Contacts of the helix formed by residues 175 - 186 (chain A) in PDB entry 3K9O
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 ASP 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY 3.8 1.2 + - - -
174A PHE* 1.3 71.2 - - - +
176A ARG* 1.3 61.5 + - - +
177A ASN* 3.4 15.2 + - - +
178A ALA* 2.9 38.0 + - + +
179A VAL* 2.9 27.5 + - - +
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Residues in contact with ARG 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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151A VAL* 5.5 5.4 - - - -
166A ILE* 3.7 21.8 - - + +
167A GLU* 5.0 9.5 - - - +
170A CYS* 3.5 39.3 - - - +
174A PHE 3.4 3.8 + - - -
175A ASP* 1.3 72.7 + - - +
177A ASN* 1.3 68.5 + - - +
179A VAL* 3.2 2.0 + - - +
180A ILE* 3.0 41.5 + - + +
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Residues in contact with ASN 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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78A LYS* 3.8 26.4 - - + +
148A TRP* 5.9 0.2 - - - -
151A VAL* 5.6 0.2 - - - +
152A TYR* 2.6 38.7 + - - +
175A ASP* 3.3 12.9 + - - +
176A ARG* 1.3 83.8 - - - +
178A ALA* 1.4 62.2 + - - +
180A ILE* 3.4 2.1 + - - +
181A VAL* 3.1 25.6 + - - +
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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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174A PHE* 5.6 0.2 - - + -
175A ASP* 2.9 30.3 + - + +
177A ASN* 1.4 76.1 - - - +
179A VAL* 1.3 58.1 + - - +
181A VAL* 3.5 9.3 + - - +
182A ALA* 3.0 30.5 + - - +
197A LEU* 3.5 19.3 - - + +
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Residues in contact with VAL 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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166A ILE* 3.8 20.4 - - + +
169A LEU* 3.7 32.0 - - + +
170A CYS* 4.1 7.2 - - - +
174A PHE* 3.5 30.7 - - + +
175A ASP 2.9 18.7 + - - +
176A ARG* 3.2 9.4 + - - +
178A ALA* 1.3 73.2 - - - +
180A ILE* 1.3 66.2 + - - +
182A ALA* 3.3 1.4 + - - +
183A LEU* 2.9 40.0 + - + +
197A LEU* 4.1 10.3 - - + -
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Residues in contact with ILE 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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147A LEU* 4.2 8.1 - - + -
148A TRP* 3.4 36.8 - - + +
151A VAL* 3.9 23.6 - - + -
152A TYR* 3.6 24.2 - - + +
166A ILE* 3.8 35.2 - - + -
176A ARG* 3.0 37.1 + - + +
177A ASN* 3.4 3.8 + - - +
179A VAL* 1.3 76.3 - - - +
181A VAL* 1.3 62.9 + - - +
183A LEU* 4.1 2.3 - - - +
184A SER* 2.7 31.7 + - - +
188A TRP* 5.2 0.9 - - + -
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Residues in contact with VAL 181 (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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80A TRP* 4.4 1.3 - - + -
86A SER* 3.9 26.7 - - - +
87A VAL* 4.9 9.6 - - + -
148A TRP* 4.0 24.9 - - + -
177A ASN 3.1 17.2 + - - +
178A ALA* 3.5 14.4 - - - +
180A ILE* 1.3 77.4 - - - +
182A ALA* 1.3 58.3 + - - +
184A SER* 3.4 0.3 + - - -
185A SER* 2.7 47.7 + - - +
196A LEU* 5.4 0.2 - - - -
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Residues in contact with ALA 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 3.0 19.7 + - - +
179A VAL 3.7 3.1 - - - +
181A VAL* 1.3 77.8 - - - +
183A LEU* 1.3 62.7 + - - +
185A SER* 3.4 0.7 + - - -
186A LYS* 3.1 27.9 + - - +
193A ALA* 3.7 26.7 - - + +
196A LEU* 3.8 20.6 - - + -
197A LEU* 3.8 15.7 - - + -
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Residues in contact with LEU 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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165A LYS* 4.0 2.9 - - + -
166A ILE* 3.9 20.4 - - + +
169A LEU* 3.9 18.2 - - + -
179A VAL* 2.9 36.8 + - + +
180A ILE 4.1 1.6 - - - +
182A ALA* 1.3 76.5 - - - +
184A SER* 1.4 62.7 + - - +
186A LYS 3.1 6.1 + - - -
188A TRP* 2.8 81.7 + - + +
190A VAL* 4.2 16.2 - - + -
193A ALA* 3.7 19.3 - - + -
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Residues in contact with SER 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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80A TRP* 3.4 25.2 - - - -
129A VAL* 5.2 0.3 - - - +
133A GLN* 3.1 27.7 + - - -
144A THR* 3.5 10.3 - - - +
148A TRP* 2.8 23.2 + - - -
180A ILE* 2.7 22.4 + - - +
181A VAL 3.8 1.8 - - - -
183A LEU* 1.4 78.0 - - - +
185A SER* 1.3 58.6 + - - +
186A LYS 3.5 0.2 + - - -
187A SER 3.9 1.9 + - - -
188A TRP* 3.5 24.7 + - - +
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Residues in contact with SER 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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80A TRP* 3.8 11.3 - - - -
86A SER* 5.1 1.4 + - - -
129A VAL* 3.8 31.2 - - - +
181A VAL* 2.7 30.9 + - - +
182A ALA 3.9 3.6 - - - -
184A SER* 1.3 75.8 - - - +
186A LYS* 1.3 69.3 + - - +
187A SER 3.6 1.0 + - - -
196A LEU* 4.5 13.2 - - - -
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Residues in contact with LYS 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 ALA 3.1 16.3 + - - +
183A LEU 3.1 4.1 + - - +
185A SER* 1.3 88.2 + - - +
187A SER* 1.3 69.9 + - - +
188A TRP 3.1 2.0 - - - -
189A ASP* 3.0 18.4 + - - +
192A THR* 3.6 37.8 + - - +
193A ALA* 3.9 11.4 - - + +
196A LEU* 3.8 31.7 - - + +
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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