Contacts of the helix formed by residues 265 - 275 (chain A) in PDB entry 3H13
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 GLU 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A GLU* 2.7 21.1 + - - -
264A THR* 1.3 74.5 - - - +
266A LEU* 1.3 57.4 + - - +
267A LEU 3.3 0.2 - - - -
268A ARG* 2.8 48.1 + - - +
269A ASP* 2.8 50.0 + - - +
280A LYS* 2.8 22.5 + - - -
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Residues in contact with LEU 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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263A GLU 3.0 12.8 + - - +
264A THR* 2.9 15.8 + - + +
265A GLU* 1.3 76.9 - - - +
267A LEU* 1.3 61.0 + - + +
269A ASP* 5.1 0.2 - - - -
270A THR* 2.9 26.0 + - - -
420A PRO* 3.5 34.3 - - + -
424A LEU* 4.4 7.4 - - + +
425A GLN* 3.8 30.5 - - + +
428A SER* 3.3 25.1 + - - +
432A ARG* 3.0 17.6 + - - +
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Residues in contact with LEU 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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256A ILE* 3.9 10.3 - - + +
263A GLU* 2.7 15.1 + - + +
266A LEU* 1.3 73.4 - - + +
268A ARG* 1.3 65.3 + - - +
269A ASP 3.2 0.4 - - - -
270A THR* 4.1 5.8 - - + -
271A PHE* 2.9 47.0 + - + +
311A VAL* 3.6 34.8 - - + -
356A PHE* 4.8 0.2 - - + -
424A LEU* 4.0 20.4 - - + +
427A LEU* 3.9 27.4 - - + -
428A SER* 3.8 34.5 - - - +
431A LEU* 5.4 0.2 - - + -
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Residues in contact with ARG 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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256A ILE* 3.6 16.7 - - + +
263A GLU* 3.0 8.2 + - - +
265A GLU* 2.8 56.8 + - - +
267A LEU* 1.3 77.8 - - - +
269A ASP* 1.3 62.5 + - - +
272A THR* 2.7 42.3 + - - +
278A VAL* 3.8 25.6 + - + +
279A GLN* 5.7 0.2 - - - +
280A LYS* 3.8 36.3 + - + +
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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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264A THR 5.1 0.2 - - - +
265A GLU* 2.8 34.6 + - - +
268A ARG* 1.3 81.6 - - - +
270A THR* 1.3 65.5 + - - +
272A THR* 3.8 4.6 - - - -
273A SER* 2.9 25.6 + - - -
432A ARG* 3.5 23.9 + - - +
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Residues in contact with THR 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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266A LEU 2.9 13.6 + - - -
267A LEU* 3.9 11.7 - - + -
268A ARG 3.4 0.2 - - - -
269A ASP* 1.3 76.6 - - - +
271A PHE* 1.3 66.7 + - + +
273A SER* 3.2 5.4 + - - -
274A LEU* 3.0 27.6 + - + +
428A SER* 2.8 32.9 + - - +
431A LEU* 3.6 35.9 - - + -
432A ARG* 3.0 25.6 + - + +
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Residues in contact with PHE 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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254A CYS* 3.6 33.4 - - + -
267A LEU* 2.9 49.3 + - + +
270A THR* 1.3 72.3 - - + +
272A THR* 1.3 66.5 + - - +
274A LEU* 3.2 18.5 + - + +
275A GLY 3.2 0.5 + - - -
276A TYR* 2.9 39.8 + + + +
278A VAL* 4.2 1.8 - - + -
309A VAL* 3.8 24.9 - - + -
311A VAL* 4.0 13.7 - - + -
356A PHE* 3.6 20.0 - + - -
427A LEU* 5.7 0.2 - - + -
431A LEU* 3.6 29.6 - - + -
477A LEU* 4.0 13.7 - - + -
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Residues in contact with THR 272 (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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268A ARG* 2.7 30.9 + - - +
269A ASP* 3.8 5.6 - - - -
271A PHE* 1.3 75.1 - - - +
273A SER* 1.3 64.2 + - - +
275A GLY* 3.1 14.9 + - - -
276A TYR 3.8 14.4 + - - +
278A VAL* 3.6 15.9 + - - +
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Residues in contact with SER 273 (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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269A ASP 2.9 18.8 + - - -
270A THR* 3.4 6.7 - - - -
272A THR* 1.3 79.5 - - - +
274A LEU* 1.3 58.2 + - - +
275A GLY* 3.5 0.3 + - - -
432A ARG* 4.5 8.1 - - - +
435A ARG* 2.9 37.9 + - - -
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Residues in contact with LEU 274 (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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251A LEU* 3.5 17.9 - - - +
270A THR* 3.0 18.3 + - + +
271A PHE* 3.2 31.6 + - + +
273A SER* 1.3 75.9 - - - +
275A GLY* 1.3 57.9 + - - +
276A TYR* 4.1 9.9 - - + -
431A LEU* 3.7 25.4 - - + +
432A ARG* 5.0 0.2 - - - -
435A ARG* 3.5 49.1 - - + +
477A LEU* 4.0 34.4 - - + +
478A SER* 5.4 2.3 - - - -
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Residues in contact with GLY 275 (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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250A PRO* 3.0 11.8 - - - +
251A LEU* 2.8 28.0 + - - -
272A THR 3.1 10.5 + - - -
273A SER 3.2 1.2 - - - -
274A LEU* 1.3 80.7 - - - +
276A TYR* 1.3 64.3 + - - +
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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