Contacts of the strand formed by residues 210 - 220 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D ILE 3.3 5.6 - - - +
44D LYS* 3.4 47.6 - - + -
45D VAL 5.7 1.3 - - - -
204D GLU* 3.3 2.0 - - - +
205D ALA* 3.0 45.2 + - + +
206D ASP* 4.5 12.3 - - + -
208D GLU 4.2 0.3 - - - -
209D THR* 1.3 100.7 - - + +
211D VAL* 1.3 68.3 + - - +
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Residues in contact with VAL 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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41D MET 3.7 0.9 - - - +
42D ARG* 3.6 1.4 - - - -
43D ILE* 2.7 41.4 + - + +
55D PHE* 3.9 30.3 - - + -
201D ARG* 3.8 27.6 - - - +
203D LYS 3.5 3.8 - - - -
204D GLU* 3.9 15.0 - - + -
208D GLU* 3.9 17.0 - - - +
209D THR 4.3 0.2 - - - -
210D TYR* 1.3 79.9 - - - +
212D GLU* 1.3 63.7 + - - +
213D GLN* 3.7 26.5 - - + -
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Residues in contact with GLU 212 (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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227C LYS* 5.3 4.3 + - - -
40D THR* 4.0 20.8 + - + +
41D MET 3.3 10.1 - - - +
42D ARG* 4.2 23.0 + - + +
201D ARG* 3.8 2.3 - - - -
202D ILE* 2.8 50.9 + - + +
203D LYS* 2.9 55.6 + - + +
211D VAL* 1.3 77.7 - - - +
213D GLN* 1.3 56.1 + - - +
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Residues in contact with GLN 213 (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 THR* 3.3 7.1 + - - +
41D MET 3.0 31.8 + - - +
43D ILE* 4.1 10.5 - - + +
55D PHE* 3.3 30.1 - - - -
56D ASP* 5.9 0.2 + - - -
59D ALA* 3.3 39.3 - - - +
62D PHE* 4.3 4.9 - - - +
63D NRQ 3.8 21.0 - - + +
199D LEU* 3.7 18.9 - - + +
200D GLU 3.4 11.7 - - - +
201D ARG* 4.9 7.3 - - - +
202D ILE* 4.2 2.7 - - - -
211D VAL* 3.7 15.2 - - + +
212D GLU* 1.3 73.3 - - - +
214D HIS* 1.3 60.5 + - - +
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Residues in contact with HIS 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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227C LYS* 3.8 31.3 + - + +
38D THR* 4.1 23.3 - - + +
39D GLN 2.9 21.4 + - - -
40D THR* 3.3 13.4 + - - +
63D NRQ 4.4 2.7 - - - -
198D ARG 3.5 1.7 - - - +
199D LEU* 3.4 4.2 - - - +
200D GLU* 2.8 42.1 + - + +
202D ILE* 3.7 24.8 - - + +
213D GLN* 1.3 75.5 - - - +
215D GLU* 1.3 84.0 + - - +
216D VAL* 4.2 9.4 + - + +
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Residues in contact with GLU 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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37D GLY 3.5 1.5 - - - +
38D THR* 3.1 5.9 - - - -
39D GLN* 2.9 50.9 + - + +
63D NRQ 3.4 59.4 + - + +
66D SER* 5.2 1.4 + - - +
70D ILE* 5.6 0.3 - - - +
197D ARG* 3.7 9.9 - - + +
198D ARG 3.5 12.3 - - - +
199D LEU* 4.2 14.8 - - + -
214D HIS* 1.3 79.7 + - - +
216D VAL* 1.3 60.8 + - - +
217D ALA* 3.2 27.5 - - - +
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Residues in contact with VAL 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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224C LEU* 3.6 18.1 - - + +
225C PRO* 3.7 42.4 - - + +
36D GLU 5.3 1.6 - - - +
37D GLY 3.2 7.0 - - - +
38D THR* 4.3 13.9 - - + -
197D ARG* 3.3 4.7 - - - -
198D ARG* 3.1 47.3 + - + +
200D GLU* 5.8 0.7 - - - +
214D HIS* 4.7 8.7 - - + +
215D GLU* 1.3 74.1 - - - +
217D ALA* 1.3 60.5 + - - +
218D VAL* 4.8 6.7 - - + -
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Residues in contact with ALA 217 (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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37D GLY* 2.6 19.3 + - - +
69D PHE 4.0 7.0 - - - +
70D ILE* 3.9 25.4 - - + -
71D ASN 3.0 21.9 + - - -
195D VAL* 4.2 10.1 - - + -
196D ASP 3.5 4.7 - - - +
197D ARG* 4.3 2.0 - - + -
215D GLU* 3.2 24.2 - - - +
216D VAL* 1.3 72.0 - - - +
218D VAL* 1.3 66.0 + - - +
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Residues in contact with VAL 218 (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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224C LEU* 3.9 26.5 - - + -
36D GLU 5.0 3.6 - - - +
71D ASN* 3.5 17.0 - - + +
73D THR* 3.7 25.4 - - + -
194D TYR 4.0 0.3 - - - +
195D VAL* 3.4 5.0 - - - +
196D ASP* 3.0 35.1 + - + +
216D VAL* 4.8 7.2 - - + -
217D ALA* 1.3 80.7 - - - +
219D ALA* 1.3 67.0 + - - +
220D ARG* 4.2 3.3 + - + +
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Residues in contact with ALA 219 (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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70D ILE* 4.0 2.6 - - + +
71D ASN 2.7 17.8 + - - +
72D HIS* 3.8 17.5 - - + -
73D THR* 2.5 34.3 + - - +
76D ILE* 3.8 3.8 - - + -
193D TYR* 3.6 30.7 - - + -
194D TYR 3.3 4.7 - - - -
195D VAL* 3.7 7.9 - - + -
218D VAL* 1.3 74.8 - - - +
220D ARG* 1.3 57.0 + - - +
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Residues in contact with ARG 220 (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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144C THR* 3.6 9.5 + - - -
196C ASP* 3.5 21.2 + - - +
220C ARG* 3.1 29.3 - - - +
73D THR* 4.7 0.9 - - - +
74D GLN* 3.6 10.3 - - - +
76D ILE* 3.5 11.0 - - - -
144D THR* 3.7 5.5 - - - +
193D TYR* 3.3 5.2 - - - +
194D TYR* 2.9 59.0 + - - +
196D ASP* 2.7 31.1 + - - +
218D VAL* 5.4 3.1 - - + +
219D ALA* 1.3 75.9 - - - +
221D TYR* 1.3 71.6 + - - +
222D CYS* 4.5 7.9 - - - +
223D ASP* 5.4 3.3 - - - +
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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