Contacts of the helix formed by residues 194 - 212 (chain A) in PDB entry 3ORO
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 ASP 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 3.8 16.3 - - + +
186A GLU* 5.4 2.2 + - - +
192A SER* 4.2 5.3 + - - +
193A VAL* 1.3 75.9 - - - +
195A ALA* 1.3 54.3 + - - +
196A ARG* 3.0 53.6 + - - +
197A SER* 2.8 34.5 + - - +
198A ASP 4.0 0.3 + - - -
259A PRO* 5.4 0.7 - - - +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A HIS* 3.5 44.0 - - + +
135A ILE* 4.3 10.1 - - + +
194A ASP* 1.3 75.2 - - - +
196A ARG* 1.3 61.5 + - + +
197A SER 3.2 0.2 - - - -
198A ASP* 3.2 17.2 + - - +
199A VAL* 3.3 14.6 + - - +
264A GLN 5.1 8.1 - - - +
265A THR* 5.7 4.5 - - + -
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Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 5.2 0.4 - - - +
194A ASP* 2.9 32.4 + - - +
195A ALA* 1.3 74.2 - - + +
197A SER* 1.3 63.6 + - - +
199A VAL* 3.4 8.4 + - - +
200A TYR 3.2 13.2 + - - -
259A PRO* 3.6 40.8 + - + +
260A GLU* 3.9 11.1 - - - +
262A ARG* 2.9 31.4 + - - +
263A TYR 3.8 9.9 - - - +
264A GLN* 3.0 54.3 + - - +
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Residues in contact with SER 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 5.4 0.4 - - - -
137A ARG* 5.6 1.0 - - - -
184A SER* 2.6 27.1 + - - -
186A GLU* 3.7 15.2 + - - -
187A GLN* 3.5 17.7 + - - +
193A VAL* 3.6 17.7 - - - -
194A ASP* 2.8 16.1 + - - -
196A ARG* 1.3 77.3 - - - +
198A ASP* 1.3 60.2 + - - -
200A TYR* 3.2 4.0 + - - +
201A SER* 3.0 30.3 + - - -
262A ARG* 4.0 1.8 - - - +
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.9 15.1 - - + +
130A HIS* 2.8 29.8 + - + +
135A ILE* 3.5 9.7 - - - +
136A HIS* 2.9 30.6 + - - +
137A ARG* 2.9 27.9 + - - -
139A VAL* 4.0 11.3 - - + +
195A ALA 3.2 9.8 + - - +
197A SER* 1.3 76.2 - - - +
199A VAL* 1.3 60.2 + - - +
201A SER* 4.0 2.5 - - - +
202A LEU* 2.8 33.1 + - - +
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 5.9 0.2 - - - -
130A HIS* 5.5 0.4 - - + -
195A ALA 3.3 12.9 + - - +
196A ARG* 3.5 11.0 - - - +
198A ASP* 1.3 79.2 - - - +
200A TYR* 1.3 57.5 + - - +
202A LEU* 3.6 6.2 - - - +
203A GLY* 2.8 26.3 + - - -
254A ALA* 4.0 18.9 - - - +
262A ARG* 4.2 4.3 - - + -
263A TYR* 3.8 33.9 - - + +
265A THR* 4.0 24.0 - - - +
266A ALA* 4.1 9.9 - - + +
269A MET* 3.9 19.7 - - - +
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Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU 3.4 19.5 - - - -
184A SER* 3.6 15.0 - - - -
185A PRO* 3.6 27.1 - - + -
196A ARG 3.2 3.2 + - - -
197A SER 3.2 8.3 + - - +
199A VAL* 1.3 78.4 - - - +
201A SER* 1.3 65.7 + - - +
203A GLY* 3.0 4.2 + - - -
204A CYS* 3.0 31.7 + - - -
216A PHE* 3.7 14.9 - - - -
228A HIS* 2.7 32.6 + - - -
254A ALA 3.3 21.5 - - - -
255A LEU* 3.5 33.8 + - + +
256A ALA 3.8 3.8 - - - -
257A LYS* 4.5 2.5 - - + +
262A ARG* 3.7 27.4 - - - +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG 5.5 2.5 + - - -
