Contacts of the helix formed by residues 183 - 190 (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 GLY 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A THR* 5.2 3.4 - - - -
79A ALA* 3.9 18.0 - - - +
82A GLN* 4.1 4.0 - - - -
164A THR* 4.0 12.3 - - - +
182A GLY* 1.3 69.2 - - - -
184A ALA* 1.3 59.3 + - - +
185A ASP 3.4 0.2 + - - -
186A ALA* 3.4 3.8 + - - +
187A VAL* 3.1 26.3 + - - +
645A GLU* 3.4 28.2 - - - +
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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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82A GLN* 3.9 14.8 - - - +
182A GLY 3.1 1.2 + - - -
183A GLY* 1.3 72.4 - - - +
185A ASP* 1.3 64.5 + - - +
187A VAL* 3.7 10.2 + - - +
188A ASP* 3.4 23.7 + - - +
645A GLU* 3.2 14.0 + - - +
671A ASN* 5.6 2.6 - - - +
674A LYS* 3.7 36.9 + - + +
675A GLN* 4.3 3.8 - - - +
744A ALA* 5.4 3.1 - - + -
745A LEU* 6.5 0.2 - - + -
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Residues in contact with ASP 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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162A ILE* 4.5 2.9 - - - -
181A VAL* 3.4 27.1 - - + +
182A GLY* 2.8 15.6 + - - +
184A ALA* 1.3 77.8 - - - +
186A ALA* 1.4 60.0 - - - +
188A ASP* 3.3 23.9 + - - +
189A VAL* 3.6 10.6 + - - +
195A TRP* 3.4 26.3 + - - +
196A GLU 5.3 0.9 - - - +
666A ARG* 5.5 0.9 + - - -
667A ILE* 6.2 0.2 - - - +
670A THR* 4.0 24.8 - - - +
671A ASN* 5.3 3.3 + - - +
674A LYS* 3.1 25.3 - - - +
738A TRP* 5.4 0.2 - - - -
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Residues in contact with ALA 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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69A VAL* 4.0 20.5 - - + +
71A MET* 5.1 1.3 - - - -
79A ALA* 5.0 3.4 - - + -
162A ILE* 4.1 12.8 - - + -
163A GLY 6.2 0.2 - - - -
164A THR* 3.7 26.2 - - + -
181A VAL* 4.4 4.9 - - + +
182A GLY 3.3 3.2 + - - -
183A GLY* 3.7 8.1 - - - +
185A ASP* 1.4 74.8 - - - +
187A VAL* 1.4 58.8 + - - +
189A VAL* 3.3 3.6 + - - +
190A MET* 2.9 38.2 + - + +
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Residues in contact with VAL 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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79A ALA 3.5 25.1 - - - +
82A GLN* 4.2 15.0 - - + +
83A PHE* 4.2 22.2 - - + +
86A SER* 5.1 2.0 - - - -
183A GLY 3.1 16.1 + - - +
184A ALA* 3.7 12.6 - - - +
185A ASP 3.4 0.4 - - - -
186A ALA* 1.4 70.3 - - - +
188A ASP* 1.3 58.3 + - - +
190A MET* 3.7 15.7 - - + +
191A ALA* 2.8 33.5 + - + +
745A LEU* 5.0 7.6 - - + -
748A MET* 4.3 21.5 - - + -
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Residues in contact with ASP 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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184A ALA 3.4 6.3 + - - +
185A ASP* 3.3 13.5 + - - +
187A VAL* 1.3 78.6 - - - +
189A VAL* 1.3 62.0 + - + +
191A ALA* 3.3 3.5 + - - +
192A GLY 3.0 8.3 + - - -
193A ILE* 2.9 59.3 + - + +
194A PRO 5.0 6.3 - - - +
195A TRP* 4.6 8.3 - - + -
196A GLU 5.7 0.2 + - - -
674A LYS* 2.7 34.4 + - - -
738A TRP* 5.2 1.4 - - - -
744A ALA* 5.4 1.7 - - - +
748A MET* 3.8 12.7 - - - +
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Residues in contact with VAL 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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66A PRO* 4.0 26.7 - - + +
69A VAL* 3.8 20.0 - - + -
92A ALA* 4.3 0.3 - - - +
93A VAL* 3.9 30.1 - - + +
162A ILE* 3.7 20.0 - - + -
185A ASP 3.6 5.1 + - - +
186A ALA 3.3 7.0 + - - +
187A VAL 3.3 0.2 - - - -
188A ASP* 1.3 72.8 - - - +
190A MET* 1.3 65.4 + - - +
191A ALA 3.1 1.6 - - - -
192A GLY* 3.2 10.7 + - - -
193A ILE 4.2 8.5 - - - +
195A TRP* 3.6 32.1 - - + -
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Residues in contact with MET 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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69A VAL* 4.3 11.9 - - + -
71A MET* 3.9 30.3 - - + -
79A ALA* 4.7 2.7 - - + +
80A MET* 4.3 12.1 - - - +
83A PHE* 3.8 39.8 - - + -
90A LYS 4.1 2.6 - - - +
91A VAL* 3.5 23.7 - - + -
92A ALA* 2.8 30.2 + - - +
93A VAL* 4.7 2.5 - - - -
95A SER* 4.0 17.0 - - - +
136A VAL* 5.2 0.2 - - - -
186A ALA* 2.9 18.1 + - + +
187A VAL* 3.3 21.5 + - + +
189A VAL* 1.3 74.0 - - - +
191A ALA* 1.3 57.9 + - - +
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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