Contacts of the helix formed by residues 190 - 204 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 4.0 10.8 - - - +
309A GLU* 5.2 0.2 - - - -
345A ILE 4.2 5.3 + - - -
346A SER* 3.9 15.5 + - - +
347A ILE 3.0 28.1 + - - +
348A THR 3.2 14.7 + - - -
349A ASP* 3.8 15.5 - - - -
375A ARG* 3.8 32.3 - - - +
159E ALA* 5.4 4.0 - - - +
188E GLY 3.5 2.9 + - - +
189E GLU* 1.3 81.1 + - - +
191E THR* 1.3 56.0 + - - +
192E ARG 3.3 0.2 - - - -
193E GLU* 3.6 33.6 + - + +
194E GLY 2.8 30.1 + - - -
222E MET* 3.7 15.5 - - - -
260E ARG* 5.0 15.2 - - - +
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Residues in contact with THR 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO 3.9 2.9 - - - +
137A GLY 3.8 7.2 - - - +
138A ILE* 3.5 23.9 - - + +
141A ARG* 3.4 32.1 - - - +
309A GLU* 3.4 27.9 + - - +
189E GLU* 3.3 4.0 + - - -
190E ARG* 1.3 72.5 - - - +
192E ARG* 1.3 58.2 + - - +
194E GLY* 3.0 2.8 + - - -
195E ASN* 3.0 25.6 + - - +
221E GLN* 4.0 26.0 + - - +
222E MET* 4.5 3.1 + - - +
223E ASN* 4.8 3.7 + - - +
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Residues in contact with ARG 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.5 18.7 - - - +
142A ARG 4.8 9.6 - - - +
144A VAL* 4.0 15.3 - - + +
164A GLY 3.8 21.7 + - - -
166A ARG* 3.6 25.0 - - - +
349A ASP* 2.8 42.5 + - - -
375A ARG* 5.2 0.6 + - - +
376A VAL* 3.6 22.0 - - - +
190E ARG 3.3 0.6 - - - -
191E THR* 1.3 78.7 - - - +
193E GLU* 1.3 91.7 + - - +
195E ASN* 3.1 6.8 + - - +
196E ASP* 2.9 47.1 + - - +
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Residues in contact with GLU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASP* 4.7 0.2 - - - +
375A ARG* 4.0 23.8 - - - +
159E ALA* 4.9 9.7 - - - +
189E GLU* 4.0 16.9 - - - +
190E ARG* 3.4 34.3 + - + +
191E THR 3.4 0.2 - - - -
192E ARG* 1.3 109.9 + - - +
194E GLY* 1.3 59.9 + - - +
196E ASP* 3.7 10.0 - - + +
197E LEU* 2.9 30.1 + - - +
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Residues in contact with GLY 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 4.2 9.5 - - - +
189E GLU* 4.1 1.1 + - - -
190E ARG 2.8 16.2 + - - -
191E THR 3.0 6.4 + - - -
193E GLU* 1.3 76.7 - - - +
195E ASN* 1.3 56.5 + - - +
197E LEU* 3.3 4.0 + - - +
198E TYR* 3.0 26.7 + - - +
219E PHE* 3.6 32.5 - - - -
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Residues in contact with ASN 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.1 35.5 + - + +
139A LEU* 4.2 4.5 + - - +
141A ARG* 3.2 47.3 + - + +
142A ARG* 3.6 8.1 + - - +
191E THR 3.0 10.5 + - - +
192E ARG* 3.1 7.4 + - - +
194E GLY* 1.3 75.3 - - - +
196E ASP* 1.3 61.2 + - - +
198E TYR* 3.2 13.5 + - - -
199E ARG* 2.9 29.0 + - - +
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Residues in contact with ASP 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ARG 3.6 17.9 - - - +
143A SER* 3.7 19.5 + - - -
144A VAL* 5.5 0.5 + - - +
192E ARG* 2.9 45.1 + - - +
193E GLU* 4.0 9.8 - - + +
195E ASN* 1.3 76.7 - - - +
197E LEU* 1.3 57.8 + - - +
199E ARG* 3.5 20.8 + - - +
200E GLU* 3.0 33.5 + - - +
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E THR* 3.3 29.4 - - - +
167E ILE* 5.4 5.8 - - + -
168E GLN* 4.6 3.8 - - + +
184E PHE* 3.6 43.1 - - + -
189E GLU* 5.6 3.6 - - - +