139A VAL* 3.5 31.3 + - - +
182A TYR* 2.5 28.4 + - - -
183A LEU* 4.2 0.7 - - - -
184A SER 4.1 9.2 + - - -
187A GLN* 4.4 4.2 + - - -
197A SER* 3.0 17.2 + - - -
198A ASP* 4.0 2.0 - - - -
200A TYR* 1.3 78.1 - - - +
202A LEU* 1.3 62.9 + - - +
204A CYS* 3.1 7.8 + - - +
205A VAL* 3.1 24.6 + - - +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.7 29.4 - - + +
122A ALA* 3.9 21.1 - - + -
123A CYS* 3.4 34.1 - - - +
126A LEU* 4.0 18.4 - - + -
139A VAL* 3.7 19.0 - - + +
144A ILE* 4.3 7.4 - - + -
198A ASP 2.8 20.1 + - - +
199A VAL* 3.6 4.7 - - - +
201A SER* 1.3 77.0 - - - +
203A GLY* 1.3 56.8 + - - +
205A VAL* 3.3 4.7 + - + +
206A LEU* 2.9 27.5 + - - +
266A ALA* 6.1 0.4 - - + -
269A MET* 4.1 10.1 - - + -
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Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL 2.8 14.3 + - - -
200A TYR 3.0 7.1 + - - -
202A LEU* 1.3 76.1 - - - +
204A CYS* 1.3 55.7 + - - +
206A LEU* 3.4 5.6 + - - +
207A TYR* 2.9 29.1 + - - +
251A VAL* 4.2 7.1 - - - +
254A ALA* 3.9 19.3 - - - -
255A LEU* 3.8 9.6 - - - -
269A MET* 4.1 6.6 - - - +
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Residues in contact with CYS 204 (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 GLN 3.9 16.4 - - - +
182A TYR* 3.9 22.9 - - + -
200A TYR* 3.0 44.5 + - - -
201A SER* 3.1 11.4 + - - +
203A GLY* 1.3 71.9 - - - +
205A VAL* 1.3 65.2 + - - +
207A TYR* 3.4 3.5 + - - +
208A GLU* 3.0 23.2 + - - +
215A PRO* 4.0 19.5 - - + +
228A HIS* 3.9 6.3 - - - -
255A LEU* 3.7 9.6 - - - -
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.7 30.7 - - + -
119A ILE* 3.9 12.3 - - + -
139A VAL* 4.1 8.7 - - + -
140A LYS* 3.7 35.4 - - - +
141A PRO* 3.8 16.4 - - + -
144A ILE* 4.3 5.8 - - + -
182A TYR* 4.6 1.8 - - + -
201A SER 3.1 13.8 + - - +
202A LEU* 3.5 8.1 - - + +
204A CYS* 1.3 73.8 - - - +
206A LEU* 1.3 60.1 + - - +
208A GLU* 3.0 7.0 + - - +
209A VAL* 2.9 30.3 + - + +
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Residues in contact with LEU 206 (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 ALA* 4.5 7.4 - - + +
116A ILE* 5.0 2.2 - - + +
119A ILE* 3.8 28.2 - - + +
202A LEU 2.9 16.9 + - - +
203A GLY* 3.6 6.1 - - - +
205A VAL* 1.3 75.3 - - - +
207A TYR* 1.3 64.3 + - - +
209A VAL* 3.4 10.4 - - + +
210A LEU* 3.1 49.5 + - + +
247A LEU* 4.9 4.5 - - + -
250A VAL* 4.8 2.0 - - + -
251A VAL* 3.7 28.9 - - + -
269A MET* 4.2 16.2 - - + -
273A LEU* 3.9 27.8 - - + -
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Residues in contact with TYR 207 (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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203A GLY 2.9 17.1 + - - +
204A CYS* 3.4 8.5 - - - +
205A VAL 3.2 0.2 - - - -
206A LEU* 1.3 76.0 - - - +
208A GLU* 1.3 58.3 + - - +
210A LEU* 3.5 4.2 + - - +
211A THR* 3.0 45.5 + - + +
213A GLU 3.1 25.4 - - - -
215A PRO* 3.5 34.1 + - + +
