Contacts of the helix formed by residues 179 - 186 (chain B) in PDB entry 1K9A
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 ALA 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.4 25.1 - - + -
78B SER 2.7 28.7 + - - +
79B LEU* 3.4 19.1 - - + -
177B VAL 2.7 2.2 + - - -
178B ALA* 1.3 71.8 - - - +
180B GLN* 1.3 64.8 + - - +
182B GLU* 3.2 1.2 + - - +
183B PHE* 3.1 31.2 + - + -
234B LEU* 4.1 13.0 - - + -
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Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B SER 3.5 9.5 + - - -
79B LEU* 3.0 36.8 + - + +
81B PRO* 5.5 3.2 - - - +
150B MET* 4.4 9.9 - - - +
178B ALA* 3.5 14.4 - - + +
179B ALA* 1.3 89.6 - - - +
181B ASP* 1.3 70.5 + - - +
183B PHE* 3.5 5.8 + - - +
184B TYR* 3.2 20.7 + - - +
256B VAL* 5.2 12.6 - - + +
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Residues in contact with ASP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ALA* 3.2 23.7 + - + +
180B GLN* 1.3 81.5 - - - +
182B GLU* 1.3 58.3 + - - +
184B TYR* 3.0 7.6 + - - +
185B ARG* 2.7 68.2 + - + +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.9 24.2 - - + -
72B LYS* 2.8 43.1 + - + +
73B ALA* 5.7 1.3 - - + -
77B LEU* 4.1 11.4 - - + -
177B VAL* 3.6 23.7 - - + +
178B ALA 3.0 12.6 + - - +
179B ALA 3.5 9.6 - - - +
181B ASP* 1.3 77.6 - - - +
183B PHE* 1.3 57.6 + - + +
185B ARG* 4.0 7.1 - - - +
186B SER* 3.0 40.8 + - - -
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Residues in contact with PHE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.8 32.3 - - + -
77B LEU* 4.4 8.7 - - + -
79B LEU* 6.0 0.7 - - + -
179B ALA* 3.1 34.2 + - + +
180B GLN* 4.0 4.7 - - - +
182B GLU* 1.3 77.4 - - + +
184B TYR* 1.3 61.4 + - - +
186B SER 3.5 1.2 + - - -
187B GLY 3.3 4.5 + - - -
188B TRP* 2.9 39.1 + - + -
189B ALA* 4.4 4.0 - - + +
233B PHE* 5.1 3.4 - + - -
234B LEU* 3.7 26.9 - - + -
237B ALA* 3.9 29.2 - - + -
238B SER* 4.1 8.3 - - - -
241B THR* 4.2 10.8 - - + -
251B LEU* 6.0 1.1 - - + -
254B VAL* 3.9 31.6 - - + -
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Residues in contact with TYR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 4.2 21.5 - - + +
66B GLN* 2.9 25.9 - - - +
180B GLN 3.2 14.0 + - - +
181B ASP* 3.0 11.1 + - - +
183B PHE* 1.3 75.0 - - - +
185B ARG* 1.3 96.8 + - - +
187B GLY* 3.2 11.1 + - - -
189B ALA* 4.0 25.9 - - + +
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLN* 3.2 25.8 + - - +
67B LYS 3.6 4.3 - - - +
69B GLU* 4.4 5.0 - - - +
181B ASP* 2.7 51.6 + - + +
182B GLU* 4.2 7.9 - - - +
184B TYR* 1.3 100.7 - - - +
186B SER* 1.3 59.2 + - - +
187B GLY 3.2 2.9 + - - -
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS 3.8 5.2 - - - -
68B ARG* 3.3 1.4 - - - +
69B GLU* 3.1 40.1 + - - +
70B GLY 4.1 0.2 + - - -
71B VAL* 3.9 8.6 - - - +
72B LYS* 3.6 23.6 + - - -
182B GLU* 3.0 22.2 + - - -
183B PHE 4.1 0.2 - - - -
184B TYR 3.2 0.2 - - - -
185B ARG* 1.3 76.8 - - - +
187B GLY* 1.3 56.8 + - - +
188B TRP* 3.0 27.5 + - - -
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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