Contacts of the strand formed by residues 206 - 216 (chain B) in PDB entry 6NQN
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 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU 3.4 3.1 - - - +
43B LYS* 3.0 43.5 + - - +
200B HIS* 3.1 23.1 - - - +
201B ASP* 2.8 34.4 + - + +
205B SER* 1.3 85.5 + - - +
207B VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET 3.5 1.4 - - - +
41B ASP* 3.2 6.9 - - - +
42B LEU* 2.8 52.8 + - + +
54B TYR* 3.7 31.9 - - + +
197B ILE* 4.1 20.4 - - + -
199B SER 3.5 3.1 - - - -
200B HIS* 4.0 2.5 - - + -
204B TYR* 3.6 37.2 - - + +
206B ASN* 1.3 79.9 - - - +
208B ASN* 1.3 71.4 + - - +
209B LEU* 4.4 1.8 - - + -
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Residues in contact with ASN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER* 5.0 2.4 + - - -
40B MET 3.3 11.2 + - - +
41B ASP* 3.1 27.2 + - - +
197B ILE* 3.6 4.5 - - - +
198B LYS* 2.9 36.9 + - - +
199B SER* 2.8 33.9 + - - +
207B VAL* 1.3 73.7 - - - +
209B LEU* 1.3 57.7 + - - +
210B HIS* 3.1 34.0 + - - -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER* 3.0 4.9 - - - -
40B MET* 2.8 43.8 + - + +
42B LEU* 3.8 22.0 - - + -
58B THR* 3.8 24.9 - - + +
61B PHE* 3.7 29.8 - - + -
63B KZ4 3.8 19.8 - - - -
195B ILE* 3.6 21.8 - - + -
196B GLU 3.5 20.4 - - - +
197B ILE* 4.0 10.1 - - + -
207B VAL* 4.4 2.7 - - + -
208B ASN* 1.3 73.8 - - - +
210B HIS* 1.3 64.0 + - - +
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN 3.3 6.6 + - - +
39B SER* 3.4 28.9 - - - -
63B KZ4 5.0 1.1 - - - -
194B HIS 4.7 0.4 - - - -
195B ILE* 3.4 5.0 - - - +
196B GLU* 2.9 38.4 + - + +
198B LYS* 3.4 41.1 + - + +
208B ASN* 3.1 29.6 + - - -
209B LEU* 1.3 74.6 - - - +
211B GLU* 1.3 63.7 + - - +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY 3.8 0.6 - - - +
37B LYS* 3.4 5.0 - - - +
38B GLN* 2.9 59.0 + - + +
63B KZ4 3.3 48.1 + - + +
65B ASN 5.1 0.9 - - - +
66B ARG* 4.6 4.2 + - - -
68B PHE 4.4 4.5 - - - +
193B HIS* 3.0 25.6 + - - -
194B HIS 3.4 15.7 - - - +
195B ILE* 4.2 3.4 - - + -
210B HIS* 1.3 77.9 - - - +
212B HIS* 1.3 67.2 + - - +
213B ALA* 3.2 16.7 - - - +
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Residues in contact with HIS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.4 26.8 - - + +
220A PRO* 4.9 10.5 + - - +
35B GLU 4.0 7.6 - - - -
36B GLY 3.2 9.4 + - - -
37B LYS* 3.8 32.7 - - + +
193B HIS* 3.4 1.7 - - - -
194B HIS* 2.9 38.8 + - + +
211B GLU* 1.3 77.2 - - - +
213B ALA* 1.3 69.4 + - - +
214B GLU* 3.5 37.3 + - + -
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.8 0.9 - - - -
36B GLY* 2.7 19.1 + - - -
66B ARG* 5.3 0.4 - - - -
68B PHE 3.6 15.3 - - - +
69B ALA* 3.9 10.8 - - + -
70B LYS 3.0 19.3 + - - -
191B VAL* 4.0 3.6 - - + -
192B ASP 3.1 12.1 - - - +
193B HIS* 3.9 7.4 - - + +
211B GLU* 3.2 23.6 - - - +
212B HIS* 1.3 73.0 + - - +
214B GLU* 1.3 67.9 + - - +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.9 21.3 - - + +
70B LYS* 3.6 39.7 - - + +
191B VAL* 3.4 3.3 - - - -
192B ASP* 2.7 39.6 + - + +
212B HIS* 3.5 26.4 + - + -
213B ALA* 1.3 78.8 - - - +
215B ALA* 1.3 63.7 + - - +
216B HIS* 4.0 3.1 - - + -
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA* 5.0 0.4 - - - +
70B LYS 2.8 18.4 + - - +
71B TYR* 3.7 42.0 - - + -
72B PRO* 3.6 20.6 - - + +
75B ILE* 4.6 1.3 - - + -
189B HIS* 4.3 2.2 - - + -
190B PHE 3.1 13.7 - - - +
191B VAL* 3.9 6.2 - - + +
214B GLU* 1.3 75.8 - - - +
216B HIS* 1.3 63.8 + - - +
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Residues in contact with HIS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 4.7 7.0 - - - -
192A ASP* 5.1 7.4 - - - -
72B PRO* 4.9 2.7 - - + -
75B ILE* 3.6 11.2 - - - +
143B THR* 4.3 4.0 - - + +
189B HIS* 3.5 4.7 - - - +
190B PHE* 2.8 59.2 + + + +
192B ASP* 2.9 44.0 + - - -
214B GLU* 4.0 5.2 - - + -
215B ALA* 1.3 77.6 - - - +
217B SER* 1.3 59.4 + - - +
218B GLY* 3.0 31.0 + - - +
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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