Contacts of the strand formed by residues 193 - 205 (chain F) 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 193 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72F HIS* 2.8 36.6 + + - -
76F ILE* 4.0 15.3 - - + -
77F PRO 5.1 1.3 + - - -
79F PHE* 5.2 1.9 - - - +
80F PHE* 4.0 15.9 - - - -
146F MET* 3.4 5.2 - - - +
147F LEU* 2.7 61.6 + - + +
154F LEU* 4.2 7.5 - - + +
190F PRO* 4.0 21.4 - - + +
191F GLY 3.3 13.0 + - - -
192F VAL* 1.3 74.1 - - - +
194F TYR* 1.3 89.9 + - - +
195F VAL* 3.7 12.1 - - + +
219F ALA* 3.6 15.9 - - + -
220F ARG 3.4 11.4 - - - +
221F TYR* 3.8 13.9 - - + -
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Residues in contact with TYR 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU* 4.1 0.9 + - - +
142E ALA* 2.4 54.7 + - + +
143E SER* 4.4 7.0 - - - -
144E THR* 4.9 4.3 - - - -
144F THR* 4.6 10.5 - - + -
145F GLU 3.2 8.5 - - - +
146F MET* 3.7 28.2 - - + -
147F LEU* 5.0 0.2 - - - -
192F VAL* 4.0 21.1 - - + +
193F TYR* 1.3 92.5 - - - +
195F VAL* 1.3 60.5 + - - +
196F ASP 4.2 0.4 - - - -
219F ALA* 3.2 3.3 - - - -
220F ARG* 2.8 74.6 + - + +
222F CYS* 4.1 18.6 - - + -
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Residues in contact with VAL 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 4.0 32.5 - - + -
144F THR* 3.3 4.8 - - - +
145F GLU* 2.9 37.0 + - + +
147F LEU* 3.8 14.6 - - + -
193F TYR* 3.7 21.5 - - + +
194F TYR* 1.3 80.2 - - - +
196F ASP* 1.3 69.0 + - - +
197F ARG* 3.7 24.6 + - - -
217F ALA* 4.2 4.5 - - + -
218F VAL 3.8 4.3 - - - +
219F ALA* 3.8 9.2 - - + -
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Residues in contact with ASP 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E ARG* 3.1 23.9 + - - +
222E CYS* 5.8 1.3 - - - -
223E ASP* 4.7 8.7 - - - +
224E LEU* 3.7 21.7 - - + +
143F SER 3.7 4.0 - - - +
144F THR* 2.7 26.2 + - - -
194F TYR 4.2 0.2 - - - -
195F VAL* 1.3 73.2 - - - +
197F ARG* 1.3 58.7 + - - +
217F ALA* 3.3 1.7 - - - -
218F VAL* 2.8 39.5 + - + +
220F ARG* 2.8 33.4 + - - -
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Residues in contact with ARG 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LEU* 3.7 5.0 - - - +
63F NRQ 3.0 51.4 + - + +
67F LYS* 5.3 2.7 - - - +
70F ILE* 6.1 0.7 - - - -
142F ALA* 3.5 4.7 - - - +
143F SER* 2.7 64.9 + - - +
144F THR 3.3 0.8 - - - +
145F GLU* 3.2 37.3 + - - +
158F SER* 2.9 31.3 + - - -
160F MET* 4.8 0.6 - - - -
174F LEU* 5.2 2.2 - - - +
195F VAL* 3.7 19.3 - - - -
196F ASP* 1.3 74.1 - - - +
198F ARG* 1.3 60.7 + - - +
215F GLU* 3.8 17.5 - - - +
216F VAL 3.2 10.1 - - - +
217F ALA* 4.0 4.0 - - + -
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Residues in contact with ARG 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E CYS* 3.5 36.8 + - - +
224E LEU* 2.5 37.4 + - + +
225E PRO 4.0 7.2 + - - +
226E SER* 4.3 12.7 - - - +
142F ALA* 4.3 16.1 - - + +
197F ARG* 1.3 73.6 - - - +
199F LEU* 1.3 60.8 + - - +
