Contacts of the helix formed by residues 192 - 202 (chain D) in PDB entry 5AQF
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 PRO 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D PHE 3.9 3.8 - - - +
191D LEU* 1.4 86.5 - - + +
193D LYS* 1.4 64.6 + - - +
194D ASP* 3.4 5.2 - - + +
195D LEU* 3.0 34.9 + - + +
196D GLN* 3.0 20.0 + - - +
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Residues in contact with LYS 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ILE* 6.1 5.4 - - + -
191D LEU 3.9 0.4 + - - -
192D PRO* 1.4 70.4 - - - +
194D ASP* 1.4 61.0 + - - +
196D GLN* 3.3 25.1 + - - +
197D ALA* 3.6 7.6 + - - +
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Residues in contact with ASP 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A THR* 4.7 13.0 - - + -
277A SER* 3.7 27.2 + - - +
279A GLN 5.7 0.7 - - - +
192D PRO* 3.4 3.4 - - + +
193D LYS* 1.4 77.0 - - - +
195D LEU* 1.4 66.7 + - + +
196D GLN 3.5 0.7 + - - -
197D ALA* 3.7 12.7 + - - +
198D GLU* 3.9 9.0 + - - +
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D LEU* 3.8 24.8 - - + +
192D PRO* 3.0 38.4 + - + +
194D ASP* 1.4 79.6 - - + +
196D GLN* 1.4 62.8 + - - +
197D ALA 3.5 0.2 - - - -
198D GLU* 3.6 24.7 + - + +
199D ALA* 3.3 16.8 + - - +
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Residues in contact with GLN 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D ILE* 3.1 36.8 + - + +
187D GLN* 3.5 23.7 + - - +
189D GLY 4.4 8.7 + - - -
191D LEU* 2.8 30.1 + - + +
192D PRO 3.0 16.5 + - - +
193D LYS* 3.3 14.8 + - - +
195D LEU* 1.4 74.7 - - - +
197D ALA* 1.4 58.0 + - - +
199D ALA 3.3 1.9 + - - -
200D LEU* 3.0 39.4 + - + +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A SER* 6.1 0.4 - - - +
193D LYS 3.6 7.0 + - - +
194D ASP* 3.9 10.8 - - - +
195D LEU 3.5 0.4 - - - -
196D GLN* 1.4 77.5 - - - +
198D GLU* 1.4 54.9 + - - +
200D LEU* 3.5 11.6 + - - +
201D CYS* 2.9 30.8 + - - +
259D CYS* 5.2 2.3 + - - -
260D GLN 6.1 0.4 - - - +
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Residues in contact with GLU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ASP 3.9 6.4 + - - +
195D LEU* 3.6 29.7 + - + +
196D GLN 3.3 0.6 - - - -
197D ALA* 1.4 74.9 - - - +
199D ALA* 1.4 63.0 + - - +
201D CYS* 3.3 7.0 + - - +
202D LYS* 3.1 46.1 + - + +
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D ILE* 3.8 24.5 - - + +
191D LEU* 3.8 28.9 - - + -
195D LEU 3.3 2.7 + - - +
196D GLN 3.3 6.1 + - - +
198D GLU* 1.4 76.9 - - - +
200D LEU* 1.4 62.3 + - - +
202D LYS* 3.2 27.8 + - + +
203D LEU* 3.7 5.9 + - - +
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D LEU* 3.4 35.0 - - + +
186D ILE* 3.7 31.9 - - + -
187D GLN* 4.4 17.5 - - + +
196D GLN* 3.0 28.0 + - + +
197D ALA* 3.6 9.0 - - - +
199D ALA* 1.4 73.5 - - - +
201D CYS* 1.4 64.0 + - - +
203D LEU* 3.2 21.4 + - + +
257D ASN 4.1 16.6 - - - +
258D ILE* 3.5 23.3 - - + +
259D CYS 5.4 0.2 - - - +
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Residues in contact with CYS 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA 2.9 18.0 + - - +
198D GLU* 3.3 6.7 + - - +
200D LEU* 1.4 73.3 - - - +
202D LYS* 1.4 60.1 + - - +
203D LEU 3.1 2.9 - - - -
204D ASP* 3.2 23.2 - - - +
259D CYS* 2.1 58.3 - - - +
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Residues in contact with LYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLU* 3.1 43.1 + - - +
199D ALA* 3.3 17.7 - - + +
200D LEU 3.2 0.6 - - - -
201D CYS* 1.4 77.4 - - - +
203D LEU* 1.4 60.3 + - + +
204D ASP 3.4 0.8 + - - -
205D ARG* 4.4 8.7 + - - +
206D ARG* 5.2 4.0 + - - +
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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