Contacts of the helix formed by residues 190 - 204 (chain F) in PDB entry 6CP3
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 ARG 190 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ARG* 4.1 10.3 - - - +
309B GLU* 4.4 2.5 - - - +
345B ILE 3.4 8.9 + - - -
346B SER 3.2 24.9 - - - -
347B ILE 2.5 24.1 + - - +
348B THR 3.6 2.7 + - - -
349B ASP* 3.6 4.9 + - - -
375B ARG* 3.1 19.2 - - - +
189F GLU* 1.3 86.7 + - - +
191F THR* 1.3 64.4 + - - +
192F ARG* 3.6 17.7 - - - +
193F GLU* 2.4 55.2 + - + +
194F GLY* 3.1 18.0 + - - -
219F PHE* 5.6 0.7 - - - -
221F GLN* 3.9 3.7 - - - +
222F MET* 3.9 16.8 - - + -
600F ADP 2.7 31.7 + - - -
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Residues in contact with THR 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PRO 3.9 2.5 - - - +
137B GLY* 4.0 1.1 - - - -
138B ILE* 3.7 35.2 - - + +
141B ARG* 3.4 28.0 + - + +
309B GLU* 3.4 25.9 + - - -
189F GLU 3.6 2.2 + - - -
190F ARG* 1.3 71.4 - - - +
192F ARG* 1.3 57.1 + - - +
194F GLY* 3.1 3.6 + - - -
195F ASN* 3.0 24.9 + - - +
221F GLN* 3.5 29.6 + - - +
223F ASN* 4.1 9.5 + - - -
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Residues in contact with ARG 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 4.1 14.9 - - + +
142B ARG 5.9 1.3 - - - +
143B SER* 5.5 11.2 - - - +
144B VAL* 5.5 5.6 - - - -
164B GLY 5.1 9.9 - - - -
166B ARG* 4.0 15.4 - - - +
312B ALA* 5.9 3.6 - - + -
349B ASP* 2.5 45.8 + - - -
375B ARG* 5.1 6.9 - - - +
376B VAL* 3.4 27.6 - - - +
190F ARG* 3.2 4.0 - - + +
191F THR* 1.3 80.4 - - - +
193F GLU* 1.3 91.2 + - - +
195F ASN* 3.1 9.4 + - + +
196F ASP* 2.9 50.0 + - - +
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Residues in contact with GLU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ARG* 4.1 6.1 + - - -
164F THR* 3.4 30.7 - - + +
168F GLN* 4.5 7.7 + - - +
189F GLU* 3.5 19.1 - - + +
190F ARG* 2.4 48.0 + - + +
191F THR 3.3 0.6 - - - -
192F ARG* 1.3 97.4 + - - +
194F GLY* 1.3 60.8 + - - +
196F ASP* 3.4 7.0 + - - +
197F LEU* 3.0 29.5 + - - +
600F ADP 4.2 4.4 + - - -
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Residues in contact with GLY 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ILE* 4.7 7.5 - - - +
184F PHE* 5.8 0.2 - - - -
190F ARG 3.1 9.5 + - - -
191F THR* 3.1 8.9 + - - -
193F GLU* 1.3 77.2 - - - +
195F ASN* 1.3 56.1 + - - +
197F LEU* 3.4 3.6 + - - +
198F TYR* 2.9 27.3 + - - +
219F PHE* 3.6 37.4 - - - -
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Residues in contact with ASN 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ILE* 3.6 21.8 - - - +
139B LEU* 5.5 0.9 - - - +
141B ARG* 2.7 45.4 + - + +
142B ARG* 3.9 4.9 - - - +
143B SER* 4.4 4.9 - - - +
191F THR 3.0 12.4 + - - +
192F ARG* 3.1 12.7 + - + +
194F GLY* 1.3 77.3 - - - +
196F ASP* 1.3 59.0 + - - +
198F TYR* 3.1 8.8 + - - +
199F ARG* 3.0 53.2 + - - +
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Residues in contact with ASP 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER* 3.4 28.8 + - - -
376B VAL* 4.2 9.2 - - - +
168F GLN* 5.3 5.6 - - - +
192F ARG* 2.9 41.1 + - - +
193F GLU* 3.9 5.8 - - - +
195F ASN* 1.3 78.0 - - - +
197F LEU* 1.3 59.3 + - - +
199F ARG* 3.4 9.7 + - - +
200F GLU* 3.0 36.3 + - + +
