Contacts of the helix formed by residues 202 - 215 (chain E) in PDB entry 1P7G
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 ASN 202 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95E PRO* 3.1 19.6 - - - +
96E ASN 2.8 9.2 + - - +
97E MSE 3.3 23.2 - - - +
98E ALA* 3.4 10.9 - - + +
102E LYS* 3.5 34.4 + - - +
103E GLY* 4.0 6.3 - - - -
200E VAL 3.1 2.6 + - - -
201E VAL* 1.3 67.6 - - - +
203E TRP* 1.3 61.3 + - - +
204E ASP* 3.2 25.3 + - - +
205E ASP* 3.5 11.5 + - - +
206E VAL* 3.2 21.4 + - - +
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Residues in contact with TRP 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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102E LYS 4.4 5.0 + - - +
104E GLY* 3.3 22.8 + - - -
105E GLY 3.1 17.8 + - - -
106E LYS 4.2 1.8 - - - +
107E PRO* 3.4 43.7 - - + +
108E GLY 5.4 1.3 - - - +
111E ILE* 4.2 11.7 - - + +
115E ILE* 4.5 3.1 - - + -
122E PHE* 3.8 19.0 - + - -
125E PHE* 3.7 26.0 - + - -
144E LEU* 5.4 0.7 - - + -
173E LEU* 3.8 14.6 - - + -
198E TRP* 3.9 12.4 + + - -
201E VAL* 3.1 34.5 + - + +
202E ASN* 1.3 69.1 - - - +
204E ASP* 1.3 59.8 + - - +
206E VAL* 3.6 32.4 - - + +
207E GLU* 2.9 29.1 + - - +
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Residues in contact with ASP 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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102E LYS* 4.5 15.7 + - + +
202E ASN* 3.1 13.4 - - - +
203E TRP* 1.3 76.2 - - - +
205E ASP* 1.3 58.6 + - - +
207E GLU* 3.2 6.1 + - - +
208E ARG* 2.8 49.7 + - - +
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Residues in contact with ASP 205 (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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95E PRO* 2.9 35.7 - - + +
96E ASN* 2.8 18.2 + - - -
202E ASN* 3.2 14.1 + - - +
204E ASP* 1.3 82.5 + - - +
206E VAL* 1.3 60.6 + - - +
208E ARG* 3.4 14.3 + - - +
209E ARG* 2.7 68.0 + - - +
222E LEU* 5.0 2.9 - - - +
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Residues in contact with VAL 206 (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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96E ASN* 4.5 4.5 - - - +
111E ILE* 3.5 27.1 - - + -
144E LEU* 5.0 0.9 - - + -
172E LEU* 3.9 26.7 - - + +
173E LEU* 3.9 29.6 - - + -
201E VAL* 4.5 0.4 - - + -
202E ASN 3.2 15.4 + - - +
203E TRP* 3.6 33.4 - - + +
204E ASP 3.2 0.6 - - - -
205E ASP* 1.3 76.7 - - - +
207E GLU* 1.3 62.1 + - - +
209E ARG* 3.0 5.7 + - - +
210E LEU* 3.0 20.3 + - - +
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Residues in contact with GLU 207 (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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108E GLY 6.1 0.2 - - - -
109E GLY* 3.4 11.4 - - - +
110E LYS* 2.9 24.7 + - - +
111E ILE* 2.8 39.3 + - + +
203E TRP 2.9 17.7 + - - +
204E ASP* 3.6 6.3 - - - +
206E VAL* 1.3 75.1 - - - +
208E ARG* 1.3 59.4 + - + +
210E LEU* 3.7 7.2 - - - +
211E GLN* 2.9 49.3 + - + +
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Residues in contact with ARG 208 (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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123A GLU* 4.1 26.9 - - - +
204E ASP* 2.8 43.7 + - - +
205E ASP* 3.6 14.4 + - - +
206E VAL 3.2 0.2 - - - -
207E GLU* 1.3 79.1 - - + +
209E ARG* 1.3 60.1 + - - +
211E GLN* 3.9 6.5 + - - +
212E LYS* 3.4 24.1 + - - +
222E LEU* 3.3 58.5 + - - +
