Contacts of the strand formed by residues 189 - 200 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71E TYR* 2.8 40.6 + + - -
75E ILE* 3.8 21.5 - - + +
145E LYS* 3.7 2.1 - - - -
146E LEU* 2.9 54.0 + - + +
153E LEU* 5.0 0.4 - - + -
186E PRO* 3.9 24.7 - - + -
187E ASP 2.8 20.3 + - - +
188E TYR* 1.3 79.5 - - - +
190E PHE* 1.3 100.0 + - - +
215E ALA* 4.3 2.0 - - + -
216E HIS 3.5 10.8 - - - +
217E SER* 4.7 3.4 - - - +
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Residues in contact with PHE 190 (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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141C PRO* 3.1 40.4 - - + -
142C SER* 4.3 8.7 - - - -
143C THR* 4.7 2.0 - - - -
143E THR* 3.9 10.5 - - + -
144E GLU 3.1 7.9 - - - +
145E LYS* 3.6 38.4 - - + -
146E LEU* 4.1 0.9 - - - -
188E TYR* 3.9 13.5 - + - -
189E HIS* 1.3 80.9 - - - +
191E VAL* 1.3 66.2 + - - +
215E ALA* 3.1 6.8 - - - +
216E HIS* 2.9 60.3 + + + +
217E SER* 3.5 22.0 - - - -
218E GLY* 3.5 16.2 - - - -
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Residues in contact with VAL 191 (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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66E ARG* 3.9 17.3 - - + -
69E ALA* 4.5 2.0 - - + -
71E TYR* 3.9 20.2 - - + +
143E THR* 4.4 0.2 - - - -
144E GLU* 2.7 35.5 + - - +
146E LEU* 3.5 21.1 - - + -
189E HIS* 4.4 0.4 - - - +
190E PHE* 1.3 79.2 - - - +
192E ASP* 1.3 72.5 + - - +
193E HIS* 3.3 35.8 - - + +
213E ALA* 4.0 8.5 - - + -
214E GLU 3.6 8.3 - - - +
215E ALA* 4.0 9.6 - - + -
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Residues in contact with ASP 192 (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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216C HIS* 5.4 8.4 - - - -
218C GLY* 5.5 1.8 - - - -
219C LEU* 3.6 33.3 + - + +
142E SER 3.3 5.8 - - - +
143E THR* 2.7 27.3 + - - +
190E PHE 4.2 0.2 - - - -
191E VAL* 1.3 72.2 - - - +
193E HIS* 1.3 60.0 + - - +
213E ALA* 3.1 8.1 - - - +
214E GLU* 2.9 35.1 + - + +
216E HIS* 2.8 35.5 + - - -
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Residues in contact with HIS 193 (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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219C LEU* 4.3 6.2 + - - +
63E KZ4 3.4 31.9 - + + -
66E ARG* 3.4 31.4 - - - -
141E PRO* 3.4 5.5 - - - +
142E SER* 2.8 48.8 + - - +
144E GLU* 2.9 28.2 + - + -
191E VAL* 3.3 36.8 - - + +
192E ASP* 1.3 73.4 - - - +
194E HIS* 1.3 64.1 + - - +
211E GLU* 2.8 24.5 + - - +
212E HIS 3.5 4.3 - - - -
213E ALA* 3.8 3.1 - - + +
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Residues in contact with HIS 194 (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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219C LEU* 4.0 26.4 + - + -
220C PRO 6.0 0.8 - - - -
63E KZ4 5.4 0.4 - - - -
138E LYS* 3.2 26.2 + - - -
139E TRP 4.6 0.9 - - - -
141E PRO* 4.3 25.8 - - + +
193E HIS* 1.3 76.4 - - - +
195E ILE* 1.3 66.0 - - - +
196E GLU* 3.4 37.1 + - + +
210E HIS 4.2 0.3 - - - +
211E GLU* 3.5 2.8 - - - +
212E HIS* 2.9 40.6 + - + +
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Residues in contact with ILE 195 (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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58E THR* 3.3 44.6 - - - +
59E THR* 3.8 6.3 - - + +
63E KZ4 3.6 40.4 + - + +
138E LYS* 4.7 1.7 + - - +
139E TRP* 3.9 43.2 + - + +
140E GLU 5.5 1.2 + - - +
194E HIS* 1.3 77.3 - - - +
196E GLU* 1.3 73.3 + - - +
209E LEU* 3.6 12.8 - - + -
210E HIS 3.4 13.7 - - - +
211E GLU* 4.0 5.6 - - + -
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Residues in contact with GLU 196 (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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138E LYS* 4.3 18.0 - - - +
194E HIS* 3.4 40.0 + - + +
195E ILE* 1.3 81.9 - - - +
197E ILE* 1.3 63.0 + - - +
198E LYS* 3.4 34.3 + - + +
209E LEU* 3.5 5.5 - - - +
210E HIS* 2.9 36.8 + - + +
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Residues in contact with ILE 197 (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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54E TYR* 4.2 16.6 - - + -
55E ASP* 3.6 24.2 - - - +
58E THR* 4.0 14.8 - - + -
138E LYS* 6.1 1.8 - - - +
196E GLU* 1.3 72.8 - - - +
198E LYS* 1.3 60.6 + - - +
199E SER 3.6 24.5 - - - +
200E HIS* 4.2 16.6 - - + -
204E TYR* 4.3 14.6 - - + -
207E VAL* 4.0 13.5 - - + -
208E ASN 3.6 3.6 - - - -
209E LEU* 3.9 17.0 - - + +
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Residues in contact with LYS 198 (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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196E GLU* 4.0 33.5 + - + +
197E ILE* 1.3 74.8 - - - +
199E SER* 1.3 62.9 + - - +
200E HIS* 6.1 0.2 - - - -
208E ASN* 2.9 20.7 + - - +
210E HIS* 3.3 46.4 - - + +
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Residues in contact with SER 199 (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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197E ILE* 3.5 6.4 - - - +
198E LYS* 1.3 81.8 - - - +
200E HIS* 1.3 70.1 + - - +
207E VAL* 3.6 1.0 - - - -
208E ASN* 3.0 41.3 + - - +
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Residues in contact with HIS 200 (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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197E ILE* 4.2 11.0 - - + -
199E SER* 1.3 83.3 + - - +
201E ASP* 1.3 83.4 + - - +
202E LYS* 4.6 6.1 - - - -
204E TYR* 3.5 51.8 + + + -
206E ASN 3.2 15.0 - - - +
207E VAL* 4.1 3.6 - - + -
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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