Contacts of the strand formed by residues 193 - 205 (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 193 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E HIS* 2.8 37.6 + + - -
76E ILE* 3.8 8.3 - - + -
77E PRO 4.9 0.9 + - - -
79E PHE 5.1 1.0 + - - -
80E PHE* 3.8 18.2 - - - -
146E MET* 3.4 5.7 - - - +
147E LEU* 2.8 70.4 + - + +
154E LEU* 4.0 8.7 - - + +
190E PRO* 3.6 27.3 - - + +
191E GLY 3.1 15.7 + - - +
192E VAL* 1.3 75.3 - - - +
194E TYR* 1.3 80.5 + - - +
195E VAL* 3.9 3.4 - - + +
219E ALA* 3.7 22.2 - - + -
220E ARG 3.5 10.5 - - - +
221E TYR* 3.9 12.1 - - + -
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Residues in contact with TYR 194 (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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144E THR* 4.1 9.6 - - + -
145E GLU 3.1 7.6 - - - +
146E MET* 3.9 29.8 - - + -
147E LEU* 4.6 0.4 - - - -
192E VAL* 4.0 20.4 - - + +
193E TYR* 1.3 88.5 - - - +
195E VAL* 1.3 63.3 + - - +
196E ASP 4.2 0.4 - - - -
219E ALA* 3.1 4.0 - - - +
220E ARG* 2.7 79.6 + - - +
222E CYS* 4.2 23.1 - - + -
141F GLU* 4.2 1.2 + - - +
142F ALA* 2.5 46.0 + - + +
143F SER* 4.6 7.2 - - - -
144F THR* 5.0 4.7 - - - -
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Residues in contact with VAL 195 (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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67E LYS* 6.0 0.2 - - - +
70E ILE* 4.1 23.8 - - + -
144E THR* 3.2 2.1 - - - -
145E GLU* 2.9 41.9 + - + +
147E LEU* 3.6 22.2 - - + +
193E TYR* 3.9 3.6 - - + +
194E TYR* 1.3 77.2 - - - +
196E ASP* 1.3 72.9 + - - +
197E ARG* 3.4 16.9 - - - -
217E ALA* 4.0 20.2 - - + -
218E VAL 3.4 10.5 - - - +
219E ALA* 3.9 17.3 - - + -
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Residues in contact with ASP 196 (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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143E SER 3.5 5.2 - - - +
144E THR* 2.9 25.1 + - - +
195E VAL* 1.3 74.4 - - - +
197E ARG* 1.3 59.1 + - - +
217E ALA* 3.5 0.9 - - - -
218E VAL* 3.1 33.4 + - + +
220E ARG* 2.7 46.9 + - - +
220F ARG* 3.3 16.7 + - - +
222F CYS* 5.6 2.2 - - - -
223F ASP* 4.9 7.2 - - - +
224F LEU* 3.4 21.1 - - + +
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Residues in contact with ARG 197 (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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63E NRQ 3.0 52.0 + - + +
142E ALA* 3.3 6.4 - - - +
143E SER* 2.5 61.5 + - - +
144E THR 3.1 16.6 - - - -
145E GLU* 3.6 23.3 + - - +
158E SER* 2.7 38.1 + - - -
160E MET* 4.9 0.2 - - - -
174E LEU* 4.6 3.6 - - - +
195E VAL* 3.4 22.4 - - - -
196E ASP* 1.3 74.3 - - - +
198E ARG* 1.3 61.0 + - - +
199E LEU 4.3 0.2 - - - -
215E GLU* 3.5 17.9 - - - +
216E VAL 3.4 8.3 - - - +
217E ALA* 4.1 6.1 - - + -
222F CYS* 5.7 0.2 - - - -
224F LEU* 3.7 5.9 - - - +
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Residues in contact with ARG 198 (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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140E TRP 6.1 0.9 - - - +
141E GLU 5.8 0.2 - - - -
142E ALA* 4.3 17.7 - - + +
197E ARG* 1.3 74.3 - - - +
199E LEU* 1.3 60.9 + - - +
200E GLU* 3.2 40.2 + - + +
214E HIS 3.8 0.9 - - - +
215E GLU* 3.3 7.4 - - - +
