Contacts of the helix formed by residues 178 - 186 (chain A) in PDB entry 4KN1
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 THR 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A TRP* 3.4 12.7 + - - +
176A PHE 3.2 0.9 + - - +
177A PRO* 1.3 90.5 - - + +
179A PRO* 1.3 77.5 - - + +
180A ALA* 3.7 7.9 + - - +
181A ALA* 3.0 28.1 + - - +
182A LEU 3.3 6.6 + - - -
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Residues in contact with PRO 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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133A CYS* 3.2 24.9 - - + +
134A GLN* 3.6 28.5 - - - +
137A TRP* 3.6 46.6 - - + -
178A THR* 1.3 87.1 - - - +
180A ALA* 1.3 63.1 + - - +
182A LEU* 3.0 5.7 + - - +
183A CYS 2.9 19.4 + - - -
193A VAL* 5.8 1.3 - - + -
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Residues in contact with ALA 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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133A CYS* 4.0 0.6 - - - -
178A THR* 3.3 7.6 + - - +
179A PRO* 1.3 78.4 - - - +
181A ALA* 1.3 57.7 + - - +
184A GLU* 2.8 48.1 + - - +
193A VAL* 3.6 28.9 - - + +
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Residues in contact with ALA 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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148A SER 4.7 0.5 - - - +
175A TYR 4.8 1.1 - - - +
176A PHE* 3.5 13.7 - - + -
177A PRO* 3.7 28.3 - - + -
178A THR* 3.0 19.3 + - - +
180A ALA* 1.3 78.6 - - - +
182A LEU* 1.3 58.0 + - - +
184A GLU* 5.2 0.2 - - - -
185A GLY* 3.1 25.6 + - - +
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Residues in contact with LEU 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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94A PHE* 4.7 3.8 - - + -
136A TRP* 3.7 27.4 - - + -
137A TRP* 3.6 42.2 - - + +
172A PHE* 4.1 14.1 - - + -
176A PHE* 3.5 43.6 - - + -
178A THR 3.3 1.8 + - - -
179A PRO 3.0 8.5 + - - +
181A ALA* 1.3 76.5 - - - +
183A CYS* 1.3 70.8 + - - +
186A LEU* 3.0 47.4 + - + +
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Residues in contact with CYS 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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128A LEU* 4.0 18.4 - - + -
133A CYS* 2.0 60.8 - - + -
136A TRP* 4.2 15.5 - - - -
179A PRO 2.9 10.2 + - - +
182A LEU* 1.3 79.5 - - - +
184A GLU* 1.3 60.2 + - - +
186A LEU* 4.3 6.2 + - - +
187A TRP 5.1 0.7 + - - -
190A SER* 4.8 1.7 + - - -
191A TYR* 3.4 33.4 + - + +
193A VAL* 4.3 10.1 - - + -
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Residues in contact with GLU 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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180A ALA* 2.8 36.1 + - - +
183A CYS* 1.3 73.5 - - - +
185A GLY* 1.3 57.5 + - - +
187A TRP 5.0 0.4 - - - -
189A HIS* 2.8 54.2 + - + +
191A TYR 3.6 18.4 - - - +
192A LYS* 3.7 7.3 - - - +
193A VAL* 3.0 38.9 + - + +
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Residues in contact with GLY 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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148A SER 3.4 17.8 - - - +
149A ASN* 3.6 12.1 + - - +
181A ALA* 3.1 19.2 + - - +
184A GLU* 1.3 77.7 - - - +
186A LEU* 1.3 67.0 + - - +
187A TRP 3.3 1.3 + - - -
188A SER* 3.5 8.1 + - - -
189A HIS* 4.9 5.4 - - - -
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Residues in contact with LEU 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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94A PHE* 3.6 14.4 - - + -
136A TRP* 3.6 34.1 - - + -
148A SER 4.0 4.6 + - - -
149A ASN* 3.7 0.5 - - - +
150A TRP* 2.9 68.2 + - + -
151A HIS 3.5 4.2 + - - -
176A PHE* 4.1 12.8 - - + -
181A ALA 4.1 0.2 + - - -
182A LEU* 3.0 24.0 + - + +
183A CYS* 4.5 4.3 - - - +
184A GLU 3.5 0.8 - - - -
185A GLY* 1.3 77.4 - - - +
187A TRP* 1.3 91.7 + - + +
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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