Contacts of the helix formed by residues 263 - 268 (chain D) in PDB entry 3A0B
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 ASN 263 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ASN* 2.4 31.6 + - - -
235A TYR* 5.7 0.2 - - - -
237A TYR* 3.7 38.4 + - - +
239A PHE* 4.4 4.3 - - + +
246D MET* 3.4 9.0 - - - +
261D PHE* 4.0 2.1 - - - -
262D SER* 1.3 80.5 - - - +
264D LYS* 1.3 59.0 + - - +
265D ARG* 3.0 10.5 + - - +
266D TRP* 2.5 33.2 + - - +
267D LEU* 3.5 7.6 + - - -
1062D MGE 3.9 11.9 + - - +
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Residues in contact with LYS 264 (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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237A TYR* 3.3 23.2 - - + -
244A GLU* 2.9 32.7 + - - +
245A THR* 3.3 24.2 - - + +
246A TYR* 3.0 22.1 - - + -
242D GLU* 3.6 14.1 + - - +
244D TYR* 3.0 37.9 + - + +
246D MET* 3.0 28.7 - - - +
263D ASN* 1.3 71.2 - - - +
265D ARG* 1.3 60.0 + - - +
266D TRP 3.3 0.4 - - - -
267D LEU* 3.8 15.9 - - + -
268D HIS* 3.2 31.7 + - + +
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Residues in contact with ARG 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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219A VAL 3.4 21.4 + - - -
220A THR* 3.3 30.0 + - - +
223A LEU* 2.9 43.1 - - - +
233A ALA* 4.0 8.5 + - - +
234A ASN* 4.0 19.5 + - - +
236A GLY 3.9 10.5 - - - +
237A TYR* 3.6 13.7 - - + -
245A THR* 2.9 37.0 - - + +
246A TYR* 4.3 4.0 - - - +
139D ARG* 3.3 12.7 - - - +
263D ASN* 2.9 16.3 - - - +
264D LYS* 1.3 79.9 - - - +
266D TRP* 1.3 59.7 + - - +
268D HIS* 3.9 6.9 + - - +
269D PHE* 3.7 16.3 + - - +
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Residues in contact with TRP 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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234A ASN* 3.9 19.7 - - + +
261D PHE* 2.8 41.9 - + - -
263D ASN* 2.5 19.6 + - - +
265D ARG* 1.3 70.5 - - - +
267D LEU* 1.3 52.9 + - - +
268D HIS 2.8 5.4 - - - -
269D PHE* 2.5 36.0 + + - +
270D PHE* 2.5 42.5 + + + +
1062D MGE 2.9 30.2 + - - +
19L LEU* 3.6 28.0 - - + -
1061L MGE 3.0 79.2 - - + +
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Residues in contact with LEU 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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214D HIS* 3.8 20.2 - - + +
244D TYR* 6.4 0.4 - - + -
246D MET* 5.8 4.0 - - + -
261D PHE* 2.9 52.3 - - + -
263D ASN 3.5 7.0 + - - +
264D LYS* 3.9 14.4 - - + +
265D ARG 3.6 0.2 - - - -
266D TRP* 1.3 79.6 - - - +
268D HIS* 1.3 84.0 + - + +
270D PHE* 4.1 1.3 - - - -
271D MET* 2.8 35.6 + - + +
1042D PQ9 3.3 32.3 - - + +
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Residues in contact with HIS 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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215A HIS* 3.0 12.6 + + - -
216A GLY* 2.4 39.4 - - - +
219A VAL* 2.5 51.3 - - + +
220A THR* 2.5 9.7 + - - +
245A THR* 6.1 0.4 - - - +
246A TYR* 3.7 26.2 - + - +
1002A FE2 2.3 29.9 - - - -
244D TYR* 4.2 3.0 + - - -
264D LYS* 3.2 17.5 + - + +
265D ARG* 4.0 7.0 + - - +
266D TRP 2.8 0.8 - - - -
267D LEU* 1.3 109.0 - - + +
269D PHE* 1.3 54.7 + - - +
270D PHE 3.6 0.4 - - - -
271D MET* 4.1 2.9 - - - -
272D LEU 4.1 0.5 + - - -
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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