Contacts of the strand formed by residues 210 - 220 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42G ARG* 3.3 29.3 - - + +
43G ILE 3.2 16.8 - - - -
44G LYS* 4.1 27.1 - - + -
203G LYS* 4.8 11.4 - - + -
204G GLU* 3.4 4.3 - - - +
205G ALA* 2.9 51.0 + - + -
206G ASP* 4.7 5.6 - - - +
208G GLU 4.2 2.5 - - - +
209G THR* 1.3 80.4 + - - +
211G VAL* 1.3 72.8 + - - +
212G GLU* 2.8 28.6 + - + -
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Residues in contact with VAL 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G MET 3.7 1.0 - - - +
42G ARG* 3.6 0.3 - - - -
43G ILE* 2.6 44.1 + - + +
55G PHE* 3.6 41.1 - - + -
201G ARG* 3.6 28.3 - - - +
203G LYS 3.7 3.4 - - - -
204G GLU* 4.3 7.6 - - + -
208G GLU* 3.7 27.1 - - + +
210G TYR* 1.3 82.4 - - - +
212G GLU* 1.3 69.5 + - - +
213G GLN* 4.1 8.3 - - - +
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Residues in contact with GLU 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G THR* 4.1 10.9 - - + +
41G MET 3.2 11.2 - - - +
42G ARG* 3.5 19.6 - - + +
201G ARG* 3.7 4.5 - - - -
202G ILE* 3.0 36.1 + - + +
203G LYS* 2.7 47.6 + - + +
210G TYR* 2.8 34.5 + - + -
211G VAL* 1.3 73.7 - - - +
213G GLN* 1.3 61.4 + - - +
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Residues in contact with GLN 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G THR* 3.2 6.0 - - - -
41G MET 2.9 37.3 + - - +
43G ILE* 4.2 11.7 - - + -
55G PHE* 3.8 20.6 - - - -
59G ALA* 2.9 40.6 + - - +
62G PHE* 4.1 9.5 - - - +
63G NRQ 3.3 30.2 - - + +
199G LEU* 3.8 25.1 - - + +
200G GLU 3.4 6.7 - - - +
201G ARG* 5.0 4.5 + - - +
202G ILE* 4.1 0.8 - - - +
211G VAL* 4.1 5.1 - - + +
212G GLU* 1.3 76.9 - - - +
214G HIS* 1.3 60.9 + - - +
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Residues in contact with HIS 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G THR* 4.1 14.8 - - + +
39G GLN 3.1 33.9 + - - -
40G THR* 3.5 14.8 + - - +
63G NRQ 4.5 0.9 - - - -
198G ARG 4.0 0.6 - - - +
199G LEU* 3.4 4.5 - - - +
200G GLU* 2.8 51.0 + - + +
202G ILE* 4.4 19.6 - - + +
213G GLN* 1.3 73.7 - - - +
215G GLU* 1.3 71.3 + - - +
216G VAL* 4.1 15.8 + - + +
225H PRO* 6.2 1.4 - - - +
227H LYS* 3.4 46.8 + - + +
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Residues in contact with GLU 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G GLY 3.3 5.9 - - - +
38G THR* 3.4 1.2 - - - -
39G GLN* 2.8 59.4 + - + +
63G NRQ 3.5 60.1 + - + +
66G SER* 5.0 1.0 + - - +
70G ILE* 5.2 3.1 - - - +
197G ARG* 3.7 5.2 - - - -
198G ARG 3.3 16.4 - - - +
199G LEU* 4.2 9.0 - - + -
214G HIS* 1.3 81.7 + - - +
216G VAL* 1.3 61.0 + - - +
217G ALA* 3.3 22.9 - - - +
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Residues in contact with VAL 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLU 4.7 2.7 - - - +
37G GLY 3.3 7.0 - - - +
38G THR* 4.3 13.7 - - + -
197G ARG* 3.3 2.8 - - - +
198G ARG* 2.8 52.9 + - + +
214G HIS* 4.1 15.8 + - + +
215G GLU* 1.3 73.6 - - - +
217G ALA* 1.3 62.6 + - - +
218G VAL* 4.5 7.2 - - + -
224H LEU* 4.1 27.2 - - + +
225H PRO* 3.8 33.2 - - + +
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Residues in contact with ALA 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G GLY* 3.0 16.6 + - - +
69G PHE 4.4 1.8 - - - +
70G ILE* 3.7 25.1 - - + -
71G ASN 3.2 19.9 + - - -
195G VAL* 4.2 3.8 - - + -
196G ASP 3.5 5.4 - - - +
197G ARG* 3.8 8.7 - - + -
215G GLU* 3.3 23.8 - - - +
216G VAL* 1.3 75.2 - - - +
218G VAL* 1.3 65.9 + - - +
224H LEU* 5.1 0.2 - - - -
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Residues in contact with VAL 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLU 4.6 4.3 - - - +
70G ILE* 3.9 3.9 - - - +
71G ASN* 3.8 31.0 - - + +
195G VAL* 4.1 1.1 - - - +
196G ASP* 3.0 36.8 + - + +
216G VAL* 4.5 8.3 - - + -
217G ALA* 1.3 80.2 - - - +
219G ALA* 1.3 73.2 + - - +
220G ARG* 5.4 0.2 - - - +
224H LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ILE* 4.0 1.8 - - + +
71G ASN 2.9 19.1 + - - +
72G HIS* 4.1 15.4 - - + +
73G THR 5.6 1.2 + - - +
74G GLN* 4.2 6.4 - - - +
76G ILE* 4.0 15.4 - - + +
193G TYR* 3.9 24.9 - - + -
194G TYR 3.2 9.2 - - - +
195G VAL* 4.1 7.2 - - + +
218G VAL* 1.3 82.8 - - - +
220G ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G GLN* 3.7 15.3 - - - +
76G ILE* 3.9 8.1 - - - -
144G THR* 3.8 5.3 - - - +
193G TYR* 3.4 3.6 - - - +
194G TYR* 2.6 68.3 + - + +
196G ASP* 2.6 42.8 + - - +
218G VAL* 6.1 0.2 - - + -
219G ALA* 1.3 77.2 - - - +
221G TYR* 1.3 71.0 + - - +
222G CYS* 5.1 5.3 - - - +
223G ASP* 4.4 16.3 - - + +
144H THR* 3.7 8.5 + - - -
196H ASP* 3.2 24.8 + - - +
220H ARG* 3.0 19.1 - - - +
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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