193E GLU 2.9 19.6 + - - +
194E GLY 3.6 4.7 - - - +
196E ASP* 1.3 77.2 - - - +
198E TYR* 1.3 55.8 + - - +
200E GLU* 3.4 4.2 + - - +
201E MET* 2.9 59.5 + - + +
219E PHE* 4.1 9.4 - - + -
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Residues in contact with TYR 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 4.8 2.5 - - + -
139A LEU* 5.4 12.8 - - + -
93E GLY 4.9 7.6 + - - -
95E ILE* 3.7 35.9 - - + -
104E ASP* 5.2 6.4 - - + +
106E ARG* 5.0 4.5 - - - -
194E GLY 3.0 14.2 + - - +
195E ASN* 3.2 20.8 + - - +
197E LEU* 1.3 78.4 - - - +
199E ARG* 1.3 58.6 + - + +
201E MET* 3.3 4.4 + - - +
202E LYS* 2.9 58.1 + - + +
207E ILE* 3.8 20.4 - - + -
209E LEU* 3.4 27.5 - - - +
217E LEU* 3.8 17.9 - - + -
219E PHE* 5.1 0.8 - - + -
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Residues in contact with ARG 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ARG* 6.0 1.6 - - - +
143A SER* 4.3 25.1 - - - +
195E ASN* 2.9 18.8 + - - +
196E ASP* 3.9 25.6 + - - +
198E TYR* 1.3 77.0 - - + +
200E GLU* 1.3 64.4 + - - +
202E LYS* 3.2 22.3 + - - +
203E GLU* 3.0 55.5 + - + +
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Residues in contact with GLU 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E THR* 3.9 22.3 + - - +
165E VAL* 4.2 14.4 - - - +
168E GLN* 3.4 21.3 - - - +
196E ASP* 3.0 20.7 + - - +
197E LEU* 3.9 4.7 - - - +
199E ARG* 1.3 84.7 + - - +
201E MET* 1.3 58.1 + - - +
203E GLU* 3.8 7.0 - - + +
204E THR* 2.9 30.1 + - - +
424E PHE* 4.0 22.6 - - + -
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Residues in contact with MET 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E ILE* 6.4 0.7 - - - -
168E GLN* 3.3 20.9 - - + +
171E ILE* 3.9 19.7 - - + -
184E PHE* 5.1 4.7 - - + -
197E LEU* 2.9 45.2 + - + +
198E TYR* 3.9 0.9 - - - +
200E GLU* 1.3 73.5 - - - +
202E LYS* 1.3 65.2 + - - +
204E THR* 3.8 3.1 - - - -
206E VAL* 3.3 14.3 + - + +
207E ILE* 2.9 38.7 + - + -
215E VAL* 3.7 41.3 - - + -
217E LEU* 4.1 20.4 - - + -
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Residues in contact with LYS 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TYR* 2.9 53.8 + - + +
199E ARG* 3.2 24.4 + - - +
201E MET* 1.3 77.4 - - - +
203E GLU* 1.3 66.4 + - + +
205E GLY* 3.1 12.8 + - - -
207E ILE* 3.5 27.8 - - + +
209E LEU* 3.9 21.9 - - + +
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Residues in contact with GLU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ARG* 3.0 47.7 + - + +
200E GLU* 3.3 6.3 + - + +
202E LYS* 1.3 79.0 - - + +
204E THR* 1.3 59.6 + - - +
205E GLY 3.3 0.4 + - - -
423E VAL* 5.1 14.1 - - + +
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Residues in contact with THR 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLN* 3.4 27.6 - - - +
172E ASN* 4.4 5.2 + - - +
200E GLU* 2.9 19.8 + - - +
201E MET 3.7 0.7 - - - +
203E GLU* 1.3 78.0 - - - +
205E GLY* 1.3 59.3 + - - +
206E VAL* 3.6 29.6 + - + +
419E ALA 5.3 2.6 - - - +
420E VAL* 3.3 35.5 + - - +
423E VAL* 6.0 4.3 - - - -
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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
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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