Contacts of the strand formed by residues 206 - 216 (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 ASN 206 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E LEU 3.3 3.4 - - - +
43E LYS* 3.5 32.6 + - - +
199E SER 5.5 0.2 - - - -
200E HIS* 3.2 23.0 - - - +
201E ASP* 2.8 33.5 + - + +
205E SER* 1.3 85.9 + - - +
207E VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 207 (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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40E MET 3.6 1.0 - - - +
41E ASP* 3.3 5.9 - - - +
42E LEU* 2.7 47.3 + - + +
54E TYR* 3.6 43.1 - - + +
197E ILE* 4.0 24.0 - - + -
199E SER 3.6 3.1 - - - -
200E HIS* 4.1 2.2 - - + -
204E TYR* 3.7 29.4 - - + +
206E ASN* 1.3 80.5 - - - +
208E ASN* 1.3 71.0 + - - +
209E LEU* 3.9 2.4 + - + -
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Residues in contact with ASN 208 (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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39E SER* 4.9 2.6 + - - -
40E MET 3.3 13.1 + - - +
41E ASP* 3.1 27.7 + - - +
197E ILE* 3.6 4.3 - - - +
198E LYS* 2.9 34.8 + - - +
199E SER* 3.0 31.2 + - - +
207E VAL* 1.3 71.9 - - - +
209E LEU* 1.3 58.1 + - - +
210E HIS* 2.9 34.8 + - - -
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Residues in contact with LEU 209 (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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39E SER* 3.1 4.3 - - - -
40E MET* 2.8 37.3 + - + +
42E LEU* 3.8 22.9 - - + -
58E THR* 3.8 26.9 - - + +
61E PHE* 3.8 28.5 - - + -
63E KZ4 3.9 17.1 - - - -
195E ILE* 3.6 20.9 - - + -
196E GLU 3.5 20.6 - - - +
197E ILE* 3.9 15.3 - - + -
207E VAL* 3.9 2.7 - - + -
208E ASN* 1.3 73.4 - - - +
210E HIS* 1.3 62.4 + - - +
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Residues in contact with HIS 210 (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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38E GLN 3.4 6.7 + - - +
39E SER* 3.4 23.2 + - - -
63E KZ4 4.9 1.1 - - - -
194E HIS 4.7 0.2 - - - -
195E ILE* 3.4 8.9 - - - +
196E GLU* 2.9 38.3 + - + +
198E LYS* 3.3 35.4 - - + +
208E ASN* 2.9 30.9 + - - -
209E LEU* 1.3 80.8 - - - +
211E GLU* 1.3 62.0 + - - +
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Residues in contact with GLU 211 (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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36E GLY 3.7 0.6 - - - +
37E LYS* 3.3 5.2 - - - +
38E GLN* 2.8 60.1 + - + +
63E KZ4 3.2 39.8 + - + +
65E ASN 5.0 0.7 - - - +
66E ARG* 4.5 4.1 + - - -
68E PHE 4.8 2.9 - - - +
193E HIS* 2.8 31.4 + - - +
194E HIS 3.5 11.9 - - - +
195E ILE* 4.0 14.1 - - + -
210E HIS* 1.3 76.2 - - - +
212E HIS* 1.3 63.3 + - - +
213E ALA* 3.5 13.9 - - - +
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Residues in contact with HIS 212 (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* 3.2 30.6 - - + +
220C PRO* 4.5 13.8 + - + -
35E GLU 4.1 3.2 + - - -
36E GLY 3.1 10.3 - - - -
37E LYS* 3.7 36.3 - - + -
193E HIS* 3.5 1.4 - - - -
194E HIS* 2.9 41.0 + - + +
211E GLU* 1.3 76.3 - - - +
213E ALA* 1.3 75.8 + - - +
214E GLU* 3.0 29.8 + - - +
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Residues in contact with ALA 213 (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* 3.8 1.3 - - - -
36E GLY* 2.7 18.0 + - - -
66E ARG* 5.2 0.4 - - - -
68E PHE 3.6 16.4 - - - +
69E ALA* 4.0 4.9 - - + -
70E LYS 3.0 19.5 + - - -
191E VAL* 4.0 8.5 - - + -
192E ASP 3.1 11.4 - - - +
193E HIS* 3.8 8.7 - - + +
211E GLU* 3.5 19.1 - - - +
212E HIS* 1.3 77.0 - - - +
214E GLU* 1.3 67.4 + - - +
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Residues in contact with GLU 214 (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 19.8 - - + +
35E GLU 4.7 0.9 - - - +
70E LYS* 3.5 38.7 + - + +
191E VAL* 4.3 2.7 - - - -
192E ASP* 2.9 34.7 + - + +
212E HIS* 3.0 28.5 + - + +
213E ALA* 1.3 80.2 - - - +
215E ALA* 1.3 65.6 + - - +
216E HIS* 3.9 3.6 - - + -
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Residues in contact with ALA 215 (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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69E ALA* 4.9 0.8 - - - +
70E LYS 2.8 17.1 + - - +
71E TYR* 3.8 41.7 - - + -
72E PRO* 3.6 20.1 - - + +
75E ILE* 4.7 0.9 - - + -
189E HIS* 4.3 2.7 - - + -
190E PHE 3.1 14.4 - - - +
191E VAL* 4.0 5.8 - - + +
214E GLU* 1.3 76.9 - - - +
216E HIS* 1.3 65.2 + - - +
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Residues in contact with HIS 216 (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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143C THR* 4.8 6.1 - - - -
192C ASP* 5.1 8.1 - - - -
72E PRO* 4.7 2.0 - - - -
75E ILE* 3.6 11.2 - - - -
143E THR* 4.3 4.5 - - + +
189E HIS* 3.5 5.0 - - - +
190E PHE* 2.9 55.5 + + + +
192E ASP* 2.8 45.3 + - - -
214E GLU* 3.9 8.1 - - + -
215E ALA* 1.3 76.1 - - - +
217E SER* 1.3 58.3 + - - +
218E GLY* 3.0 30.6 + - - -
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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