Contacts of the helix formed by residues 166 - 174 (chain A) in PDB entry 1B0K
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 SER 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ASP* 1.3 74.6 + - - +
167A HIS* 1.3 61.3 + - - +
168A THR 3.1 2.8 + - - -
169A PRO* 3.5 12.7 - - - +
180A GLY* 4.4 7.4 - - - -
261A ALA* 3.7 14.0 - - - +
447A ARG* 2.8 25.6 + - - -
641A GLY 4.0 5.8 - - - -
643A SER* 3.2 20.8 + - - -
667A ILE* 4.3 9.6 - - - -
756A FLC 2.7 28.8 + - - -
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Residues in contact with HIS 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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147A HIS* 3.4 21.9 + - + +
165A ASP* 2.9 12.3 + - - +
166A SER* 1.3 76.7 + - - +
168A THR* 1.4 60.8 + - - +
169A PRO* 3.4 3.1 - - - -
170A ASN* 3.4 18.4 + - - +
258A ASN* 3.2 39.3 + - - +
261A ALA* 4.0 5.0 - - + +
262A GLU* 2.9 22.4 + - - -
358A CYS* 4.1 4.3 - - - -
446A ASN* 3.0 32.1 - - - -
447A ARG* 3.5 24.0 + - - -
755A SF4 3.1 9.0 - - - -
1100A O 2.9 20.1 + - - +
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Residues in contact with THR 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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146A ILE* 5.5 0.9 - - - +
147A HIS* 3.6 18.6 + - + +
150A ILE* 5.8 4.0 - - + +
161A LEU* 4.1 12.1 - - + -
163A GLY* 3.6 33.3 - - - +
165A ASP* 2.7 24.2 + - - +
166A SER 3.1 0.8 - - - -
167A HIS* 1.4 74.1 - - - +
169A PRO* 1.4 62.4 - - - +
170A ASN* 3.0 8.5 + - - +
171A GLY* 3.2 5.9 + - - -
178A CYS* 3.2 25.2 - - + +
179A ILE 3.9 13.2 - - - +
180A GLY* 4.1 0.2 - - - -
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Residues in contact with PRO 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER 3.5 14.8 - - - +
167A HIS* 3.5 1.6 - - - +
168A THR* 1.4 84.7 - - - +
170A ASN* 1.4 52.9 + - - +
171A GLY 3.0 3.6 - - - -
172A GLY* 2.8 26.2 + - - -
178A CYS* 3.2 21.1 - - + +
180A GLY 4.2 7.0 - - - +
257A CYS* 3.3 30.7 - - - +
258A ASN* 4.8 3.8 - - - +
260A GLY 6.0 0.4 - - - -
261A ALA* 5.4 6.7 - - + +
265A ALA 5.4 2.5 - - - +
266A THR 4.4 4.9 - - - +
267A THR* 3.5 28.7 - - - +
268A SER 3.9 2.9 - - - +
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Residues in contact with ASN 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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147A HIS* 3.4 39.1 + - + +
148A GLN* 5.1 4.0 - - - +
151A LEU* 3.9 12.3 - - - +
167A HIS 3.4 16.2 + - - +
168A THR 3.0 2.4 + - - +
169A PRO* 1.4 73.8 - - - +
171A GLY* 1.4 56.2 + - - +
173A GLY* 3.1 18.4 + - - -
254A ALA* 3.5 45.9 - - - +
255A THR* 4.6 0.5 + - - -
257A CYS* 4.3 0.2 - - - +
258A ASN* 3.2 31.9 + - - +
358A CYS 3.6 10.7 + - - +
359A THR* 5.1 0.2 - - - -
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Residues in contact with GLY 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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150A ILE* 5.5 6.3 - - - -
151A LEU* 4.4 10.1 - - - -
155A ALA* 4.5 10.9 - - - +
156A TYR 5.8 0.2 + - - -
159A VAL* 6.0 0.2 - - - +
168A THR 3.2 5.8 + - - -
169A PRO 2.9 2.2 + - - -
170A ASN* 1.4 73.9 - - - +
172A GLY* 1.4 57.7 + - - +
173A GLY 3.1 3.1 - - - -
174A LEU* 3.0 24.3 + - - +
176A GLY* 3.9 7.1 + - - -
178A CYS* 3.5 25.6 - - - -
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Residues in contact with GLY 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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169A PRO 2.8 10.5 + - - -
171A GLY* 1.4 76.3 - - - +
173A GLY* 1.4 55.0 + - - +
174A LEU 3.1 0.4 - - - -
175A GLY* 3.2 14.4 + - - -
176A GLY 3.4 17.5 + - - -
178A CYS* 4.2 2.0 - - - +
257A CYS* 3.7 7.0 - - - -
268A SER 3.3 22.9 - - - -
269A VAL* 3.7 1.0 - - - -
270A PHE* 3.3 22.7 + - - +
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Residues in contact with GLY 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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151A LEU* 4.5 2.2 - - - -
170A ASN 3.1 9.6 + - - -
171A GLY 3.1 2.0 - - - -
172A GLY* 1.4 75.2 - - - +
174A LEU* 1.4 57.2 + - - +
175A GLY 3.6 0.2 - - - -
250A CYS* 3.7 19.8 - - - +
253A MET* 3.8 17.0 - - - +
254A ALA* 3.7 26.9 - - - -
257A CYS* 3.7 4.4 - - - -
270A PHE* 4.9 0.2 - - - -
276A MET* 3.4 14.2 - - - +
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Residues in contact with LEU 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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151A LEU* 3.7 28.2 - - + +
155A ALA* 3.5 32.5 - - + +
156A TYR 3.4 2.5 - - - -
157A PRO* 3.0 35.7 - - + +
171A GLY 3.0 10.6 + - - +
173A GLY* 1.4 74.3 - - - +
175A GLY* 1.4 56.2 + - - +
176A GLY 3.5 2.7 - - - -
250A CYS* 3.3 27.4 - - - -
276A MET* 3.5 31.6 - - + +
279A TYR* 3.8 19.1 - - + -
280A LEU* 4.4 8.7 - - + -
285A ARG* 3.9 5.6 - - - +
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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