Contacts of the helix formed by residues 187 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A CYS* 1.3 75.8 - - - +
188A THR* 1.3 64.6 + - - +
189A ARG 3.2 3.5 + - - -
190A LYS* 3.2 24.0 + - - +
191A LYS* 3.0 39.2 + - - +
288A SER 4.0 0.9 + - - -
289A GLU* 2.8 30.2 + - - -
290A GLY 3.0 6.2 + - - +
291A LYS* 3.7 36.6 - - + -
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Residues in contact with THR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA* 5.8 0.3 - - - +
180A ILE* 4.3 10.8 - - + -
181A GLY* 4.3 5.4 - - - -
186A CYS* 3.5 19.7 - - - -
187A THR* 1.3 75.4 - - - +
189A ARG* 1.3 63.0 + - - +
191A LYS 4.7 0.2 - - - +
192A THR* 2.8 42.7 + - - +
194A VAL* 3.7 14.1 - - + +
289A GLU* 2.4 44.2 + - - +
1338A IMP 4.2 3.3 - - - -
318B TYR* 3.7 17.6 + - + +
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 4.5 15.6 + - - -
180A ILE 2.6 30.5 + - - -
181A GLY* 3.2 38.4 + - - +
182A PRO* 3.5 11.1 - - - +
186A CYS 5.6 0.2 + - - -
187A THR 3.2 0.6 - - - -
188A THR* 1.3 77.6 - - - +
190A LYS* 1.3 58.8 + - + +
193A GLY* 2.8 27.6 + - - +
194A VAL 3.5 12.6 - - - +
196A TYR 3.4 27.1 + - - +
197A PRO* 4.7 1.0 - - - +
198A GLN 5.3 0.2 - - - +
16B LEU* 3.4 41.3 - - + +
224B CYS* 5.3 0.7 - - - -
226B GLY* 4.3 1.7 - - - -
230B LYS* 5.0 3.5 + - - -
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Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A CYS 4.3 4.8 + - - -
187A THR* 3.2 40.3 + - + +
189A ARG* 1.3 77.7 - - + +
191A LYS* 1.3 62.7 + - + +
192A THR 3.4 0.2 - - - -
291A LYS* 4.8 8.8 - - - +
224B CYS* 3.2 33.5 - - + +
225B PRO* 3.7 0.5 - - - +
226B GLY 2.8 20.1 + - - -
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A THR* 3.0 33.6 + - - +
188A THR 4.1 1.3 - - - +
190A LYS* 1.3 80.0 - - + +
192A THR* 1.3 65.5 + - + +
288A SER* 3.4 43.1 + - - +
289A GLU* 4.5 4.3 - - + -
290A GLY 6.2 0.2 - - - -
225B PRO* 3.4 31.1 - - + +
226B GLY 3.5 4.0 + - - +
307B ASP* 4.8 22.9 + - - +
311B GLY* 3.1 28.1 - - - -
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A THR* 2.8 22.2 + - - +
191A LYS* 1.3 85.8 - - + +
193A GLY* 1.3 59.4 + - - +
194A VAL* 3.2 25.8 + - - +
289A GLU* 3.9 15.0 - - - +
17B LEU* 4.0 0.7 - - - +
226B GLY* 3.7 7.6 - - - -
229B ALA* 3.7 5.1 - - - +
311B GLY* 3.6 10.5 - - - +
314B SER* 3.4 26.5 - - - +
315B THR* 2.8 40.5 + - - +
318B TYR* 4.1 1.7 - - + -
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Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ARG 2.8 22.6 + - - -
192A THR* 1.3 76.3 + - - +
194A VAL* 1.3 52.4 + - - +
16B LEU* 3.3 13.5 - - - -
17B LEU* 2.7 36.3 + - - +
226B GLY* 3.5 5.7 - - - -
230B LYS* 3.8 20.8 - - - -
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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