Contacts of the strand formed by residues 206 - 216 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D LEU 3.4 3.1 - - - +
43D LYS* 3.5 25.2 - - - +
200D HIS* 3.1 23.8 - - - +
201D ASP* 3.0 33.0 + - + +
205D SER* 1.3 86.4 + - - +
207D VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 207 (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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40D MET 3.6 1.4 - - - +
41D ASP* 3.4 6.1 - - - +
42D LEU* 2.9 40.8 + - + +
54D TYR* 3.6 37.7 - - + +
197D ILE* 3.9 27.6 - - + -
199D SER 3.5 3.1 - - - -
200D HIS* 4.0 1.6 - - + -
204D TYR* 3.6 35.9 - - + +
206D ASN* 1.3 81.2 - - - +
208D ASN* 1.3 67.3 + - - +
209D LEU* 4.0 2.8 + - + +
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Residues in contact with ASN 208 (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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39D SER* 4.9 2.0 + - - -
40D MET 3.5 12.9 + - - +
41D ASP* 3.2 25.7 + - - +
197D ILE* 3.5 5.4 - - - +
198D LYS* 2.8 43.5 + - - +
199D SER* 2.8 35.0 + - - +
207D VAL* 1.3 71.9 - - - +
209D LEU* 1.3 55.9 + - - +
210D HIS* 3.0 35.1 + - - -
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Residues in contact with LEU 209 (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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38D GLN 4.6 0.2 - - - -
39D SER* 3.1 5.2 - - - -
40D MET* 3.0 36.4 + - + +
42D LEU* 3.9 22.7 - - + -
58D THR* 3.9 32.3 - - + +
61D PHE* 3.8 22.0 - - + -
63D KZ4 3.7 27.1 - - - -
195D ILE* 3.7 19.3 - - + -
196D GLU 3.4 21.1 - - - +
197D ILE* 3.9 6.3 - - + -
207D VAL* 4.5 2.5 - - + -
208D ASN* 1.3 74.8 - - - +
210D HIS* 1.3 63.6 + - - +
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Residues in contact with HIS 210 (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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38D GLN 3.4 6.7 - - - -
39D SER* 3.4 27.0 + - - -
63D KZ4 5.0 0.7 - - - -
194D HIS 4.6 0.4 - - - -
195D ILE* 3.3 6.8 - - - +
196D GLU* 2.7 47.2 + - + +
198D LYS* 3.3 39.8 + - + +
208D ASN* 3.0 31.7 + - - -
209D LEU* 1.3 75.6 - - - +
211D GLU* 1.3 61.9 + - - +
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Residues in contact with GLU 211 (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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36D GLY 3.6 1.0 - - - +
37D LYS* 3.4 5.5 - - - +
38D GLN* 2.9 57.1 + - + +
63D KZ4 3.2 40.6 + - + +
65D ASN 5.1 0.9 - - - +
66D ARG* 4.6 4.0 + - - -
68D PHE 4.7 4.4 - - - +
193D HIS* 2.9 29.3 + - - -
194D HIS 3.4 12.8 - - - +
195D ILE* 4.0 14.6 - - + -
210D HIS* 1.3 76.4 - - - +
212D HIS* 1.3 65.0 + - - +
213D ALA* 3.5 15.1 - - - +
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Residues in contact with HIS 212 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D GLU 4.0 5.4 + - - -
36D GLY 3.1 11.2 - - - +
37D LYS* 3.8 34.7 - - + -
192D ASP 3.9 0.2 - - - +
193D HIS* 3.5 2.6 - - - -
194D HIS* 2.9 41.6 + - + +
211D GLU* 1.3 76.5 - - - +
213D ALA* 1.3 76.3 + - - +
214D GLU* 3.1 32.6 + - + +
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Residues in contact with ALA 213 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLY* 2.8 14.7 + - - -
66D ARG* 5.3 0.4 - - - -
68D PHE 3.5 17.2 + - - +
69D ALA* 3.9 11.2 - - + -
70D LYS 3.0 19.5 + - - -
191D VAL* 3.9 2.9 - - + -
192D ASP 3.1 11.4 - - - +
193D HIS* 3.9 9.2 - - + +
211D GLU* 3.5 19.1 - - - +
212D HIS* 1.3 76.5 - - - +
214D GLU* 1.3 68.7 + - - +
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Residues in contact with GLU 214 (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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35D GLU 4.7 0.5 - - - +
70D LYS* 3.6 37.0 - - + +
191D VAL* 4.2 4.0 - - - -
192D ASP* 2.8 43.1 + - + +
212D HIS* 3.1 31.3 + - + +
213D ALA* 1.3 79.4 - - - +
215D ALA* 1.3 64.4 + - - +
216D HIS* 3.9 3.5 - - + -
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Residues in contact with ALA 215 (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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69D ALA* 5.1 0.8 - - - +
70D LYS 2.9 15.8 + - - +
71D TYR* 3.6 43.7 - - + -
72D PRO* 3.5 21.1 - - + +
75D ILE* 4.4 3.6 - - + -
189D HIS* 4.4 0.4 - - + -
190D PHE 3.2 13.0 - - - +
191D VAL* 4.1 4.6 - - + +
214D GLU* 1.3 76.8 - - - +
216D HIS* 1.3 65.5 + - - +
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Residues in contact with HIS 216 (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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72D PRO* 4.7 2.7 - - - -
75D ILE* 3.5 15.5 - - - +
143D THR* 4.3 5.2 - - + -
189D HIS* 3.6 0.9 - - - +
190D PHE* 2.9 56.9 + + + +
192D ASP* 2.8 45.9 + - - -
214D GLU* 3.9 10.1 - - + -
215D ALA* 1.3 76.5 - - - +
217D SER* 1.3 60.1 + - - +
218D GLY* 3.0 30.7 + - - +
143F THR* 4.7 6.1 - - - -
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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