216E VAL* 3.0 41.1 + - + +
222F CYS* 3.5 38.3 + - - +
224F LEU* 2.8 33.8 + - + +
225F PRO 3.7 7.1 + - - -
226F SER* 3.8 14.6 - - - +
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Residues in contact with LEU 199 (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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59E ALA* 3.9 20.9 - - + +
60E THR* 5.3 1.6 - - + -
63E NRQ 3.6 75.6 + - + +
140E TRP* 4.4 34.5 + - + +
141E GLU 5.6 1.8 + - - -
142E ALA* 5.6 1.4 - - - +
197E ARG 4.3 0.4 - - - -
198E ARG* 1.3 72.3 - - - +
200E GLU* 1.3 66.4 + - - +
201E ARG* 6.3 0.2 - - + -
213E GLN* 3.6 33.0 - - + +
214E HIS 3.4 4.5 - - - +
215E GLU* 4.2 3.8 - - + -
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Residues in contact with GLU 200 (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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198E ARG* 3.2 31.5 + - + +
199E LEU* 1.3 82.4 - - - +
201E ARG* 1.3 61.5 + - - +
202E ILE* 3.6 6.5 + - + -
213E GLN* 3.5 1.7 - - - -
214E HIS* 2.7 57.2 + - + +
216E VAL* 5.1 0.3 - - - +
225F PRO 4.4 1.7 - - - +
226F SER* 2.7 29.3 + - - -
227F LYS* 2.9 25.6 + - - +
228F LEU* 3.7 24.9 + - + +
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Residues in contact with ARG 201 (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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55E PHE* 3.6 34.6 - - - +
56E ASP* 3.4 28.3 + - - +
199E LEU* 4.3 0.8 + - - +
200E GLU* 1.3 71.3 - - - +
202E ILE* 1.3 64.0 + - - +
203E LYS 3.5 24.2 - - - +
204E GLU* 3.5 29.7 + - - -
208E GLU* 3.5 31.1 + - - +
211E VAL* 3.8 15.9 - - + +
212E GLU 3.5 6.7 - - - +
213E GLN* 4.6 4.2 + - + +
228F LEU* 3.3 24.4 - - + +
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Residues in contact with ILE 202 (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* 5.7 1.1 - - - +
200E GLU* 4.6 3.1 - - + +
201E ARG* 1.3 75.0 - - - +
203E LYS* 1.3 61.3 + - + +
212E GLU* 2.7 45.5 + - + +
214E HIS* 4.0 23.1 - - + +
227F LYS* 3.5 47.6 - - + +
228F LEU* 3.9 11.4 - - + +
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Residues in contact with LYS 203 (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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201E ARG* 3.5 11.4 - - - +
202E ILE* 1.3 84.5 - - + +
204E GLU* 1.3 75.1 - - - +
205E ALA* 5.7 4.3 - - - -
210E TYR* 4.5 19.7 - - + -
211E VAL* 3.5 2.1 - - - -
212E GLU* 3.1 48.6 + - + +
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Residues in contact with GLU 204 (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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201E ARG* 3.5 35.6 + - - +
203E LYS* 1.3 85.6 - - - +
205E ALA* 1.3 62.9 + - - +
208E GLU* 3.7 20.4 + - + +
210E TYR* 3.3 11.7 - - - +
211E VAL* 4.7 3.4 - - + -
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Residues in contact with ALA 205 (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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203E LYS* 5.7 5.4 - - - -
204E GLU* 1.3 77.9 - - - +
206E ASP* 1.3 81.9 + - - +
207E LYS 3.6 1.7 + - - -
208E GLU 3.9 1.8 + - - +
209E THR* 3.5 2.6 + - - -
210E TYR* 3.1 43.8 + - + +
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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