Contacts of the helix formed by residues 261 - 271 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A HIS* 3.7 29.4 + - - -
92A PRO* 4.2 11.5 - - - +
253A LEU* 4.9 2.1 - - - +
259A ALA 3.6 1.2 + - - -
260A TRP* 1.3 94.5 - - - +
262A ASP* 1.3 61.3 + - - +
263A ALA* 3.0 27.5 + - - +
264A VAL* 3.7 16.3 + - - +
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Residues in contact with ASP 262 (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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246A ARG* 3.1 26.3 + - - +
260A TRP* 3.1 21.1 - - - +
261A SER* 1.3 69.1 + - - +
263A ALA* 1.3 62.8 + - - +
264A VAL* 2.9 7.8 + - - -
265A LEU* 2.9 21.3 + - - +
266A HIS* 3.1 29.3 + - - -
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Residues in contact with ALA 263 (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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90A ALA* 4.2 15.4 - - - +
91A HIS* 4.9 0.4 - - - +
92A PRO* 5.2 2.5 - - + -
261A SER* 3.0 15.1 + - - +
262A ASP* 1.3 76.6 + - - +
264A VAL* 1.3 54.8 + - - +
266A HIS* 2.6 44.3 + - - +
267A HIS* 3.2 2.3 + - - -
270A LEU* 4.1 21.8 - - + -
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Residues in contact with VAL 264 (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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87A MET* 3.2 53.9 - - - +
88A LEU* 5.2 0.4 - - - -
90A ALA* 4.9 0.9 - - - -
91A HIS* 5.1 10.5 - - + +
249A LEU* 3.1 50.0 - - + -
253A LEU* 4.4 15.9 - - + -
260A TRP* 4.8 2.7 - - + -
261A SER* 3.7 17.0 + - - +
262A ASP 4.3 0.2 - - - +
263A ALA* 1.3 77.8 - - - +
265A LEU* 1.3 76.9 + - + +
266A HIS 3.3 1.0 + - - -
267A HIS* 3.5 5.9 + - - +
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Residues in contact with LEU 265 (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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87A MET* 5.2 2.2 - - - -
245A PRO* 3.8 18.4 - - + +
246A ARG* 3.3 63.0 - - + +
249A LEU* 5.1 0.2 - - + -
260A TRP* 4.1 11.2 - - + -
262A ASP* 2.9 19.8 + - - +
264A VAL* 1.3 90.2 - - + +
266A HIS* 1.3 63.9 + - + +
267A HIS* 3.5 5.9 - - - -
268A GLU* 3.4 10.6 - - - +
292A PRO* 5.0 1.9 - - - +
293A VAL* 5.2 4.0 - - - +
340A PHE* 3.4 38.9 - - + -
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Residues in contact with HIS 266 (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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262A ASP* 3.1 38.3 + - - -
263A ALA* 2.6 21.3 + - - +
265A LEU* 1.3 81.1 + - + +
267A HIS* 1.3 63.4 + - - +
268A GLU* 3.1 22.4 + - - +
269A ASP* 2.9 30.4 + - + +
270A LEU* 3.9 7.1 + - + +
340A PHE* 4.9 13.1 - + - -
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Residues in contact with HIS 267 (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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1A A3P 4.0 7.6 + - - -
83A LEU* 4.2 8.3 - - + +
86A ALA* 3.9 24.5 - - - +
87A MET* 3.9 23.8 - - + -
90A ALA* 4.0 10.8 - - + -
263A ALA 3.2 5.1 + - - -
264A VAL 3.5 10.1 + - - +
265A LEU 3.5 2.2 - - - -
266A HIS* 1.3 76.4 - - - +
268A GLU* 1.3 68.5 + - - +
269A ASP 2.8 0.7 + - - -
270A LEU* 2.7 33.8 + - - +
271A ILE* 4.0 5.4 + - - +
277A VAL* 4.3 5.7 - - + +
289A VAL* 3.1 36.0 + - + +
291A LYS 3.2 11.7 - - - -
292A PRO* 3.5 2.2 - - + +
293A VAL* 3.5 32.2 + - + +
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Residues in contact with GLU 268 (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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265A LEU 3.4 7.0 - - - +
266A HIS* 3.2 32.5 + - - -
267A HIS* 1.3 83.7 + - - +
269A ASP* 1.3 82.2 + - - +
270A LEU 3.3 1.5 + - - -
271A ILE* 3.5 23.9 + - - +
290A ILE 3.6 18.8 - - - +
291A LYS 4.1 0.4 - - - -
292A PRO* 3.5 40.0 - - + +
340A PHE* 5.9 1.0 - - - -
347A ARG* 4.0 13.2 + - - +
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Residues in contact with ASP 269 (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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266A HIS* 2.9 23.9 + - + +
267A HIS 2.8 2.0 + - - -
268A GLU* 1.3 104.2 - - - +
270A LEU* 1.3 64.1 + - + +
271A ILE 3.8 0.9 - - - -
273A LYS* 3.3 20.1 + - - +
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Residues in contact with LEU 270 (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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90A ALA* 3.4 37.7 - - + +
263A ALA* 4.1 15.7 - - + -
266A HIS* 4.4 7.0 - - + +
267A HIS 2.7 18.1 + - - +
269A ASP* 1.3 81.1 - - + +
271A ILE* 1.3 60.3 + - - +
273A LYS* 3.5 28.3 + - + +
274A PRO 5.2 6.5 - - - +
276A GLY* 4.4 4.7 - - - -
277A VAL* 3.0 30.5 + - + -
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Residues in contact with ILE 271 (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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267A HIS* 4.3 5.6 - - - +
268A GLU* 3.5 28.2 + - - +
269A ASP 3.8 1.4 - - - -
270A LEU* 1.3 75.4 - - - +
272A GLY* 1.3 61.9 + - - +
273A LYS* 2.9 19.1 + - - +
277A VAL* 3.4 17.7 - - + +
279A LEU* 4.0 32.3 - - + -
289A VAL* 4.3 6.3 - - + +
290A ILE* 3.9 35.4 - - + +
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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