Contacts of the helix formed by residues 183 - 195 (chain A) in PDB entry 5HKZ
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 LYS 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A ILE* 3.6 3.6 - - - +
182A THR* 1.3 88.3 - - + +
184A ALA* 1.3 61.3 + - - +
185A ASP* 4.7 2.2 - - + +
186A ALA* 3.0 19.3 + - + +
187A ALA* 2.8 27.2 + - - +
242A ASP* 4.5 0.6 + - - -
245A THR* 4.0 23.1 + - - +
246A ARG* 4.5 10.5 - - + -
249A GLN* 2.9 40.7 + - + +
250A PRO* 6.1 1.1 - - - -
251A TRP* 5.9 4.3 - - + +
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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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181A ILE 5.5 0.4 - - - -
182A THR 3.6 3.8 + - - -
183A LYS* 1.3 73.2 - - - +
185A ASP* 1.3 63.3 + - - +
187A ALA* 3.3 8.8 + - - +
188A GLU* 3.0 31.2 + - - +
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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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183A LYS* 3.3 1.9 - - + +
184A ALA* 1.3 80.9 - - - +
186A ALA* 1.3 62.9 + - - +
188A GLU* 3.4 7.3 + - - +
189A PHE* 3.2 19.8 + - - +
251A TRP* 3.6 38.8 + - + +
252A SER* 4.9 7.1 + - - -
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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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181A ILE* 4.1 3.1 - - + -
183A LYS* 3.0 14.7 + - + +
185A ASP* 1.3 76.7 - - - +
187A ALA* 1.3 65.1 + - - +
189A PHE* 3.1 3.0 + - - +
190A TRP 3.0 18.0 + - - -
241A PHE* 3.3 21.4 - - + -
245A THR* 3.6 37.2 - - + +
251A TRP* 3.8 16.4 - - + +
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Residues in contact with ALA 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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181A ILE* 3.5 36.8 - - + +
183A LYS 2.8 12.1 + - - +
184A ALA* 3.6 12.1 - - - +
186A ALA* 1.3 76.5 - - - +
188A GLU* 1.3 63.1 + - - +
190A TRP* 3.3 2.6 + - - +
191A ARG* 3.0 25.6 + - - +
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Residues in contact with GLU 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 3.0 16.7 + - - +
185A ASP* 3.8 6.5 - - - +
186A ALA 3.2 0.2 - - - -
187A ALA* 1.3 76.9 - - - +
189A PHE* 1.3 62.6 + - - +
191A ARG* 3.4 24.8 + - - +
192A LYS* 3.0 32.8 + - - +
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Residues in contact with PHE 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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185A ASP 3.2 8.1 + - - +
186A ALA 3.1 7.5 + - - +
188A GLU* 1.3 77.9 - - - +
190A TRP* 1.3 65.7 + + - +
192A LYS* 3.9 4.4 - - - +
193A ALA* 3.0 28.0 + - + +
194A PHE* 4.4 11.4 - + - -
205A PHE* 4.1 12.6 - + - -
208A ALA* 3.4 28.9 - - + -
209A LEU* 3.6 33.4 - - + -
212A VAL* 4.0 19.3 - - + -
241A PHE* 3.5 28.7 - + - -
251A TRP* 3.5 31.0 - + + +
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Residues in contact with TRP 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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181A ILE* 3.5 29.6 - - + -
186A ALA 3.0 10.0 + - - +
187A ALA 3.3 0.6 + - - +
189A PHE* 1.3 82.4 - + - +
191A ARG* 1.3 59.1 + - - +
193A ALA 4.6 0.2 - - - +
194A PHE* 2.7 58.4 + + + +
195A GLY 3.4 13.5 + - - -
196A GLU 5.5 0.2 - - - -
197A LYS 2.9 29.9 + - - -
198A THR 4.3 5.4 - - - -
200A VAL* 4.4 11.9 - - + -
205A PHE* 4.0 16.8 - + - -
236A ILE* 3.8 16.2 - - + -
237A SER 3.9 0.9 - - - -
238A VAL* 3.7 34.9 - - + +
241A PHE* 3.6 39.9 - + + -
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Residues in contact with ARG 191 (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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187A ALA 3.0 17.4 + - - +
188A GLU* 3.7 23.3 - - - +
190A TRP* 1.3 77.5 - - - +
192A LYS* 1.3 60.7 + - - +
195A GLY* 3.0 39.5 + - - +
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Residues in contact with LYS 192 (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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188A GLU* 3.0 23.9 + - - +
189A PHE* 3.9 4.5 - - - +
191A ARG* 1.3 80.1 - - - +
193A ALA* 1.3 62.8 + - - +
195A GLY 4.8 0.2 + - - -
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Residues in contact with ALA 193 (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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189A PHE* 3.0 24.8 + - + +
192A LYS* 1.3 78.4 - - + +
194A PHE* 1.4 90.1 + - + +
195A GLY 3.9 0.2 - - - -
197A LYS* 5.7 0.7 + - - -
208A ALA* 4.0 17.9 - - + -
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Residues in contact with PHE 194 (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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189A PHE* 4.4 4.5 - + - -
190A TRP* 2.7 52.5 + + + +
193A ALA* 1.4 93.6 - - + +
195A GLY* 1.3 63.8 + - - +
197A LYS* 3.0 46.1 + - + +
200A VAL* 3.6 26.5 - - + -
204A SER* 3.9 19.7 - - - -
205A PHE* 3.9 28.3 - + - -
208A ALA* 3.6 24.2 - - + -
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Residues in contact with GLY 195 (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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190A TRP* 3.4 16.2 + - - -
191A ARG* 3.0 32.9 + - - +
192A LYS 4.8 0.4 + - - -
193A ALA 3.9 0.6 - - - -
194A PHE* 1.3 77.0 - - - +
196A GLU* 1.3 63.2 + - - +
197A LYS 3.7 0.3 + - - -
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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