Contacts of the strand formed by residues 189 - 200 (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 HIS 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D TYR* 2.8 42.2 + + - -
75D ILE* 3.7 21.2 - - + +
76D VAL 4.7 0.2 - - - -
145D LYS* 3.7 3.1 - - - -
146D LEU* 2.8 55.8 + - + +
153D LEU* 4.7 3.4 - - + -
186D PRO* 3.7 27.4 - - + -
187D ASP 2.8 19.6 + - - +
188D TYR* 1.3 78.4 - - - +
190D PHE* 1.3 94.7 + - - +
191D VAL* 4.5 0.2 - - + -
215D ALA* 4.4 1.8 - - + -
216D HIS 3.6 11.2 - - - +
217D SER* 4.8 2.9 - - - +
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Residues in contact with PHE 190 (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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143D THR* 3.9 7.6 - - + -
144D GLU 3.1 8.1 - - - +
145D LYS* 3.6 45.3 - - + -
146D LEU* 4.1 0.9 - - - -
188D TYR* 3.8 15.0 - + - -
189D HIS* 1.3 84.7 - - - +
191D VAL* 1.3 66.5 + - - +
215D ALA* 3.2 6.8 - - - +
216D HIS* 2.9 50.4 + + + +
217D SER* 3.5 8.7 - - - -
218D GLY* 3.4 34.3 - - - -
141F PRO* 3.0 41.5 - - + -
142F SER* 4.2 4.0 - - - -
143F THR* 4.8 2.0 - - - -
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Residues in contact with VAL 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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66D ARG* 4.0 13.7 - - + -
69D ALA* 4.4 2.9 - - + -
71D TYR* 4.0 20.6 - - + +
144D GLU* 2.8 33.7 + - - +
146D LEU* 3.6 19.7 - - + +
189D HIS* 4.5 0.4 - - + -
190D PHE* 1.3 79.4 - - - +
192D ASP* 1.3 70.7 + - - +
193D HIS* 3.3 37.9 - - + +
213D ALA* 3.9 11.4 - - + -
214D GLU 3.4 9.0 - - - +
215D ALA* 4.1 10.1 - - + -
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Residues in contact with ASP 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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142D SER 3.3 5.2 - - - +
143D THR* 2.6 29.2 + - - +
191D VAL* 1.3 73.2 - - - +
193D HIS* 1.3 60.4 + - - +
212D HIS 3.9 0.2 - - - +
213D ALA* 3.1 7.6 - - - +
214D GLU* 2.8 40.0 + - + +
216D HIS* 2.8 32.7 + - - -
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Residues in contact with HIS 193 (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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63D KZ4 3.4 31.3 - + + -
66D ARG* 3.5 35.4 - - - -
141D PRO* 3.3 5.7 - - - +
142D SER* 2.8 48.6 + - - +
144D GLU* 2.8 29.4 + - + +
191D VAL* 3.3 35.1 - - + +
192D ASP* 1.3 73.8 - - - +
194D HIS* 1.3 64.1 + - - +
211D GLU* 2.9 20.2 + - - +
212D HIS 3.5 4.7 - - - -
213D ALA* 3.9 2.8 - - + +
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Residues in contact with HIS 194 (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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63D KZ4 5.2 0.4 - - - -
138D LYS* 2.9 29.3 + - - -
139D TRP 4.4 1.1 - - - -
140D GLU 4.6 0.2 - - - -
141D PRO* 3.9 33.2 - - + +
193D HIS* 1.3 75.3 - - - +
195D ILE* 1.3 72.2 + - - +
196D GLU* 3.8 27.0 + - + +
210D HIS 4.1 0.5 - - - +
211D GLU* 3.4 3.4 - - - -
212D HIS* 2.9 41.3 + - + +
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Residues in contact with ILE 195 (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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58D THR* 3.3 44.0 - - - +
59D THR* 3.8 6.7 - - + +
63D KZ4 3.7 40.3 + - + +
138D LYS* 4.5 2.6 + - - +
139D TRP* 3.9 43.3 + - + +
140D GLU 5.5 0.8 + - - +
193D HIS 4.3 0.2 - - - -
194D HIS* 1.3 80.7 + - - +
196D GLU* 1.3 67.7 + - - +
209D LEU* 3.7 12.8 - - + -
210D HIS 3.3 12.8 - - - +
211D GLU* 4.0 7.2 - - + -
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Residues in contact with GLU 196 (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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138D LYS* 4.5 14.4 - - - +
194D HIS* 3.8 34.2 + - + +
195D ILE* 1.3 82.2 - - - +
197D ILE* 1.3 65.1 + - - +
198D LYS* 3.5 28.3 + - + +
209D LEU* 3.4 6.6 - - - +
210D HIS* 2.7 47.1 + - + +
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Residues in contact with ILE 197 (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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54D TYR* 4.2 7.9 - - + -
55D ASP* 3.8 21.8 - - - +
58D THR* 4.1 14.1 - - + -
138D LYS* 6.1 2.0 - - - +
196D GLU* 1.3 74.0 - - - +
198D LYS* 1.3 60.7 + - - +
199D SER 3.5 27.1 - - - +
200D HIS* 4.0 15.9 - - + -
204D TYR* 4.1 20.6 - - + -
207D VAL* 3.9 15.9 - - + -
208D ASN 3.5 6.3 - - - +
209D LEU* 3.9 17.0 - - + +
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Residues in contact with LYS 198 (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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196D GLU* 3.5 31.2 + - + +
197D ILE* 1.3 77.4 - - - +
199D SER* 1.3 59.4 + - - -
200D HIS* 6.0 0.2 - - - -
208D ASN* 2.8 26.6 + - - +
210D HIS* 3.3 48.2 + - + +
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Residues in contact with SER 199 (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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197D ILE* 3.5 7.7 - - - +
198D LYS* 1.3 81.1 - - - +
200D HIS* 1.3 68.4 + - - +
208D ASN* 2.8 44.4 + - - +
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Residues in contact with HIS 200 (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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197D ILE* 4.0 13.7 - - + -
199D SER* 1.3 78.4 + - - +
201D ASP* 1.3 81.9 + - - +
202D LYS* 4.9 2.9 - - - -
204D TYR* 3.3 54.2 + + + -
206D ASN 3.1 15.7 - - - +
207D VAL* 4.0 3.4 - - + -
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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