEU* 1.3 75.5 - - - +
181A SER* 1.3 65.4 + - - +
183A LEU 3.1 0.9 + - - -
184A ALA* 2.8 30.7 + - - +
203A THR* 4.0 2.2 + - - -
205A PRO* 3.6 9.7 - - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLY 3.0 17.5 + - - -
178A ALA* 3.1 8.8 + - - -
180A SER* 1.3 81.9 + - - +
182A THR* 1.3 65.3 + - - +
184A ALA* 3.4 1.2 + - - +
185A LEU 3.2 17.0 + - - -
203A THR* 3.7 12.8 - - - -
205A PRO* 4.0 11.2 - - - -
211A ALA* 5.6 1.0 - - - +
220A PHE* 3.2 22.6 - - - -
286A ILE* 3.6 32.1 - - - +
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Residues in contact with THR 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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113A TRP* 3.8 28.2 - - + -
125A ILE* 5.2 3.1 - - + -
129A THR* 5.0 12.2 - - - +
133A LEU* 4.2 18.2 - - + -
178A ALA 2.6 21.9 + - - -
179A LEU* 3.2 9.1 + - + -
180A SER 3.2 0.6 - - - -
181A SER* 1.3 80.5 + - - +
183A LEU* 1.3 63.4 + - - +
185A LEU* 3.2 8.0 + - - +
186A TRP* 3.1 17.2 + - - +
211A ALA* 3.3 20.7 - - + +
216A PHE* 4.3 13.6 - - + -
220A PHE* 5.2 0.4 - - - -
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Residues in contact with LEU 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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73A MET* 3.9 28.3 - - + -
87A ILE* 4.4 9.6 - - + -
89A ILE* 4.0 10.3 - - + -
133A LEU* 4.0 17.9 - - + +
136A LEU* 4.2 17.0 - - + -
152A ILE* 5.0 4.7 - - + -
170A VAL* 4.1 15.7 - - + -
179A LEU 2.6 21.3 + - - +
180A SER 3.6 3.1 - - - +
182A THR* 1.3 73.3 - - - +
184A ALA* 1.3 64.2 + - - +
186A TRP* 3.0 31.3 + - + +
187A LEU* 3.0 36.4 + - + +
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Residues in contact with ALA 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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170A VAL* 3.8 24.0 - - + -
180A SER 2.8 15.9 + - - +
181A SER 3.6 6.1 - - - +
183A LEU* 1.3 78.2 - - - +
185A LEU* 1.3 54.9 + - - +
187A LEU* 3.3 5.4 + - - +
188A LYS* 3.0 30.6 + - - +
201A ILE* 3.9 14.1 - - + +
203A THR* 3.9 21.5 - - + -
224A LEU* 4.5 4.3 - - + -
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Residues in contact with LEU 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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113A TRP* 3.7 9.9 - - + -
181A SER 3.2 12.9 + - - +
182A THR* 3.2 9.4 + - - +
184A ALA* 1.3 72.9 - - - +
186A TRP* 1.3 59.9 + - - +
188A LYS* 3.2 8.2 + - + +
189A ASP* 2.8 37.9 + - - +
216A PHE* 3.8 29.6 - - + -
219A TYR* 3.9 33.9 - - + -
220A PHE* 3.9 21.9 - - + -
223A CYS* 3.9 22.9 - - + -
224A LEU* 4.0 10.8 - - + -
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Residues in contact with TRP 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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113A TRP* 3.9 18.5 - - + -
115A TYR* 3.5 39.4 - + + -
133A LEU* 4.5 5.2 - - + -
137A GLN* 3.3 40.4 - - + +
152A ILE* 4.1 20.6 - - + -
153A LEU* 4.0 30.7 - - + -
182A THR 3.1 10.4 + - - +
183A LEU* 3.0 31.0 + - + +
185A LEU* 1.3 77.2 - - - +
187A LEU* 1.3 85.4 + - + +
189A ASP* 3.3 3.5 + - - +
190A ILE* 3.2 44.0 + - + +
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Residues in contact with LEU 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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87A ILE* 4.0 19.1 - - + -
152A ILE* 5.8 1.3 - - + -
153A LEU* 4.9 2.5 - - + -
156A LEU* 4.1 17.5 - - + -
168A ILE* 5.1 5.2 - - + -
170A VAL* 4.6 9.4 - - + -
183A LEU* 3.0 38.5 + - + +
184A ALA 3.6 4.3 - - - +
185A LEU 3.3 0.2 - - - -
186A TRP* 1.3 100.6 - - + +
188A LYS* 1.3 64.1 + - - +
190A ILE* 3.4 11.0 + - + +
191A GLN* 3.2 24.8 + - - +
195A LEU* 3.7 20.7 - - + +
201A ILE* 3.6 20.6 - - + -
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Residues in contact with LYS 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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184A ALA 3.0 15.1 + - - +
185A LEU* 3.3 20.2 - - + +
187A LEU* 1.3 77.2 - - - +
189A ASP* 1.3 62.1 + - - +
191A GLN* 3.2 39.5 + - - +
201A ILE* 3.7 31.1 - - + +
223A CYS* 3.6 29.3 + - + +
224A LEU* 4.8 14.4 - - + +
227A GLN* 5.8 3.9 - - - +
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Residues in contact with ASP 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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113A TRP* 2.7 31.2 + - - -
115A TYR* 3.5 35.5 - - + +
116A ALA* 3.7 2.5 - - - +
185A LEU* 2.8 29.7 + - - +
186A TRP 3.3 2.4 + - - +
188A LYS* 1.3 74.4 - - - +
190A ILE* 1.3 59.6 + - - +
191A GLN 3.4 2.3 + - - +
193A VAL* 5.4 2.8 - - - +
219A TYR* 2.4 31.4 + - - -
223A CYS* 4.8 1.0 - - - -
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Residues in contact with ILE 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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115A TYR* 4.2 14.6 - - + -
153A LEU* 3.9 32.3 - - + -
186A TRP* 3.4 50.7 - - + +
187A LEU* 3.4 17.9 - - + +
189A ASP* 1.3 78.6 - - - +
191A GLN* 1.3 63.4 + - - +
193A VAL* 3.1 8.7 + - + +
194A LYS* 2.8 50.7 + - + +
195A LEU* 3.3 7.9 + - + -
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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