Contacts of the helix formed by residues 166 - 176 (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 VAL 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A HIS 4.0 5.8 - - - +
122A CYS* 3.0 7.3 + - - +
124A ILE 3.6 24.9 - - - +
125A ASN* 3.9 13.0 - - + -
126A SER 5.2 0.9 - - - +
164A PRO* 4.3 2.0 - - - -
165A LEU* 1.3 83.0 - - - +
167A GLY* 1.3 67.6 + - - +
168A SER* 3.7 13.5 - - - +
169A ILE* 3.2 33.3 + - + +
170A ALA* 3.1 20.4 + - - +
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Residues in contact with GLY 167 (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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164A PRO* 4.8 7.6 - - - +
165A LEU 3.9 3.4 + - - -
166A VAL* 1.3 72.2 - - - +
168A SER* 1.3 61.9 + - - +
170A ALA* 3.1 7.5 + - - +
171A THR* 3.0 32.6 + - - +
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Residues in contact with SER 168 (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* 5.5 0.4 - - - -
166A VAL* 3.7 13.5 - - - +
167A GLY* 1.3 75.1 - - - +
169A ILE* 1.3 61.7 + - - +
171A THR* 3.0 20.0 + - - -
172A GLN* 3.1 17.0 + - - +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE 5.5 0.7 - - - +
120A TYR* 3.7 44.6 - - + +
121A HIS 3.8 17.0 - - - +
122A CYS* 3.7 18.6 - - + +
124A ILE 5.5 0.2 - - - +
166A VAL* 3.2 34.5 + - + +
168A SER* 1.3 79.6 - - - +
170A ALA* 1.3 59.6 + - - +
172A GLN* 3.3 5.7 + - - +
173A TYR* 2.9 27.0 + - - +
180A HIS* 3.5 27.3 - - + +
187A TRP* 6.1 1.3 - - + -
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Residues in contact with ALA 170 (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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122A CYS* 3.6 14.9 - - + +
161A PRO* 4.3 11.8 - - + +
164A PRO* 3.5 37.5 - - + -
166A VAL 3.1 4.9 + - - -
167A GLY 3.1 6.9 + - - +
169A ILE* 1.3 76.3 - - - +
171A THR* 1.3 65.1 + - + +
173A TYR* 3.2 7.1 + - - +
174A MET* 3.1 28.5 + - + +
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Residues in contact with THR 171 (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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167A GLY* 3.0 15.8 + - - +
168A SER* 3.0 14.6 + - - -
170A ALA* 1.3 76.2 - - + +
172A GLN* 1.3 59.3 + - - +
174A MET* 3.2 7.2 + - - +
175A THR* 2.8 41.6 + - - +
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Residues in contact with GLN 172 (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* 2.5 35.9 + - - -
168A SER 3.1 14.4 + - - +
169A ILE 3.6 2.6 + - - +
171A THR* 1.3 84.0 + - - +
173A TYR* 1.3 57.0 + - - +
175A THR* 4.0 5.4 - - - -
176A ASN* 2.7 55.1 + - + +
179A GLU* 3.5 20.4 + - + +
180A HIS* 3.3 29.3 - - - +
183A MET* 4.6 2.6 - - - +
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Residues in contact with TYR 173 (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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122A CYS* 5.5 0.9 - - - -
158A ASP* 5.6 2.1 - - - -
159A CYS* 3.5 35.0 + - - -
161A PRO* 3.9 28.9 - - + -
169A ILE 2.9 14.4 + - - +
170A ALA* 3.2 12.1 + - - +
172A GLN* 1.3 76.3 - - - +
174A MET* 1.3 69.3 + - - +
177A ARG* 3.4 65.8 + - - +
180A HIS* 3.6 38.9 - + + +
181A ASP* 4.9 0.4 - - - -
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Residues in contact with MET 174 (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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161A PRO* 3.8 30.7 - - + -
170A ALA* 3.1 17.2 + - + +
171A THR* 3.6 8.7 - - - +
172A GLN 3.2 0.2 - - - -
173A TYR* 1.3 84.9 - - - +
175A THR* 1.3 67.9 + - + +
177A ARG* 5.1 1.1 + - - +
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Residues in contact with THR 175 (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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171A THR* 2.8 30.3 + - - +
172A GLN* 4.0 3.1 - - - -
174A MET* 1.3 87.5 - - + +
176A ASN* 1.3 63.8 + - - +
177A ARG 3.9 1.1 - - - -
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Residues in contact with ASN 176 (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* 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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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