Contacts of the helix formed by residues 265 - 279 (chain B) in PDB entry 5H65
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 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B GLY* 1.3 71.7 - - - -
266B GLU* 1.3 59.0 + - - +
267B HIS 3.4 0.2 - - - -
268B GLN* 3.4 22.3 + - - +
269B GLY* 2.7 31.7 + - - -
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B GLY* 3.7 9.6 - - - -
265B SER* 1.3 87.1 + - - +
267B HIS* 1.3 60.4 + - - +
269B GLY* 3.5 2.0 + - - +
270B ALA* 3.0 25.8 + - - +
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ILE* 6.0 0.4 - - + -
445A LEU* 3.4 27.9 + - + -
446A PRO 2.8 27.9 + - - -
447A LEU* 4.0 25.9 - - + +
448A SER 4.8 0.2 - - - -
264B GLY* 3.5 12.8 + - - +
265B SER 3.4 0.2 - - - -
266B GLU* 1.3 77.2 - - - +
268B GLN* 1.3 65.6 + - - +
270B ALA* 3.2 11.2 + - - +
271B LEU* 3.1 37.4 + - + +
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Residues in contact with GLN 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A ASN* 5.7 0.2 + - - -
420A ASP* 3.3 33.2 + - + +
422A LYS* 4.8 16.5 + - - +
438A PHE* 6.2 1.3 - - + -
445A LEU* 3.6 28.9 - - + +
264B GLY 3.5 5.5 + - - +
265B SER* 3.4 31.8 + - - +
267B HIS* 1.3 78.0 - - - +
269B GLY* 1.3 63.5 + - - +
271B LEU* 3.1 5.6 + - - +
272B VAL* 3.0 30.0 + - + +
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Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B SER 2.7 20.1 + - - -
266B GLU* 3.8 3.6 - - - -
267B HIS 3.3 0.4 - - - -
268B GLN* 1.3 74.1 + - - +
270B ALA* 1.3 60.5 + - - +
272B VAL* 3.3 9.0 + - - +
273B CYS* 3.0 31.2 + - - -
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLU 3.0 14.7 + - - +
267B HIS* 3.2 15.0 + - - +
269B GLY* 1.3 74.9 - - - +
271B LEU* 1.3 61.2 + - + +
273B CYS* 3.3 8.0 + - - +
274B LEU* 2.9 34.5 + - + +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A PHE* 3.5 14.8 - - + -
445A LEU* 3.9 23.8 - - + -
446A PRO 3.6 19.5 - - - +
448A SER* 3.7 36.6 - - - +
451A CYS* 4.3 18.4 - - + -
470A PHE* 3.4 11.6 - - + -
267B HIS* 3.1 27.1 + - + +
268B GLN* 3.1 7.2 + - - +
270B ALA* 1.3 78.5 - - + +
272B VAL* 1.3 57.9 + - - +
274B LEU* 3.3 9.0 + - + -
275B ALA* 2.8 26.7 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LYS* 4.0 35.2 - - + +
424A TRP* 3.7 17.9 - - + -
438A PHE* 3.9 19.3 - - + -
268B GLN* 3.0 30.2 + - + +
269B GLY* 3.5 11.4 - - - +
271B LEU* 1.3 75.1 - - - +
273B CYS* 1.3 61.8 + - - +
275B ALA* 3.4 2.3 + - - +
276B GLU* 2.9 33.9 + - - +
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Residues in contact with CYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLY 3.0 20.8 + - - -
270B ALA* 3.3 9.6 + - - +
272B VAL* 1.3 76.0 - - - +
274B LEU* 1.3 59.3 + - + +
276B GLU* 3.3 9.9 + - - +
277B SER* 2.9 30.4 + - - -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A SER* 3.8 31.2 - - - +
469A LYS* 3.9 24.7 - - + +
470A PHE* 3.8 12.3 - - + -
270B ALA* 2.9 21.6 + - + +
271B LEU* 3.5 16.8 - - + +
273B CYS* 1.3 74.7 - - - +
275B ALA* 1.3 62.6 + - - +
277B SER* 2.7 23.0 + - - +
278B CYS* 3.5 11.8 - - - -
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TRP* 4.0 10.3 - - + -
436A VAL* 4.6 7.0 - - + -
438A PHE* 3.6 23.8 - - + -
466A LEU* 3.8 19.9 - - + +
470A PHE* 3.8 3.9 - - + -
271B LEU 2.8 17.8 + - - +
272B VAL 3.5 5.4 - - - +
273B CYS 3.3 0.2 - - - -
274B LEU* 1.3 75.7 - - - +
276B GLU* 1.3 62.4 + - - +
278B CYS* 3.0 19.9 + - - +
279B LEU* 3.5 14.0 + - - +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TRP* 3.2 34.2 + - + +
272B VAL* 2.9 22.8 + - - +
273B CYS* 3.7 10.5 - - - +
275B ALA* 1.3 75.3 - - - +
277B SER* 1.3 62.5 + - - +
279B LEU* 3.1 29.2 + - - +
281B LEU* 4.5 11.3 - - + +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LYS* 5.3 2.6 + - - +
469A LYS* 3.3 22.5 - - - +
273B CYS 2.9 14.7 + - - -
274B LEU* 2.7 24.0 + - - +
276B GLU* 1.3 75.8 - - - +
278B CYS* 1.3 58.9 + - - +
279B LEU 3.7 4.5 + - - +
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Residues in contact with CYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU* 3.7 16.3 - - - +
465A LYS* 3.6 57.7 - - + +
466A LEU* 3.6 22.7 - - + -
469A LYS* 3.6 25.4 - - - -
274B LEU 3.5 15.7 - - - -
275B ALA 3.0 9.0 + - - +
277B SER* 1.3 78.0 + - - +
279B LEU* 1.3 62.9 + - - +
280B THR* 4.8 1.9 + - - -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TRP* 3.6 50.0 - - + +
434A VAL* 4.2 18.6 - - + -
436A VAL* 4.7 2.5 - - + -
455A ILE* 4.8 1.3 - - + -
462A GLU* 3.6 16.6 - - + +
466A LEU* 4.2 23.1 - - + -
275B ALA 3.6 16.4 - - - +
276B GLU* 3.1 17.3 + - - +
277B SER 4.1 4.7 - - - +
278B CYS* 1.3 83.5 - - - +
280B THR* 1.3 63.1 + - - +
281B LEU* 3.8 22.6 + - + +
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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