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Residues in contact with LEU 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F GLN* 4.3 27.0 - - + +
171F ILE* 4.0 18.8 - - + -
184F PHE* 3.6 51.8 - - + -
193F GLU 3.0 19.0 + - - +
194F GLY* 3.9 5.2 - - - +
196F ASP* 1.3 76.4 - - - +
198F TYR* 1.3 55.9 + - - +
200F GLU* 3.3 12.0 + - + -
201F MET* 2.9 58.8 + - + +
217F LEU* 5.0 3.6 - - + -
219F PHE* 5.0 2.2 - - + -
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Residues in contact with TYR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ILE* 5.2 2.7 - - + -
139B LEU* 4.9 14.2 - - + +
93F GLY 5.0 5.2 + - - -
95F ILE* 3.6 26.8 - - + +
104F ASP* 5.0 7.9 - - + +
106F ARG* 5.3 3.5 - - - -
194F GLY 2.9 14.5 + - - +
195F ASN* 3.1 14.1 + - - +
197F LEU* 1.3 76.2 - - - +
199F ARG* 1.3 82.2 + - - +
201F MET* 3.2 5.0 + - - +
202F LYS* 3.0 52.3 + - + +
207F ILE* 3.6 23.3 - - + -
209F LEU* 3.6 21.7 - - - +
217F LEU* 3.6 26.8 - - + +
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Residues in contact with ARG 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 5.1 10.5 + - - +
141B ARG 3.9 13.7 + - - -
142B ARG* 5.3 7.3 - - - +
143B SER* 5.5 4.5 - - - +
315B SER* 5.7 3.8 - - - -
195F ASN* 3.0 43.2 + - - +
196F ASP* 3.9 11.7 - - - +
198F TYR* 1.3 97.9 - - - +
200F GLU* 1.3 61.2 + - + +
202F LYS* 3.2 39.0 + - - +
203F GLU* 3.0 41.4 + - + +
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Residues in contact with GLU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F GLN* 5.4 7.4 - - - +
196F ASP* 3.0 23.9 + - + +
197F LEU* 3.7 16.8 - - + +
198F TYR 3.3 0.2 - - - -
199F ARG* 1.3 78.2 - - - +
201F MET* 1.3 55.8 + - - +
203F GLU* 4.6 10.5 - - - +
204F THR* 2.6 50.2 + - + +
420F VAL* 6.5 1.6 - - + -
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Residues in contact with MET 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F ILE* 3.8 28.7 - - + -
175F ALA* 6.1 0.9 - - + -
184F PHE* 5.3 2.0 - - + -
197F LEU* 2.9 50.1 + - + +
198F TYR* 3.7 5.6 - - - +
200F GLU* 1.3 78.2 - - - +
202F LYS* 1.3 62.2 + - - +
204F THR* 4.1 1.8 - - - -
205F GLY 3.7 0.3 + - - -
206F VAL* 3.3 38.3 + - + -
207F ILE* 2.8 48.7 + - + +
215F VAL* 4.4 24.5 - - + -
217F LEU* 5.1 7.4 - - + -
254F PHE* 6.2 1.1 - - + -
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Residues in contact with LYS 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F TYR* 3.0 41.1 + - + +
199F ARG* 3.2 45.1 + - - +
201F MET* 1.3 78.9 - - - +
203F GLU* 1.3 67.3 + - + +
205F GLY* 3.4 8.7 + - - -
207F ILE* 3.5 28.5 - - + +
209F LEU* 3.8 26.4 - - + +
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Residues in contact with GLU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F ARG* 3.0 25.4 + - + +
200F GLU* 4.6 11.6 - - - +
202F LYS* 1.3 80.8 - - + +
204F THR* 1.3 64.4 + - + +
205F GLY* 3.1 4.6 + - - -
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Residues in contact with THR 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F ASN* 5.6 2.2 - - - +
176F LYS* 3.7 35.1 + - - +
200F GLU* 2.6 37.7 + - + +
201F MET* 5.3 0.5 - - - -
203F GLU* 1.3 79.2 - - + +
205F GLY* 1.3 60.6 + - - +
206F VAL* 3.2 21.8 + - - +
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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