200F GLU* 3.1 39.1 + - + +
214F HIS* 3.6 1.9 - - - +
215F GLU* 3.1 7.0 - - - -
216F VAL* 2.8 47.4 + - + +
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ALA* 3.7 37.9 - - + +
60F THR* 4.6 2.5 - - + -
63F NRQ 3.6 57.7 + - + +
140F TRP* 4.1 35.3 + - + +
141F GLU 5.6 1.2 + - - -
142F ALA* 5.5 1.8 - - - +
160F MET* 5.8 0.2 - - + -
197F ARG 4.2 0.4 - - - -
198F ARG* 1.3 73.4 - - - +
200F GLU* 1.3 68.4 + - - +
201F ARG* 4.2 2.3 + - + +
213F GLN* 3.7 28.5 - - + +
214F HIS 3.3 7.0 - - - +
215F GLU* 4.4 5.4 - - + +
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Residues in contact with GLU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E PRO 4.6 0.5 - - - +
226E SER* 2.7 25.7 + - - -
227E LYS* 3.0 26.5 + - + +
228E LEU* 3.8 29.2 - - + +
140F TRP 5.8 2.0 - - - +
198F ARG* 3.1 35.5 + - + +
199F LEU* 1.3 78.2 - - - +
201F ARG* 1.3 63.5 + - - +
202F ILE* 3.3 10.7 + - + +
213F GLN* 3.7 3.5 - - - -
214F HIS* 2.7 45.0 + - + +
216F VAL* 5.9 0.2 - - - +
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Residues in contact with ARG 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E LEU* 3.7 18.8 - - - +
55F PHE* 3.5 24.9 - - - +
56F ASP* 3.3 33.4 + - - +
139F GLY* 5.8 6.5 - - - -
199F LEU* 4.2 4.0 + - + +
200F GLU* 1.3 69.6 - - - +
202F ILE* 1.3 63.9 + - - +
203F LYS 4.0 9.6 - - - +
204F GLU* 3.2 38.7 + - + +
208F GLU* 2.8 31.5 + - - +
211F VAL* 3.4 34.9 - - - +
212F GLU 3.8 3.4 - - - -
213F GLN* 4.6 8.8 + - + +
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Residues in contact with ILE 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E LYS* 3.7 53.2 - - + +
228E LEU* 4.3 15.3 - - + +
40F THR* 6.0 2.5 - - + -
200F GLU* 3.8 16.2 - - + +
201F ARG* 1.3 77.6 - - - +
203F LYS* 1.3 69.9 + - + +
204F GLU* 5.8 0.5 - - - +
212F GLU* 2.9 23.8 + - + +
213F GLN 4.7 1.1 - - - -
214F HIS* 4.0 16.4 - - + +
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Residues in contact with LYS 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F ARG* 4.0 1.8 - - - -
202F ILE* 1.3 87.4 - - + +
204F GLU* 1.3 75.6 + - - +
205F ALA* 4.5 11.7 - - - +
210F TYR* 4.2 12.4 - - + -
211F VAL* 3.4 5.2 - - - +
212F GLU* 2.8 62.6 + - + +
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Residues in contact with GLU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F ARG* 3.2 40.7 + - + +
202F ILE 5.8 0.7 - - - +
203F LYS* 1.3 86.4 + - - +
205F ALA* 1.3 63.5 + - - +
208F GLU* 3.7 19.6 + - - +
210F TYR* 3.3 11.4 - - - +
211F VAL* 4.5 2.7 - - + -
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Residues in contact with ALA 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F LYS* 4.5 9.4 - - - +
204F GLU* 1.3 78.7 - - - +
206F ASP* 1.3 79.1 + - - +
207F LYS 3.5 1.8 - - - -
208F GLU 3.2 2.3 + - - -
209F THR 3.1 18.5 + - - -
210F TYR* 3.0 31.2 + - + -
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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