Contacts of the helix formed by residues 183 - 193 (chain D) in PDB entry 4GJ0
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 GLN 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A TYR* 3.4 26.5 - - - -
192A ASP* 4.5 6.7 - - - +
193A ASP* 2.9 38.3 + - - +
255B GLN* 3.4 28.7 - - - +
182D LYS* 1.3 75.3 - - - +
184D TRP* 1.3 68.3 + - - +
185D VAL* 3.9 5.2 + - - +
186D HIS* 3.1 13.6 + - + +
187D ALA* 2.9 18.9 + - - +
220D TRP* 3.4 1.1 - - - -
273D CYS 3.5 9.8 - - - +
274D ASP* 3.6 21.8 + - - +
275D ARG 3.2 14.6 + - - +
276D LYS* 4.0 1.4 - - + +
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Residues in contact with TRP 184 (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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272B PHE* 5.1 5.4 - + - -
183D GLN* 1.3 70.4 - - - +
185D VAL* 1.3 88.2 + - + +
187D ALA* 3.1 6.1 + - - +
188D ARG* 2.9 53.2 + - - -
198D LEU* 3.2 22.6 - - + +
220D TRP* 3.4 40.9 - + + +
221D ILE 3.0 23.1 + - - -
222D GLY 4.4 1.3 - - - -
223D LEU 4.5 4.0 + - - -
224D ARG* 3.3 49.1 - - + -
235D VAL* 3.6 17.5 - - + -
259D CYS* 3.4 27.9 - - + -
260D VAL 4.8 0.2 - - - -
273D CYS* 3.0 23.7 + - + +
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Residues in contact with VAL 185 (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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189A TYR* 3.3 45.1 - - + +
255B GLN* 5.5 2.2 - - + -
256B GLY* 6.4 2.0 - - - -
183D GLN* 3.9 7.8 - - - +
184D TRP* 1.3 97.9 - - + +
186D HIS* 1.3 67.6 + - - +
188D ARG* 3.2 10.1 + - - +
189D TYR* 3.0 56.8 + - + +
273D CYS* 4.7 1.0 + - - +
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Residues in contact with HIS 186 (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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186A HIS* 3.7 14.2 + + - -
189A TYR* 3.7 16.9 + - + -
190A ALA* 3.6 21.4 - - - -
193A ASP* 2.7 35.3 + - + +
181D THR 4.4 2.2 - - - -
182D LYS* 3.8 18.7 - - + +
183D GLN* 3.1 14.5 + - + +
185D VAL* 1.3 83.5 - - - +
187D ALA* 1.3 62.4 + - - +
189D TYR* 3.2 6.3 + - - -
190D ALA* 3.0 18.5 + - - +
301D GOL 2.9 42.8 + - - -
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Residues in contact with ALA 187 (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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182D LYS* 3.8 14.2 - - + +
183D GLN 2.9 12.8 + - - +
184D TRP 3.5 7.6 - - - +
186D HIS* 1.3 75.0 - - - +
188D ARG* 1.3 63.7 + - - +
190D ALA* 3.2 4.0 + - - +
191D CYS* 3.1 26.7 + - - -
198D LEU* 4.1 10.1 - - + -
220D TRP* 4.0 13.2 - - + -
280D TRP* 3.6 32.5 - - + -
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Residues in contact with ARG 188 (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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274B ASP* 3.1 32.1 + - - +
184D TRP* 2.9 33.4 + - + +
185D VAL* 3.3 22.3 - - - +
186D HIS 3.2 0.2 - - - -
187D ALA* 1.3 78.0 - - - +
189D TYR* 1.3 68.5 + - - +
191D CYS* 3.3 4.2 + - - +
192D ASP* 3.1 38.7 + - - +
198D LEU* 3.7 23.2 + - + +
224D ARG* 3.7 19.0 - - - +
235D VAL* 4.4 24.9 + - + +
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Residues in contact with TYR 189 (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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183A GLN* 5.1 8.3 - - + -
185A VAL* 3.6 34.7 - - + +
186A HIS* 3.6 39.0 - + + +
189A TYR* 4.1 14.3 - + - -
303A SO4 5.0 3.3 + - - -
185D VAL* 3.0 45.9 + - + +
186D HIS* 3.2 6.9 + - - +
188D ARG* 1.3 83.6 + - - +
190D ALA* 1.3 66.0 + - - +
192D ASP* 3.2 20.7 + - + +
193D ASP* 3.0 29.3 + - - +
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Residues in contact with ALA 190 (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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186A HIS* 3.9 3.5 - - - -
182D LYS* 3.9 19.5 - - + -
186D HIS 3.0 11.1 + - - +
187D ALA 3.2 9.2 + - - +
189D TYR* 1.3 77.2 - - - +
191D CYS* 1.3 62.9 + - - +
193D ASP* 3.4 8.9 + - - +
194D MET* 3.5 19.8 - - - +
280D TRP* 4.0 19.5 - - + -
301D GOL 3.5 23.8 - - - +
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Residues in contact with CYS 191 (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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187D ALA 3.1 15.1 + - - +
188D ARG 3.5 8.1 - - - +
189D TYR 3.1 0.2 - - - -
190D ALA* 1.3 72.2 - - - +
192D ASP* 1.3 66.0 + - - +
193D ASP 3.0 1.8 - - - -
194D MET* 3.0 15.1 + - - +
196D GLY* 3.0 18.1 + - - -
197D GLN* 3.6 20.2 - - - -
198D LEU* 3.7 22.2 - - - +
280D TRP* 4.2 4.0 - - - -
281D VAL 4.2 0.2 - - - -
282D CYS* 2.1 55.2 - - + -
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Residues in contact with ASP 192 (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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276A LYS* 5.4 1.2 + - - -
188D ARG* 3.1 29.7 + - - +
189D TYR* 3.5 32.0 - - + +
191D CYS* 1.3 75.2 - - - +
193D ASP* 1.3 67.1 + - - +
195D GLU* 3.2 18.0 + - - +
196D GLY 3.4 14.3 - - - +
197D GLN* 4.5 10.4 + - - +
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Residues in contact with ASP 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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181A THR 3.9 16.2 - - - +
182A LYS* 4.5 2.2 - - - +
183A GLN* 5.4 6.6 + - - +
186A HIS* 2.5 36.5 + - + +
276A LYS* 3.3 26.9 + - - +
189D TYR* 3.0 15.4 + - - +
190D ALA* 3.8 6.1 - - - +
191D CYS 3.0 0.6 + - - -
192D ASP* 1.3 84.1 - - - +
194D MET* 1.3 61.3 + - + +
195D GLU* 3.3 11.9 + - - +
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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