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Residues in contact with ARG 209 (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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92E ILE* 3.8 12.6 - - - +
95E PRO* 3.1 34.1 - - - +
96E ASN* 3.2 6.0 - - - +
171E VAL 3.8 10.8 - - - -
172E LEU* 3.4 31.6 - - + -
205E ASP* 2.7 34.4 + - - +
206E VAL 3.0 7.7 + - - +
208E ARG* 1.3 76.1 - - - +
210E LEU* 1.3 58.4 + - - +
212E LYS* 3.3 3.5 + - - +
213E ALA* 3.1 21.7 + - - +
219E ALA* 3.2 42.4 + - + +
222E LEU* 4.0 11.5 + - - +
305E ACT 2.6 34.3 + - - +
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Residues in contact with LEU 210 (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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110E LYS* 3.7 3.4 - - + -
111E ILE* 3.2 50.0 - - + +
114E LEU* 3.4 31.6 - - + -
146E TYR* 3.9 12.1 - - + -
153E LEU* 4.3 0.9 - - + -
172E LEU* 3.7 29.7 - - + +
206E VAL 3.0 12.0 + - - +
207E GLU* 3.7 9.4 - - - +
209E ARG* 1.3 75.5 - - - +
211E GLN* 1.3 55.7 + - - +
213E ALA* 3.0 2.1 + - + -
214E LEU* 2.7 47.1 + - + +
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Residues in contact with GLN 211 (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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110E LYS* 4.0 15.0 - - - +
207E GLU* 2.9 38.2 + - + +
208E ARG* 3.9 10.3 - - - +
210E LEU* 1.3 76.7 - - - +
212E LYS* 1.3 63.5 + - + +
214E LEU* 3.5 15.5 + - - +
215E ASN* 2.9 39.7 + - - +
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Residues in contact with LYS 212 (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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195A ASP* 4.4 15.6 + - - +
208E ARG 3.4 13.0 - - - +
209E ARG* 3.3 6.2 + - - +
210E LEU 3.2 0.4 - - - -
211E GLN* 1.3 74.5 - - + +
213E ALA* 1.3 65.0 + - - +
215E ASN 3.2 6.2 + - - -
217E GLN* 2.8 65.0 + - + +
218E ILE 3.4 24.2 - - - +
219E ALA* 4.2 7.4 - - + -
220E LEU 3.8 14.1 - - - +
221E LYS 4.5 5.3 + - - -
222E LEU* 3.3 26.8 + - - +
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Residues in contact with ALA 213 (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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146E TYR* 3.7 46.4 - - + -
170E GLN* 4.4 9.9 - - + -
172E LEU* 4.0 5.4 - - + -
209E ARG 3.1 12.7 + - - +
210E LEU* 3.0 14.1 + - + +
212E LYS* 1.3 77.3 - - - +
214E LEU* 1.3 62.4 + - - +
216E GLY* 3.0 14.2 + - - -
217E GLN 3.8 11.4 + - - +
219E ALA* 4.9 0.4 - - - +
218H ILE* 4.8 2.7 - - - +
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Residues in contact with LEU 214 (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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110E LYS* 3.7 44.9 - - + +
114E LEU* 3.4 29.8 - - + -
146E TYR* 3.9 21.6 + - + +
210E LEU* 2.7 32.2 + - + +
211E GLN* 3.7 17.7 - - - +
212E LYS 3.3 0.2 - - - -
213E ALA* 1.3 72.6 - - - +
215E ASN* 1.3 65.0 + - - +
216E GLY* 3.1 1.6 + - - -
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Residues in contact with ASN 215 (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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134A LYS* 4.3 17.0 - - - +
189A ASP* 4.2 16.1 - - - +
191A GLY* 6.4 3.1 - - - -
192A SER* 5.6 0.4 - - - +
195A ASP* 4.8 0.2 + - - -
211E GLN* 2.9 31.5 + - - +
212E LYS 3.2 7.8 + - - +
214E LEU* 1.3 79.7 - - - +
216E GLY* 1.3 59.9 + - - +
217E GLN* 3.7 25.4 + - - +
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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