Contacts of the helix formed by residues 187 - 193 (chain B) in PDB entry 2BZN
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 THR 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B CYS* 1.3 77.8 - - - +
188B THR* 1.3 65.2 + - - +
189B ARG* 3.2 3.4 - - - -
190B LYS* 3.1 29.3 + - + +
191B LYS* 2.9 37.9 + - - +
288B SER 3.9 0.9 + - - -
289B GLU* 2.8 35.4 + - - -
290B GLY 3.1 8.2 + - - +
291B LYS* 3.8 30.5 - - + -
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA* 6.0 0.3 - - - +
180B ILE* 4.0 16.8 - - + -
181B GLY* 4.2 4.4 + - - -
186B CYS* 3.2 23.8 - - - -
187B THR* 1.3 75.2 - - - +
189B ARG* 1.3 56.9 + - - +
191B LYS* 4.6 0.2 - - - -
192B THR* 2.7 44.0 + - - +
194B VAL 3.5 18.6 - - - +
289B GLU* 2.7 39.9 + - - +
1338B IMP 4.1 2.1 - - - -
318D TYR* 3.9 13.5 + - + +
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 4.4 11.5 + - - -
180B ILE 3.4 13.3 + - - -
181B GLY* 3.3 39.8 + - - +
182B PRO* 3.6 7.6 - - - +
186B CYS* 5.2 0.4 - - - -
187B THR 3.2 1.4 - - - -
188B THR* 1.3 79.9 - - - +
190B LYS* 1.3 61.2 + - + +
193B GLY* 3.0 24.7 + - - +
194B VAL 3.6 20.4 - - - +
196B TYR 3.6 23.4 + - - +
197B PRO* 3.9 9.5 - - - +
16D LEU* 3.4 40.5 - - + +
224D CYS* 5.3 0.5 - - - -
226D GLY* 4.4 1.6 - - - -
230D LYS* 5.0 4.2 + - - -
336D VAL* 4.9 2.6 - - - +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B CYS 3.7 20.4 + - - -
187B THR* 3.1 24.3 + - + +
189B ARG* 1.3 79.6 - - + +
191B LYS* 1.3 65.5 + - + +
291B LYS* 4.2 18.9 - - - +
224D CYS* 3.2 30.3 - - + +
225D PRO* 3.7 0.7 - - - +
226D GLY 2.9 21.5 + - - -
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B THR* 2.9 31.5 + - - +
188B THR 4.1 1.8 - - - +
190B LYS* 1.3 82.8 - - + +
192B THR* 1.3 65.5 + - + +
272B GLU* 5.2 3.6 + - - -
288B SER* 3.1 44.7 + - - +
289B GLU* 4.5 4.3 - - + -
225D PRO* 3.3 26.5 - - + +
226D GLY 3.5 2.8 + - - +
307D ASP* 2.4 44.6 + - - +
311D GLY* 3.2 26.6 - - - -
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B THR* 2.7 26.9 + - - +
191B LYS* 1.3 80.1 - - + +
193B GLY* 1.3 62.4 + - - +
194B VAL* 3.1 26.4 + - - +
289B GLU* 3.9 16.8 - - + +
17D LEU* 4.1 0.5 - - - +
226D GLY* 3.8 5.8 - - - -
229D ALA* 3.6 5.4 - - - +
311D GLY* 3.7 10.1 - - - +
314D SER* 3.7 25.8 - - - +
315D THR* 2.7 40.4 + - - +
318D TYR* 4.1 2.1 - - + -
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Residues in contact with GLY 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ARG 3.0 21.6 + - - -
192B THR* 1.3 78.4 + - - +
194B VAL* 1.3 53.1 + - - +
16D LEU* 3.2 14.1 - - - -
17D LEU* 2.7 35.6 + - - +
226D GLY* 3.6 6.7 - - - -
230D LYS* 3.8 20.1 - - - -
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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