Contacts of the strand formed by residues 198 - 208 (chain E) in PDB entry 3BZE
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 GLU 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193E PRO* 4.0 1.2 - - - +
194E ILE* 3.2 20.7 + - + +
195E SER* 2.7 36.6 + - - +
196E ASP 3.6 0.4 - - - -
197E HIS* 1.3 90.1 - - - +
199E ALA* 1.3 65.8 + - - +
248E VAL* 3.6 25.5 - - + +
249E VAL 3.2 11.8 - - - +
250E PRO* 4.6 6.6 - - + +
251E SER* 3.6 6.2 + - - +
105G PRO* 3.8 8.0 - - - +
106G ASP* 3.2 39.0 + - + +
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Residues in contact with ALA 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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191E HIS* 3.3 37.0 - - + +
192E HIS 3.1 10.8 - - - +
193E PRO* 3.8 2.9 - - + -
194E ILE* 3.9 5.8 - - - +
198E GLU* 1.3 79.7 - - - +
200E THR* 1.3 63.4 + - - +
201E LEU* 5.6 1.6 - - + -
247E VAL 3.7 0.2 - - - +
248E VAL* 3.3 4.9 - - - -
249E VAL* 2.7 43.0 + - + +
251E SER* 5.3 6.3 - - - +
254E GLU* 6.1 0.9 - - + -
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Residues in contact with THR 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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190E THR 3.5 3.1 - - - +
191E HIS* 3.6 2.4 - - - -
192E HIS* 2.6 53.2 + - + +
194E ILE* 3.5 23.9 - - - +
199E ALA* 1.3 75.2 - - - +
201E LEU* 1.3 67.4 + - - +
202E ARG* 3.9 18.8 - - - +
246E ALA* 3.7 26.9 - - + -
247E VAL 3.5 7.4 - - - +
248E VAL* 4.2 7.9 - - + +
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Residues in contact with LEU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E VAL* 4.3 11.0 - - + -
190E THR 3.4 9.9 - - - +
191E HIS* 3.9 27.1 - - + -
199E ALA* 5.3 1.8 - - + +
200E THR* 1.3 81.4 - - - +
202E ARG* 1.3 60.6 + - - +
203E CYS 3.8 0.2 - - - -
217E TRP* 3.7 21.5 - - + -
246E ALA* 3.2 3.3 - - - -
247E VAL* 2.8 42.6 + - + +
249E VAL* 4.2 16.2 - - + -
254E GLU* 4.1 20.0 - - + +
257E TYR* 4.1 27.1 - - + -
273E ARG 4.8 4.9 - - - +
274E TRP* 4.7 6.3 - - + -
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Residues in contact with ARG 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E VAL* 3.7 0.6 - - - -
190E THR* 3.0 38.9 + - - +
192E HIS* 3.9 14.8 + - + +
200E THR* 3.9 17.6 - - - +
201E LEU* 1.3 71.0 - - - +
203E CYS* 1.3 58.2 - - - +
204E TRP* 3.1 44.9 - - + +
217E TRP* 4.8 0.4 - - - -
244E TRP* 3.0 60.2 - - + -
245E ALA 3.7 2.7 - - - -
246E ALA* 3.1 14.1 - - - +
98F ASP* 2.8 19.4 + - - +
99F MET* 3.7 19.2 - - - +
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Residues in contact with CYS 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E THR* 4.3 6.1 - - - -
188E HIS 4.0 2.5 - - - -
189E VAL* 4.6 4.7 - - + -
201E LEU 3.7 1.8 + - - -
202E ARG* 1.3 70.3 - - - +
204E TRP* 1.3 62.7 + - - +
215E LEU* 4.0 4.8 - - + +
217E TRP* 3.6 15.2 - - + +
244E TRP* 3.1 25.6 - - - +
245E ALA* 2.8 20.4 + - + +
259E CYS* 2.0 49.6 - - - -
261E VAL* 4.4 3.1 - - - -
272E LEU* 4.0 17.0 - - - -
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Residues in contact with TRP 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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186E LYS 4.2 1.1 - - - -
187E THR* 2.9 31.4 + - - +
188E HIS* 2.9 53.6 + + + +
190E THR* 3.3 24.1 + - + +
192E HIS* 6.1 0.2 - + - -
202E ARG* 3.1 44.7 - - - +
203E CYS* 1.3 77.7 - - - +
205E ALA* 1.3 61.9 + - - +
206E LEU* 4.1 24.5 - - + -
234E ARG* 3.6 16.2 - - - -
242E GLN* 6.1 0.2 - - + -
243E LYS 3.9 4.0 - - - -
244E TRP* 3.4 23.6 - + + -
261E VAL* 5.3 0.2 - - - +
97F ARG 4.6 4.7 - - - -
98F ASP* 3.3 15.7 - - - -
99F MET* 3.4 29.2 - - - -
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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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185E PRO* 4.1 6.7 - - + -
186E LYS 3.6 4.0 - - - -
187E THR* 4.1 4.5 - - - +
204E TRP* 1.3 76.1 - - - +
206E LEU* 1.3 61.5 + - - +
208E PHE* 3.2 10.7 - - + -
213E ILE* 3.8 28.3 - - + -
215E LEU* 4.0 16.2 - - + -
242E GLN* 3.2 2.8 - - - +
243E LYS 3.0 35.9 + - - +
261E VAL* 5.1 0.2 - - + -
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Residues in contact with LEU 206 (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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185E PRO* 3.4 1.6 - - - +
186E LYS* 2.9 52.0 + - + +
188E HIS* 3.9 28.0 - - + +
204E TRP* 4.1 22.7 - - + -
205E ALA* 1.3 81.1 - - - +
207E GLY* 1.3 65.2 + - - +
208E PHE* 3.4 2.9 - - - -
241E PHE 4.1 0.9 - - - -
242E GLN* 3.4 35.7 - - + +
243E LYS 5.1 0.2 - - - +
12F ARG 5.8 0.7 - - - +
14F PRO* 4.4 25.6 - - + -
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Residues in contact with GLY 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E GLU* 3.2 24.4 - - - +
184E PRO 3.8 4.3 - - - +
186E LYS* 3.8 8.5 + - - -
206E LEU* 1.3 74.8 - - - +
208E PHE* 1.3 59.8 + - - +
236E ALA* 5.6 0.4 - - - +
240E THR* 3.3 25.2 - - - +
241E PHE 3.0 8.2 + - - -
242E GLN* 4.5 4.2 - - - +
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Residues in contact with PHE 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E GLU* 3.0 12.6 - - - +
184E PRO 4.3 0.4 - - - -
185E PRO* 3.8 27.1 - - + -
205E ALA* 3.2 30.7 - - + -
207E GLY* 1.3 77.8 - - - +
209E TYR* 1.3 65.7 + - - +
210E PRO 3.4 18.6 - - - -
211E ALA 3.4 22.9 - - - -
213E ILE* 3.7 25.1 - - + -
233E THR* 4.4 2.5 - - + -
240E THR* 3.3 4.5 - - - -
241E PHE* 2.8 65.4 + - + -
242E GLN* 3.4 5.8 - - - -
243E LYS* 3.7 11.7 - - + -
263E HIS* 3.7 14.4 - + + -
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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