Contacts of the strand formed by residues 210 - 220 (chain E) in PDB entry 3BXB
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 TYR 210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E ARG* 3.3 43.7 - - + +
43E ILE 2.9 25.6 - - - -
44E LYS* 3.9 27.1 - - + -
203E LYS* 4.5 28.7 - - + -
204E GLU* 3.3 6.6 - - - +
205E ALA* 3.1 48.9 + - + +
206E ASP* 5.3 1.3 - - - +
208E GLU 4.5 0.2 - - - -
209E THR* 1.3 82.0 + - - +
211E VAL* 1.3 70.7 + - - +
212E GLU* 4.0 8.0 + - - -
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Residues in contact with VAL 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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41E MET 3.5 2.8 - - - +
42E ARG* 4.7 0.4 - - - -
43E ILE* 2.8 40.8 + - + +
55E PHE* 4.1 42.6 - - + -
201E ARG* 3.8 29.2 - - + +
203E LYS 3.5 7.2 - - - +
204E GLU* 4.7 1.6 - - + -
208E GLU* 4.2 20.4 - - + +
210E TYR* 1.3 82.4 - - - +
212E GLU* 1.3 72.1 + - - +
213E GLN* 4.2 10.8 - - + +
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Residues in contact with GLU 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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40E THR* 4.0 18.1 + - + +
41E MET 3.4 7.9 - - - +
42E ARG* 4.0 21.9 + - + +
201E ARG* 3.5 6.1 - - - +
202E ILE* 2.7 55.2 + - + +
203E LYS* 3.1 37.9 + - + +
210E TYR* 4.0 14.6 + - + +
211E VAL* 1.3 74.3 - - - +
213E GLN* 1.3 58.0 + - - +
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Residues in contact with GLN 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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40E THR* 3.3 5.1 - - - +
41E MET* 2.8 44.3 + - + +
43E ILE* 3.9 12.9 - - + +
55E PHE* 3.7 22.2 - - - -
59E ALA* 2.7 43.2 + - - +
62E PHE* 3.7 15.6 - - - +
63E NRQ 3.4 17.4 - - - +
199E LEU* 3.6 26.4 - - + +
200E GLU 3.5 5.4 - - - +
201E ARG* 4.6 3.2 + - + +
202E ILE* 5.0 0.4 - - - -
211E VAL* 4.2 6.8 - - + +
212E GLU* 1.3 76.1 - - - +
214E HIS* 1.3 60.6 + - - +
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Residues in contact with HIS 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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38E THR* 4.2 11.3 - - + +
39E GLN 2.9 33.1 + - - -
40E THR* 3.3 14.1 + - - +
63E NRQ 4.0 2.7 - - - -
198E ARG 3.8 0.5 - - - +
199E LEU* 3.4 4.9 - - - +
200E GLU* 2.7 63.9 + - + +
202E ILE* 4.0 19.7 - - + +
213E GLN* 1.3 74.1 - - - +
215E GLU* 1.3 70.3 + - - +
216E VAL* 4.1 12.8 + - + +
225F PRO 5.6 1.4 + - - -
227F LYS* 4.0 33.0 + - + +
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Residues in contact with GLU 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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37E GLY 3.5 2.1 - - - +
38E THR* 3.5 3.1 - - - -
39E GLN* 2.9 56.7 + - + +
63E NRQ 2.8 66.6 + - + +
66E SER* 5.1 1.0 + - - +
197E ARG* 3.5 11.6 - - - +
198E ARG 3.3 14.6 - - - +
199E LEU* 4.2 4.3 - - + -
214E HIS* 1.3 79.4 + - - +
216E VAL* 1.3 69.6 + - - +
217E ALA* 4.1 12.2 - - + +
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Residues in contact with VAL 216 (chain E).
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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36E GLU 5.0 2.2 - - - +
37E GLY 3.4 5.2 - - - +
38E THR* 4.0 22.4 - - + -
197E ARG* 3.4 1.0 - - - -
198E ARG* 3.0 45.2 + - + +
200E GLU* 5.1 0.2 - - - +
214E HIS* 4.1 11.1 + - + +
215E GLU* 1.3 74.5 - - - +
217E ALA* 1.3 67.0 + - - +
218E VAL* 4.8 7.0 - - + -
224F LEU* 4.1 18.2 - - + +
225F PRO* 3.4 45.8 - - + +
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Residues in contact with ALA 217 (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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37E GLY* 3.0 16.7 + - - +
39E GLN* 6.2 0.4 - - - +
69E PHE 4.6 1.1 - - - +
70E ILE* 4.3 17.7 - - + -
71E ASN 3.0 22.6 + - - -
195E VAL* 4.0 16.2 - - + -
196E ASP 3.5 5.6 - - - -
197E ARG* 4.1 9.6 - - + -
215E GLU* 4.1 13.7 - - - +
216E VAL* 1.3 79.4 - - - +
218E VAL* 1.3 65.4 + - - +
219E ALA 4.4 0.2 - - - -
224F LEU* 5.1 0.2 - - - -
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Residues in contact with VAL 218 (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 GLU 4.8 5.2 - - - +
71E ASN* 3.7 22.0 - - + +
73E THR* 3.0 28.3 - - + +
194E TYR 4.0 0.3 - - - +
195E VAL* 3.4 4.2 - - - -
196E ASP* 3.1 35.0 + - - +
216E VAL* 4.8 4.0 - - + -
217E ALA* 1.3 82.3 - - - +
219E ALA* 1.3 63.8 + - - +
220E ARG* 5.1 0.6 - - + +
224F LEU* 3.7 24.9 - - + -
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Residues in contact with ALA 219 (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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70E ILE* 3.9 4.5 - - + +
71E ASN 3.0 12.9 + - - +
72E HIS* 3.8 19.7 - - + +
73E THR* 2.8 25.1 + - - -
76E ILE* 3.8 6.7 - - + -
193E TYR* 3.7 30.3 - - + -
194E TYR 3.1 7.2 - - - +
195E VAL* 3.9 8.3 - - + -
218E VAL* 1.3 74.7 - - - +
220E ARG* 1.3 65.0 + - - +
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Residues in contact with ARG 220 (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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74E GLN* 3.4 15.9 - - - +
76E ILE* 3.6 7.9 - - - -
144E THR* 3.9 6.7 - - - +
193E TYR* 3.5 2.8 - - - +
194E TYR* 2.7 61.0 + - - +
196E ASP* 2.7 41.9 + - - +
218E VAL* 5.8 0.7 - - + -
219E ALA* 1.3 77.4 - - - +
221E TYR* 1.3 68.0 + - - +
222E CYS* 4.5 4.6 - - - +
223E ASP* 3.5 34.2 + - - +
144F THR* 3.5 9.9 + - - -
196F ASP* 3.1 27.7 + - - +
220F ARG* 3.2 8.1 - - - +
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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