Contacts of the helix formed by residues 180 - 186 (chain A) in PDB entry 6KI3
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 180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ILE* 4.6 7.0 - - + +
179A ASP* 1.3 71.8 - - - +
181A ALA* 1.3 60.7 + - - +
183A ILE* 3.4 11.6 - - - +
184A TRP* 3.1 24.4 + - - +
190A ILE* 3.7 15.6 - - + +
217A PHE* 5.0 0.4 - - + -
218A HIS 3.2 9.4 + - - +
219A LEU* 4.0 10.9 - - + -
220A ASN 2.7 37.0 + - - -
241A ILE* 4.6 0.7 - - - -
242A TRP* 3.9 11.6 - - + -
257A PHE* 4.0 38.4 - - + -
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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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179A ASP* 3.2 11.3 + - - +
180A THR* 1.3 82.7 + - - +
182A HIS* 1.3 58.6 + - - +
184A TRP* 3.8 1.7 - - - +
185A SER* 3.1 25.5 + - - -
220A ASN* 3.6 24.7 - - + +
221A ASP 3.8 11.0 - - - +
222A ALA* 4.1 18.1 - - + +
231A ASP* 4.3 4.3 - - - +
232A ARG 5.3 0.4 - - - +
233A HIS* 4.1 15.7 - - + -
241A ILE* 4.3 1.6 - - - -
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Residues in contact with HIS 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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115A HIS* 5.0 4.9 - + - -
142A GLU* 3.1 17.1 + - - -
143A THR* 2.8 30.5 + - - +
144A PRO* 3.4 12.1 - - + +
145A HIS* 4.0 22.6 - + - +
179A ASP* 3.0 17.9 + - - +
181A ALA* 1.3 75.9 - - - +
183A ILE* 1.3 60.7 + - - +
184A TRP 3.1 1.1 - - - -
185A SER* 3.1 3.3 + - - -
186A SER* 2.8 32.2 + - - -
231A ASP* 3.3 15.5 + - - -
233A HIS* 4.0 0.4 - - - -
301A ZN 2.1 32.1 - - - -
303A ZN 4.6 0.2 - - - -
10D 3DR 2.9 22.9 + - - -
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Residues in contact with ILE 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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143A THR* 3.7 30.1 - - + +
154A SER* 3.4 32.5 - - - +
178A ILE* 4.6 4.5 - - + -
179A ASP 3.2 5.6 + - - +
180A THR* 3.4 15.5 - - - +
182A HIS* 1.3 76.1 - - - +
184A TRP* 1.3 63.2 + - - +
186A SER 3.4 0.7 + - - -
187A GLY 3.1 6.4 + - - -
188A VAL* 2.8 33.4 + - + +
190A ILE* 3.9 31.4 - - + -
199A TRP* 4.2 29.4 - - + -
257A PHE* 4.5 6.5 - - + -
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Residues in contact with TRP 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 THR 3.1 19.3 + - - +
181A ALA 3.8 1.6 - - - +
183A ILE* 1.3 75.6 - - - +
185A SER* 1.3 66.8 + - - +
187A GLY* 3.0 12.6 + - - -
188A VAL 3.5 24.7 - - - +
189A ASN* 4.0 12.6 - - - -
190A ILE* 4.1 4.7 - - + -
191A SER* 3.2 27.8 - - - -
222A ALA* 3.5 22.4 - - + +
224A THR* 3.0 21.2 + - + -
225A GLU* 3.4 4.9 - - - -
226A CYS* 3.4 41.2 - - + +
227A GLY 3.1 12.1 + - - -
240A MET* 3.9 27.4 - - + -
241A ILE* 3.4 30.0 - - + +
244B SER* 4.6 11.7 - - - -
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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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145A HIS* 3.6 12.5 - - - +
146A ASN 4.1 0.7 - - - +
181A ALA 3.1 16.0 + - - -
182A HIS 3.1 6.3 + - - -
184A TRP* 1.3 84.1 - - - +
186A SER* 1.3 56.9 + - - +
187A GLY 3.2 0.2 - - - -
224A THR* 4.5 3.4 - - - -
225A GLU 4.5 1.3 - - - -
227A GLY 3.1 4.9 - - - -
228A SER 3.1 14.4 + - - +
229A GLY* 3.0 35.5 + - - -
230A ILE 3.0 29.3 + - - -
231A ASP* 5.2 2.2 - - - -
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Residues in contact with SER 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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144A PRO 3.2 21.3 + - - -
145A HIS* 3.4 10.6 - - - -
146A ASN 3.6 12.4 + - - -
152A LYS* 3.5 33.3 - - - +
154A SER* 3.2 28.0 + - - -
182A HIS 2.8 8.1 + - - -
183A ILE 3.6 1.3 - - - -
184A TRP 3.1 0.2 - - - -
185A SER* 1.3 76.4 - - - +
187A GLY* 1.3 58.2 + - - +
188A VAL* 3.9 2.2 - - - +
227A GLY* 4.4 2.5 - - - -
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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