Contacts of the helix formed by residues 176 - 192 (chain A) in PDB entry 3BZH
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 ASN 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLN* 2.7 25.8 + - + +
175A THR* 1.3 80.3 + - - +
177A ARG* 1.3 65.3 + - - +
178A ALA* 4.1 6.1 + - - +
179A GLU* 3.4 31.2 + - - +
180A HIS 3.0 17.7 + - - -
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Residues in contact with ARG 177 (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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90A VAL* 6.2 1.0 - - - +
172A GLN 3.5 1.3 + - - -
173A TYR* 3.4 67.0 + - - +
174A MET 5.1 1.1 - - - +
175A THR 3.9 0.8 - - - -
176A ASN* 1.3 74.7 - - - +
178A ALA* 1.3 58.9 + - - +
180A HIS* 3.1 4.9 + - - +
181A ASP* 2.8 53.9 + - - +
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Residues in contact with ALA 178 (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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176A ASN* 3.2 6.7 + - - +
177A ARG* 1.3 79.4 - - - +
179A GLU* 1.3 56.9 - - - +
181A ASP* 3.9 4.7 - - - +
182A ARG* 2.9 29.5 + - - +
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Residues in contact with GLU 179 (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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172A GLN* 3.5 18.6 - - - +
176A ASN* 3.1 34.1 + - - +
178A ALA* 1.3 75.8 - - - +
180A HIS* 1.3 66.3 + - - +
182A ARG* 2.6 48.2 + - - +
183A MET* 2.9 32.1 + - + +
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Residues in contact with HIS 180 (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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90A VAL* 5.1 3.4 - - + -
91A TYR* 4.7 8.7 + - - -
120A TYR* 3.8 10.7 + + - -
121A HIS* 5.1 0.2 - - - -
122A CYS* 4.9 4.4 + - - +
159A CYS* 5.2 5.3 - - + -
169A ILE* 3.5 44.2 - - + +
172A GLN* 3.3 18.2 - - + +
173A TYR* 3.6 39.5 - + + +
176A ASN 3.0 12.4 + - - +
177A ARG* 3.1 8.9 + - - +
179A GLU* 1.3 78.1 - - - +
181A ASP* 1.3 79.0 + - - +
183A MET* 3.3 2.8 + - - +
184A ALA* 2.8 36.7 + - + +
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Residues in contact with ASP 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.6 27.3 - - + +
173A TYR* 4.9 0.2 - - - -
177A ARG* 2.8 51.3 + - - +
178A ALA* 4.0 4.3 - - - +
180A HIS* 1.3 93.8 + - - +
182A ARG* 1.3 67.2 + - - +
184A ALA* 3.8 2.0 - - - +
185A ARG* 2.9 34.3 + - - +
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Residues in contact with ARG 182 (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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178A ALA 2.9 19.3 + - - +
179A GLU* 2.6 44.9 + - - +
181A ASP* 1.3 78.1 - - - +
183A MET* 1.3 72.6 + - - +
185A ARG* 3.3 6.9 + - - +
186A GLN* 3.0 55.5 + - - +
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Residues in contact with MET 183 (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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120A TYR* 3.7 33.4 - - + +
172A GLN* 4.6 2.0 - - - +
179A GLU* 2.9 35.6 + - + +
180A HIS 3.6 3.6 - - - +
182A ARG* 1.3 98.0 - - - +
184A ALA* 1.3 57.7 + - - +
186A GLN* 3.2 17.7 + - - +
187A TRP* 2.8 68.7 + - + +
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Residues in contact with ALA 184 (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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90A VAL* 3.6 29.4 - - + -
91A TYR* 4.0 5.7 - - + +
120A TYR* 3.8 30.9 - - + +
180A HIS* 2.8 24.4 + - + +
181A ASP* 3.3 3.8 + - - +
183A MET* 1.3 72.6 - - - +
185A ARG* 1.3 57.4 + - - +
187A TRP* 3.5 1.9 + - - +
188A THR* 2.8 32.8 + - - -
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Residues in contact with ARG 185 (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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89A SER 5.3 0.6 + - - -
90A VAL* 3.6 38.7 - - + +
181A ASP* 2.9 24.6 + - - +
182A ARG* 3.7 6.7 - - - +
184A ALA* 1.3 76.5 - - - +
186A GLN* 1.3 62.9 + - - +
188A THR* 3.2 4.4 + - - -
189A LYS* 3.0 23.7 + - - +
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Residues in contact with GLN 186 (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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182A ARG* 3.0 45.2 + - + +
183A MET* 3.2 27.1 + - - +
185A ARG* 1.3 76.9 - - - +
187A TRP* 1.3 64.4 + - + +
189A LYS* 3.3 6.7 + - - +
190A ARG* 2.9 33.7 + - + +
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Residues in contact with TRP 187 (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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118A ARG* 4.2 30.2 - - + +
119A ILE* 3.7 21.8 - - - -
120A TYR* 3.6 48.9 - + + +
169A ILE* 6.1 1.6 - - + -
183A MET* 2.8 45.2 + - + +
184A ALA 3.9 2.2 - - - +
186A GLN* 1.3 86.6 + - + +
188A THR* 1.3 57.7 + - - +
190A ARG* 4.3 2.2 - - + -
191A TYR* 3.0 66.8 + + + +
192A ALA 3.9 0.3 + - - -
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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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90A VAL 3.5 12.3 + - - -
91A TYR* 3.5 39.0 - - - +
92A GLU 3.9 8.7 - - - +
93A GLY 4.4 1.1 - - - -
94A GLY* 3.6 21.1 - - - +
96A PHE* 4.2 5.4 - - + -
184A ALA 2.8 18.8 + - - -
185A ARG* 3.4 9.9 - - - -
186A GLN 3.2 0.6 - - - -
187A TRP* 1.3 78.3 - - - +
189A LYS* 1.3 59.4 + - - +
192A ALA* 2.9 36.1 + - - +
193A THR* 3.4 2.3 - - + +
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Residues in contact with LYS 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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185A ARG 3.0 12.1 + - - +
186A GLN* 3.3 8.5 + - - +
188A THR* 1.3 77.7 - - - +
190A ARG* 1.3 62.5 - - - +
193A THR* 2.5 37.5 + - + +
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Residues in contact with ARG 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 GLN* 2.9 21.2 + - + +
187A TRP* 4.0 4.9 - - + +
189A LYS* 1.3 79.4 - - - +
191A TYR* 1.3 90.0 + - + +
193A THR 4.7 4.4 - - - +
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Residues in contact with TYR 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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117A THR* 3.4 13.1 - - + +
118A ARG* 3.7 65.7 + - + +
187A TRP* 3.0 63.5 + + + +
190A ARG* 1.3 99.0 - - + +
192A ALA* 1.3 60.9 + - - +
193A THR 3.6 5.1 - - - +
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Residues in contact with ALA 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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93A GLY 4.1 0.7 - - - +
94A GLY* 3.4 2.4 - - - -
95A VAL* 2.9 49.1 + - - +
96A PHE* 3.5 37.9 - - + -
117A THR* 3.9 2.7 - - + -
118A ARG 5.0 0.4 - - - +
187A TRP 3.9 0.6 + - - +
188A THR* 2.9 14.0 + - - +
191A TYR* 1.3 79.3 - - - +
193A THR* 1.3 65.5 + - - +
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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