Contacts of the helix formed by residues 266 - 271 (chain B) in PDB entry 6AHU
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 LEU 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LEU* 4.4 20.6 - - + -
262B ILE* 3.3 27.1 - - + +
263B LEU 3.2 4.4 + - - +
265B ALA* 1.3 91.9 - - + +
267B SER* 1.3 61.8 + - - +
268B GLY 3.3 2.9 - - - -
269B MET* 3.4 43.3 + - + +
270B CYS* 3.9 11.3 + - - -
278B PHE* 4.1 28.6 - - + -
310B PHE* 5.8 1.3 - - + -
327B LEU* 4.8 10.1 - - + -
343B ILE* 4.1 16.8 - - + -
346B ALA* 5.5 1.6 - - + -
347B CYS* 4.4 14.1 - - - -
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Residues in contact with SER 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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263B LEU 2.8 16.2 + - - -
264B LYS* 3.6 15.2 + - - -
265B ALA 3.7 0.6 - - - -
266B LEU* 1.3 78.6 - - - +
268B GLY* 1.3 59.0 + - - +
269B MET 3.2 3.6 + - - -
270B CYS* 4.2 15.5 + - - -
271B ASN* 4.4 5.0 + - - -
272B ILE* 4.6 14.0 - - - +
278B PHE* 6.0 0.2 - - - -
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Residues in contact with GLY 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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264B LYS 5.0 1.4 + - - -
265B ALA 5.2 1.2 + - - -
266B LEU* 3.3 1.2 - - - +
267B SER* 1.3 79.8 + - - +
269B MET* 1.3 57.1 + - - +
271B ASN* 5.1 7.9 - - - +
295B TYR* 5.6 0.2 - - - +
296B ARG 3.0 15.8 - - - +
297B VAL* 3.4 2.1 - - - -
298B ASN* 3.2 40.3 + - - -
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Residues in contact with MET 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 ALA 5.2 2.2 - - - +
266B LEU* 3.6 45.3 - - + +
267B SER 3.2 0.8 - - - -
268B GLY* 1.3 80.6 - - - +
270B CYS* 1.3 60.7 + - - +
271B ASN* 3.6 2.0 - - - -
278B PHE* 5.5 3.1 - - + -
294B LEU* 3.6 35.5 - - + -
295B TYR* 2.9 59.8 + - - +
296B ARG 3.6 6.7 - - - +
297B VAL* 5.8 0.7 - - - -
329B ILE* 5.7 3.6 - - + -
342B GLU* 3.3 30.7 - - - +
343B ILE* 4.0 11.2 - - + -
346B ALA* 5.7 1.3 - - - -
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Residues in contact with CYS 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 LEU 3.9 7.4 + - - +
267B SER* 4.2 5.8 - - - -
269B MET* 1.3 78.0 - - - +
271B ASN* 1.3 73.6 + - - +
272B ILE* 3.7 29.8 - - - -
274B THR* 4.2 2.3 + - - -
275B GLY* 5.0 2.8 + - - -
276B LEU 4.9 7.0 - - - +
277B THR* 5.3 3.6 - - - -
278B PHE* 3.6 38.6 - - + -
279B ALA* 5.8 1.3 - - - -
292B LEU* 4.2 15.4 - - + +
293B VAL 4.3 8.7 - - - +
294B LEU* 5.1 1.8 - - + +
295B TYR* 4.2 7.9 - - - -
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Residues in contact with ASN 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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267B SER 4.4 5.6 + - - -
268B GLY* 5.1 6.7 - - - +
269B MET 3.6 2.4 - - - +
270B CYS* 1.3 80.1 - - - +
272B ILE* 1.3 64.3 + - - +
273B ASP 3.3 2.7 - - - -
274B THR* 2.6 42.2 + - + +
275B GLY 3.5 3.8 + - - +
295B TYR* 3.3 39.2 - - + +
300B TYR* 3.9 28.5 - - - +
302B ARG* 4.3 8.1 - - - +
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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