Contacts of the helix formed by residues 199 - 214 (chain A) in PDB entry 1O94
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 ALA 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.8 10.3 - - + +
195A LEU* 2.8 17.0 + - + +
196A GLU 3.9 2.7 - - - +
197A ASN 3.2 0.2 - - - -
198A ARG* 1.3 77.0 - - - +
200A ARG* 1.3 59.0 + - - +
201A PHE 3.3 0.7 - - - -
202A TRP* 3.3 6.7 + - - +
203A LEU* 2.9 42.0 + - + +
243A PHE* 3.7 29.2 - - + -
246A MET* 4.0 9.4 - - - -
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Residues in contact with ARG 200 (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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190A LYS* 2.8 41.4 + - - +
191A TYR* 3.7 25.6 - - + -
196A GLU* 3.3 16.8 + - - +
197A ASN* 3.0 41.0 + - - +
199A ALA* 1.3 76.3 - - - +
201A PHE* 1.3 59.1 - - - +
203A LEU* 3.9 7.2 - - - +
204A GLU* 2.9 57.2 + - + +
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Residues in contact with PHE 201 (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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139A MET* 4.1 7.6 - - + -
144A ILE* 3.7 22.2 - - + -
147A VAL* 4.3 8.5 - - + -
148A GLN* 3.6 30.5 + - + +
151A TYR* 4.3 9.9 - + - -
175A LEU* 3.5 29.8 - - + -
176A PRO* 4.2 14.8 - - + -
179A PHE* 3.5 54.7 - + + -
191A TYR* 3.8 10.8 - - + -
198A ARG 4.4 1.2 + - - -
199A ALA 3.3 0.6 - - - -
200A ARG* 1.3 80.3 - - - +
202A TRP* 1.3 60.8 + - - +
205A THR* 2.8 50.3 + - - -
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Residues in contact with TRP 202 (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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168A VAL* 3.7 16.2 - - + +
170A GLY* 3.3 28.9 - - - -
176A PRO* 3.5 32.0 + - + +
177A LEU* 4.2 9.0 - - + -
180A LEU* 4.1 11.0 - - + -
198A ARG 5.2 0.8 + - - +
199A ALA* 3.3 9.6 + - - +
201A PHE* 1.3 82.7 - - - +
203A LEU* 1.3 59.3 + - - +
205A THR* 3.4 4.1 + - - -
206A LEU* 3.0 42.4 + - + +
221A THR* 3.0 35.6 + - + -
222A ARG 3.6 10.8 - - - -
223A PHE* 3.4 33.2 - + + -
243A PHE* 3.4 30.1 - + + -
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Residues in contact with LEU 203 (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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196A GLU* 5.0 3.1 - - - +
199A ALA* 2.9 39.1 + - + +
200A ARG* 3.9 6.5 - - - +
202A TRP* 1.3 77.2 - - - +
204A GLU* 1.3 57.5 + - + +
206A LEU* 3.4 2.3 + - + -
207A GLU* 3.0 29.1 + - - +
243A PHE* 4.1 7.2 - - + -
246A MET* 3.8 21.8 - - + +
247A ALA* 3.6 40.6 - - + +
250A LEU* 3.6 19.1 - - + +
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Residues in contact with GLU 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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148A GLN* 3.0 30.1 + - - +
190A LYS* 5.1 3.6 + - - -
191A TYR* 2.5 33.6 + - - -
200A ARG* 2.9 35.2 + - + +
203A LEU* 1.3 74.7 - - + +
205A THR* 1.3 61.6 + - - +
207A GLU* 3.7 13.3 - - - +
208A LYS* 3.0 43.6 + - - +
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Residues in contact with THR 205 (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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148A GLN* 3.6 16.5 - - + +
151A TYR* 3.7 37.5 - - + -
168A VAL* 4.0 24.0 - - + -
201A PHE* 2.8 37.6 + - + -
202A TRP* 3.6 8.7 - - - -
203A LEU 3.3 0.2 - - - -
204A GLU* 1.3 78.7 - - - +
206A LEU* 1.3 56.9 + - - +
208A LYS* 3.4 4.3 + - - +
209A VAL* 2.9 31.0 + - - +
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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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168A VAL* 3.9 20.9 - - + -
202A TRP* 3.0 43.4 + - + +
203A LEU* 3.7 5.6 - - - +
204A GLU 3.3 0.2 - - - -
205A THR* 1.3 72.5 - - - +
207A GLU* 1.3 61.3 + - - +
209A VAL* 3.4 1.1 + - - +
