Contacts of the helix formed by residues 193 - 198 (chain D) in PDB entry 4UX9
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 193 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D TYR 3.6 1.2 + - - -
192D ARG* 1.3 74.4 - - - +
194D PRO* 1.4 76.1 - - + +
195D GLU* 3.7 24.5 - - + +
196D VAL* 3.0 24.2 + - + +
197D ILE* 3.1 10.9 + - - +
206D VAL* 4.0 12.5 - - + +
209D TRP* 3.4 26.5 - - + -
210D SER* 5.2 0.4 + - - -
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Residues in contact with PRO 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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192D ARG 3.9 0.6 - - - +
193D ALA* 1.4 85.1 - - + +
195D GLU* 1.3 57.4 + - - +
197D ILE* 3.2 14.0 + - + -
198D LEU* 2.8 45.6 + - + +
200D MET* 4.7 0.2 - - - -
209D TRP* 3.7 30.3 - - + -
234D TRP* 3.9 21.3 - - + -
237D VAL* 4.7 2.2 - - + -
248D PHE* 4.4 2.5 - - + -
304D ILE* 3.7 39.9 - - + +
309D ARG* 3.8 4.0 - - - +
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Residues in contact with GLU 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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193D ALA* 3.7 5.6 - - + -
194D PRO* 1.3 75.8 - - - +
196D VAL* 1.4 61.7 + - - +
199D GLY* 3.2 2.6 + - - -
200D MET* 2.8 52.9 + - + +
201D GLY 3.6 23.6 - - - +
202D TYR* 4.1 5.7 - - + -
203D LYS 5.2 0.2 + - - -
205D ASN* 4.3 0.2 - - - +
206D VAL* 3.0 32.9 + - + +
248D PHE* 5.5 0.7 - - - -
304D ILE 3.8 5.0 - - - +
306D ALA* 3.4 15.8 + - + +
309D ARG* 2.9 42.4 + - - -
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Residues in contact with VAL 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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150D ARG* 5.4 10.8 - - - +
180D PHE* 5.7 0.3 - - - +
181D MET* 3.8 36.9 + - + +
189D ARG* 5.9 2.8 + - - +
192D ARG* 3.6 31.2 - - + +
193D ALA* 3.0 19.3 + - + +
195D GLU* 1.4 78.4 - - + +
197D ILE* 1.4 62.0 + - - +
198D LEU 3.5 0.5 + - - -
199D GLY* 3.6 7.6 + - - -
202D TYR* 5.1 10.8 - - + -
206D VAL* 4.2 29.4 - - + -
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Residues in contact with ILE 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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189D ARG* 5.6 10.8 - - + +
192D ARG* 3.8 27.4 - - + +
193D ALA 3.1 15.2 + - - +
194D PRO* 3.6 13.7 - - + +
196D VAL* 1.4 74.8 - - - +
198D LEU* 1.3 72.3 + - + +
199D GLY 3.4 0.4 + - - -
230D TYR 4.2 17.5 - - - +
233D GLN* 3.8 34.1 - - + -
234D TRP* 4.5 19.7 - - + -
237D VAL* 4.8 8.1 - - + -
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Residues in contact with LEU 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 PRO 2.8 21.8 + - - +
197D ILE* 1.3 80.9 - - + +
199D GLY* 1.3 63.2 + - - +
200D MET* 3.5 6.9 - - + +
234D TRP* 3.6 46.2 - - + -
248D PHE* 3.7 25.6 - - + -
252D LEU* 3.8 18.5 - - + +
253D GLN* 5.5 3.5 + - - +
256D VAL* 3.6 33.6 - - + +
259D TYR* 6.1 0.9 - - + -
260D VAL* 3.8 26.0 - - + -
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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