233A PRO* 4.5 6.5 - - + -
234A ILE* 2.5 34.4 + - - +
236A PRO* 4.0 18.4 - - + -
239A ARG* 2.9 34.4 + - - -
251A VAL* 3.7 23.6 - - + -
252A LEU* 5.3 0.7 - - + -
255A LEU* 3.9 10.3 - - + -
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Residues in contact with GLU 208 (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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101A ARG* 6.1 0.3 - - - +
104A VAL* 4.1 25.1 - - + +
105A HIS* 5.0 9.4 - - - -
109A PRO* 5.0 0.2 - - - +
141A PRO* 3.7 10.6 - - + +
181A GLN* 5.2 0.2 - - - +
182A TYR* 2.5 41.1 + - - -
204A CYS 3.0 14.8 + - - +
205A VAL* 3.0 6.3 + - - +
207A TYR* 1.3 76.1 - - - +
209A VAL* 1.3 59.8 + - + +
212A GLY* 2.7 33.1 + - - +
213A GLU 3.2 22.6 + - - +
214A PRO* 3.6 19.1 - - + +
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Residues in contact with VAL 209 (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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100A LEU* 4.1 32.1 - - + -
103A ILE* 6.5 0.4 - - + -
104A VAL* 4.0 22.9 - - + -
109A PRO* 3.2 5.4 - - - +
110A MET* 2.8 47.3 + - + +
115A ALA* 4.0 19.7 - - + -
118A VAL* 6.4 0.7 - - + -
119A ILE* 4.5 9.4 - - + -
141A PRO* 5.8 1.6 - - + -
205A VAL* 2.9 20.7 + - + +
206A LEU* 3.4 22.4 - - + +
208A GLU* 1.3 78.1 - - + +
210A LEU* 1.3 57.7 + - - +
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Residues in contact with LEU 210 (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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109A PRO* 3.5 12.2 - - - +
110A MET 4.5 5.1 - - - +
112A PRO* 3.8 15.3 - - + +
115A ALA* 3.6 23.6 - - + -
116A ILE* 5.5 0.4 - - + +
206A LEU* 3.1 38.6 + - + +
207A TYR* 3.8 4.9 - - - +
209A VAL* 1.3 77.3 - - - +
211A THR* 1.3 60.1 + - + +
236A PRO* 4.9 4.3 - - + -
240A HIS* 3.9 14.4 - - - +
243A LEU* 4.2 26.7 - - + +
247A LEU* 3.6 39.3 - - + -
251A VAL* 4.0 13.5 - - + -
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Residues in contact with THR 211 (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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109A PRO* 4.0 6.9 - - - +
207A TYR* 3.0 24.7 + - + +
210A LEU* 1.3 80.0 - - + +
212A GLY* 1.3 59.6 + - - +
213A GLU* 2.9 36.6 + - - +
236A PRO* 3.8 42.4 - - + +
239A ARG* 4.4 12.6 - - + +
240A HIS* 3.5 24.9 + - + +
243A LEU* 4.3 2.9 - - + -
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Residues in contact with GLY 212 (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 VAL* 4.1 17.3 - - - +
109A PRO* 4.0 20.1 - - - +
208A GLU* 2.7 26.5 + - - +
210A LEU 3.8 0.8 - - - -
211A THR* 1.3 71.0 - - - +
213A GLU* 1.3 71.8 + - - +
214A PRO* 4.8 0.3 - - - +
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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
------------------------------------------------------------
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