Contacts of the helix formed by residues 261 - 271 (chain D) in PDB entry 3AP3
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 SER 261 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D HIS* 3.6 31.9 + - - -
92D PRO* 4.1 12.2 - - - +
253D LEU* 4.5 3.0 - - - +
259D ALA 3.7 0.8 + - - -
260D TRP* 1.3 90.1 - - - +
262D ASP* 1.3 60.6 + - - +
263D ALA* 3.3 20.6 + - - +
264D VAL* 3.1 27.4 + - - +
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Residues in contact with ASP 262 (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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246D ARG* 3.3 27.9 + - - -
260D TRP* 3.2 19.5 - - - +
261D SER* 1.3 69.3 + - - +
263D ALA* 1.4 55.7 + - - +
264D VAL 2.6 17.3 + - - -
265D LEU* 2.7 25.8 + - - +
266D HIS* 3.3 22.9 + - - -
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Residues in contact with ALA 263 (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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90D ALA* 4.0 17.2 - - - +
92D PRO* 5.3 2.2 - - + -
261D SER* 3.3 13.1 + - - +
262D ASP* 1.4 77.5 - - - +
264D VAL* 1.3 54.5 + - - +
265D LEU 3.2 0.2 - - - -
266D HIS* 2.8 40.9 + - - +
267D HIS 3.4 0.9 + - - -
270D LEU* 4.0 19.7 - - + -
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Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D MET* 3.6 40.8 - - + +
88D LEU* 6.3 0.2 - - + -
90D ALA* 4.9 1.7 - - - +
91D HIS* 4.7 9.6 - - + +
249D LEU* 3.3 37.0 - - + -
253D LEU* 3.9 23.8 - - + -
260D TRP* 4.3 2.9 - - + -
261D SER* 3.1 30.0 + - - +
262D ASP 2.6 4.1 + - - +
263D ALA* 1.3 74.1 - - - +
265D LEU* 1.3 78.3 + - + +
266D HIS 3.3 1.0 + - - -
267D HIS* 3.5 9.0 + - - +
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Residues in contact with LEU 265 (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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87D MET* 5.4 2.9 - - - -
245D PRO* 3.8 43.7 - - + +
246D ARG* 3.7 26.9 - - + +
249D LEU* 5.3 0.7 - - + -
260D TRP* 4.1 13.2 - - + -
262D ASP* 2.7 34.7 + - - +
264D VAL* 1.3 84.9 - - + +
266D HIS* 1.3 65.3 - - + +
267D HIS* 3.4 7.5 - - - -
268D GLU* 3.5 10.6 - - - +
292D PRO* 5.1 0.7 - - - +
293D VAL* 5.0 3.4 - - - +
340D PHE* 3.5 36.6 - - + -
344D ASN* 5.0 0.7 + - - -
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Residues in contact with HIS 266 (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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262D ASP* 3.3 32.5 + - - -
263D ALA* 2.8 16.6 + - + +
265D LEU* 1.3 89.9 + - + +
267D HIS* 1.3 65.3 + - - +
268D GLU* 3.1 16.0 + - - -
269D ASP* 3.1 35.9 + - + +
270D LEU* 4.0 7.9 + - + +
340D PHE* 4.9 13.4 - + - -
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Residues in contact with HIS 267 (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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1D A3P 3.8 6.5 + - - -
83D LEU* 4.2 8.0 - - + +
86D ALA* 4.1 18.9 - - + +
87D MET* 4.1 20.9 - - + -
90D ALA* 4.1 13.7 - - + -
263D ALA 3.4 1.4 + - - -
264D VAL 3.5 8.3 + - - +
265D LEU 3.4 4.9 - - - -
266D HIS* 1.3 76.5 - - - +
268D GLU* 1.3 75.6 + - - +
270D LEU* 2.7 35.2 + - - +
271D ILE* 4.0 3.2 + - - +
277D VAL* 4.1 6.2 - - + +
289D VAL* 3.2 21.2 + - + +
291D LYS 2.8 26.0 - - - -
292D PRO* 3.1 19.4 - - + +
293D VAL* 3.2 25.7 + - + +
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Residues in contact with GLU 268 (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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265D LEU 3.5 3.9 - - - +
266D HIS* 3.2 23.1 + - - -
267D HIS* 1.3 101.0 + - + +
269D ASP* 1.3 74.7 + - - +
270D LEU 3.2 1.3 + - - -
271D ILE* 3.6 20.9 + - - +
290D ILE 3.3 22.9 - - - +
291D LYS 3.9 2.0 - - - -
292D PRO* 3.3 39.2 - - + +
340D PHE* 5.8 0.7 - - - -
347D ARG* 4.1 8.9 + - - +
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Residues in contact with ASP 269 (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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266D HIS* 3.1 26.8 + - + +
267D HIS 2.9 0.8 + - - -
268D GLU* 1.3 97.9 - - - +
270D LEU* 1.3 61.9 + - + +
271D ILE 3.7 1.6 - - - -
273D LYS* 3.3 21.7 + - - +
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Residues in contact with LEU 270 (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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90D ALA* 3.2 39.3 - - + +
263D ALA* 4.0 16.6 - - + -
266D HIS* 4.0 11.7 - - + +
267D HIS 2.7 18.4 + - - +
269D ASP* 1.3 80.2 - - + +
271D ILE* 1.3 57.9 + - - +
272D GLY 3.5 0.5 + - - -
273D LYS* 3.7 23.6 + - + +
274D PRO 5.7 2.2 - - - +
276D GLY* 3.7 11.9 - - - +
277D VAL* 2.8 39.0 + - + +
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Residues in contact with ILE 271 (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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267D HIS* 4.4 7.0 - - - +
268D GLU* 3.6 22.2 + - - +
269D ASP 3.7 2.6 + - - -
270D LEU* 1.3 73.2 - - - +
272D GLY* 1.3 61.8 + - - +
273D LYS* 3.1 14.7 + - - +
277D VAL* 3.6 11.7 - - + +
279D LEU* 3.8 31.0 - - + +
289D VAL* 4.5 3.4 - - + +
290D ILE* 3.5 44.6 - - + +
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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