210A LYS* 2.8 34.1 + - - +
219A ILE* 3.8 27.5 - - + +
220A ALA 4.5 0.2 - - - +
221A THR* 4.2 14.1 - - + +
247A ALA* 4.3 16.6 - - + -
250A LEU* 4.0 18.2 - - + +
251A VAL* 4.0 24.2 - - + -
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Residues in contact with GLU 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 LEU 3.0 17.6 + - - +
204A GLU* 3.7 16.4 - - - +
205A THR 3.3 0.2 - - - -
206A LEU* 1.3 76.7 - - - +
208A LYS* 1.3 60.5 + - + +
210A LYS* 3.8 2.2 - - - +
211A HIS* 2.9 31.1 + - + +
250A LEU* 4.1 24.5 - - + +
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Residues in contact with LYS 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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145A ALA* 5.2 8.9 + - - +
148A GLN* 3.4 39.7 + - + +
149A GLN* 6.2 0.4 - - - -
152A VAL* 3.6 25.4 - - + +
204A GLU* 3.0 29.2 + - - +
205A THR* 3.8 3.8 - - - +
207A GLU* 1.3 77.0 - - + +
209A VAL* 1.3 60.0 + - - +
211A HIS* 3.4 7.8 + - - +
212A ALA* 3.0 28.1 + - - +
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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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104A LEU* 4.7 3.1 - - + -
151A TYR* 4.0 37.9 - - + +
152A VAL* 4.4 2.9 - - + +
155A ALA* 3.9 18.6 - - + -
166A VAL* 4.1 12.8 - - + +
168A VAL* 4.3 17.3 - - + -
205A THR 2.9 19.5 + - - +
206A LEU* 4.0 2.7 - - - +
208A LYS* 1.3 73.4 - - - +
210A LYS* 1.3 65.8 + - - +
212A ALA* 3.1 5.3 + - - +
213A VAL* 2.9 25.4 + - + +
219A ILE* 4.1 22.0 - - + -
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Residues in contact with LYS 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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206A LEU 2.8 22.1 + - - +
207A GLU* 3.8 4.5 - - - +
209A VAL* 1.3 71.7 - - - +
211A HIS* 1.3 61.9 + - - +
214A GLY* 2.7 32.8 + - - +
215A SER 4.4 0.5 + - - -
219A ILE* 3.9 21.9 - - + +
249A SER 4.1 13.9 + - - -
250A LEU* 3.4 40.0 + - + +
252A ASP* 3.4 29.3 + - - -
292A LYS* 5.6 0.8 - - - +
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Residues in contact with HIS 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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207A GLU* 2.9 21.3 + - + +
208A LYS* 3.6 8.3 + - - +
209A VAL 3.2 0.2 - - - -
210A LYS* 1.3 79.4 - - - +
212A ALA* 1.3 64.9 + - - +
214A GLY 4.7 0.5 + - - -
215A SER 5.7 0.5 + - - -
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Residues in contact with ALA 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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152A VAL* 3.9 26.5 - - + +
155A ALA* 5.3 0.4 - - + -
156A LYS* 4.1 17.0 - - + +
159A ARG* 3.0 21.3 + - - -
208A LYS 3.0 16.9 + - - +
209A VAL* 3.1 5.4 + - - +
211A HIS* 1.3 83.4 + - - +
213A VAL* 1.4 61.9 + - + +
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Residues in contact with VAL 213 (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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155A ALA* 3.4 45.1 - - + +
156A LYS* 3.8 9.4 - - + +
159A ARG* 3.7 18.2 - - + +
166A VAL* 4.5 6.3 - - + -
209A VAL* 2.9 20.1 + - + +
212A ALA* 1.4 82.7 - - + +
214A GLY* 1.3 61.2 + - - +
215A SER 3.3 3.4 - - - -
216A ASP* 2.9 11.1 + - - +
217A CYS* 2.8 41.2 + - + -
219A ILE* 3.8 17.0 - - + -
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Residues in contact with GLY 214 (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 PRO* 3.7 12.1 - - - +
210A LYS* 2.7 36.2 + - - -
211A HIS 4.7 0.2 + - - -
212A ALA 3.8 0.4 - - - -
213A VAL* 1.3 73.5 - - - +
215A SER* 1.3 60.4 + - - +
216A ASP 3.1 0.7 + - - -
217A CYS 3.3 19.1 - - - +
219A ILE* 4.1 10.1 - - - -
252A ASP* 5.3 0.9 - - - +
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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