Contacts of the helix formed by residues 184 - 192 (chain D) in PDB entry 3N2N
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 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D ASP 4.9 0.8 + - - -
151D GLY* 6.0 1.2 - - - -
182D ASP 4.0 0.2 + - - -
183D PHE* 1.3 73.8 - - - +
185D GLU* 1.3 62.4 + - - +
186D THR* 3.0 18.4 + - - +
187D GLN* 3.0 42.8 + - + +
188D LEU* 3.2 22.0 + - - +
209E GLN* 5.3 0.9 - - - +
210E GLY* 3.1 31.6 + - - +
213E HIS* 3.7 17.2 - - + +
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Residues in contact with GLU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D PHE* 3.8 28.4 + - + -
184D ASN* 1.3 72.5 - - - +
186D THR* 1.3 63.8 + - - +
188D LEU* 3.5 2.2 + - - +
189D ALA* 2.9 29.1 + - - +
195D LYS* 4.4 29.3 + - - +
198D VAL* 4.0 17.0 - - + +
199E PHE* 5.9 1.9 - - - -
207E ALA* 5.1 11.7 - - - +
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ASN* 3.0 11.4 + - - +
185D GLU* 1.3 78.4 - - - +
187D GLN* 1.3 66.0 + - - +
189D ALA* 3.3 13.9 + - - +
190D ARG* 3.6 12.0 + - + +
195D LYS* 3.2 35.5 + - - +
207E ALA 4.7 1.0 + - - -
210E GLY* 4.0 0.9 - - - -
211E ILE* 3.4 27.5 + - + +
214E SER* 3.7 22.2 - - - +
215E ILE* 6.2 0.9 - - + -
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Residues in contact with GLN 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D GLY* 5.3 2.2 - - - +
158D PHE* 3.5 36.2 - - + -
184D ASN* 3.0 37.5 - - + +
186D THR* 1.3 75.9 - - - +
188D LEU* 1.3 64.1 + - + +
190D ARG* 2.8 52.0 + - - +
191D ILE 3.9 0.3 + - - -
213E HIS* 4.8 6.0 + - + -
214E SER* 3.0 29.6 + - - +
217E LYS* 3.9 27.7 - - - +
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D MET* 5.4 1.1 - - + -
149D THR* 3.9 20.9 - - + +
151D GLY* 3.8 27.8 - - - -
158D PHE* 4.7 7.2 - - + -
177D ALA* 4.1 18.5 - - + +
179D GLY* 3.8 22.9 - - - +
183D PHE* 3.7 26.2 - - + -
184D ASN 3.2 15.0 + - - +
185D GLU 4.0 3.8 - - - +
187D GLN* 1.3 79.8 - - + +
189D ALA* 1.3 56.1 + - - +
190D ARG 3.1 0.9 - - - -
191D ILE* 3.0 14.7 + - + +
192D ALA* 2.8 29.1 + - - +
198D VAL* 3.9 14.4 - - + -
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D GLU 2.9 18.8 + - - +
186D THR* 3.4 9.2 - - + +
187D GLN 3.2 0.6 - - - -
188D LEU* 1.3 73.4 - - - +
190D ARG* 1.3 60.2 + - - +
191D ILE 3.3 0.2 - - - -
192D ALA 3.1 18.8 - - - +
193D ASP 4.6 0.9 - - - +
194D SER* 4.4 8.3 + - - -
195D LYS* 3.4 37.7 - - + +
198D VAL* 3.8 8.0 - - - +
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Residues in contact with ARG 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D PHE* 3.3 47.6 + - + +
159D PHE* 5.6 1.0 - - - +
162D GLU* 2.7 65.5 + - + +
166D ASN* 4.7 0.2 - - - +
169D ARG* 3.7 10.6 + - - -
186D THR* 3.7 10.5 - - + +
187D GLN* 2.8 41.7 + - - +
189D ALA* 1.3 78.3 - - - +
191D ILE* 1.3 61.9 + - - +
192D ALA 4.0 0.5 - - - +
214E SER* 4.2 8.1 + - - +
217E LYS* 5.6 3.6 + - - +
218E LYS* 5.0 25.5 - - - +
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D MET* 3.7 16.4 - - + -
124D PHE* 3.5 34.5 - - + -
147D ALA* 5.1 4.5 - - + -
158D PHE* 3.7 27.1 - - + -
161D SER* 3.7 17.7 - - - -
162D GLU* 3.6 30.5 - - + +
165D ALA* 3.4 9.8 - - + +
169D ARG* 2.8 30.3 + - - -
175D VAL* 3.6 5.4 - - + +
177D ALA* 5.1 5.4 - - + -
187D GLN 4.2 1.6 - - - +
188D LEU* 3.0 15.6 + - + +
190D ARG* 1.3 77.4 - - - +
192D ALA* 1.3 57.1 - - - +
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ARG* 3.3 6.1 + - - -
175D VAL* 3.4 19.1 - - - +
177D ALA* 3.8 10.5 - - + +
188D LEU 2.8 18.0 + - - +
189D ALA* 3.1 12.0 - - - +
190D ARG 4.0 1.7 - - - +
191D ILE* 1.3 79.9 - - - +
193D ASP* 1.3 66.2 + - - +
194D SER 3.3 13.5 - - - +
197D HIS 3.8 18.6 - - - +
198D VAL* 3.8 6.5 - - + -
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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