Contacts of the helix formed by residues 264 - 268 (chain B) in PDB entry 3P9K
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 ILE 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL 3.5 16.6 - - - +
205B GLY* 3.4 25.4 - - - +
249B MET* 3.9 31.4 - - + -
261B MET* 3.9 16.1 - - + -
262B LYS 3.2 24.2 - - - +
263B TRP* 1.3 76.9 - - - +
265B LEU* 1.3 68.2 + - - +
266B HIS 3.2 1.1 - - - -
267B ASP* 2.9 24.6 + - - +
268B TRP* 3.3 10.1 - - - +
276B LEU* 3.9 16.8 - - + -
294B GLN* 3.0 1.6 + - - -
402B SAH 3.6 26.5 - - + +
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Residues in contact with LEU 265 (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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261B MET* 4.1 18.1 - - + +
264B ILE* 1.3 79.8 - - - +
266B HIS* 1.3 60.0 + - - +
267B ASP 3.0 1.4 + - - -
268B TRP* 3.2 13.4 + - + +
273B CYS* 3.4 28.9 - - + -
276B LEU* 4.2 17.0 - - + -
277B LEU* 4.0 24.9 - - + -
292B LEU* 3.6 40.4 - - + +
294B GLN* 3.1 8.1 + - - +
327B ARG* 2.9 20.6 + - - +
332B PHE* 4.2 17.3 - - + -
335B LEU* 4.5 5.2 - - + -
358B PHE* 4.7 0.7 - - + -
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Residues in contact with HIS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B TRP* 3.1 46.1 + + - -
265B LEU* 1.3 75.4 - - - +
267B ASP* 1.3 74.3 + - - +
268B TRP 3.4 0.4 - - - -
294B GLN* 3.2 21.1 + - + +
313B VAL* 3.8 7.3 - - + +
317B MET* 3.3 15.4 - - - +
324B GLY* 2.9 4.6 - - - -
325B ARG 2.9 41.9 + - - +
326B GLU* 3.0 28.2 + - - +
327B ARG* 3.9 1.8 - - - +
332B PHE* 5.8 3.6 - - + -
602B CIY 2.7 40.2 + + - -
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Residues in contact with ASP 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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160B PHE* 3.6 10.0 - - + -
263B TRP 3.2 15.0 - - - +
264B ILE* 2.9 15.6 + - - +
266B HIS* 1.3 83.1 + - - +
268B TRP* 1.3 71.5 + - + +
317B MET* 3.2 1.7 - - - +
321B ASN* 3.1 44.3 + - - +
322B PRO* 3.6 9.7 - - - +
324B GLY* 3.3 11.1 + - - -
402B SAH 3.6 18.2 - - - +
602B CIY 2.7 25.2 - - - +
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Residues in contact with TRP 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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160B PHE* 3.7 30.0 - + - -
249B MET* 3.5 15.5 - - + +
250B PHE* 3.5 34.5 - + + -
264B ILE* 3.3 23.2 + - + +
265B LEU* 3.2 8.9 + - - +
267B ASP* 1.3 90.5 + - + +
269B SER* 1.3 57.0 + - - +
272B HIS* 3.5 40.2 - + + -
273B CYS* 3.7 8.0 - - - +
276B LEU* 5.2 2.7 - - + -
322B PRO* 3.5 34.5 - - + -
323B GLY 3.6 9.2 - - - +
324B GLY* 3.8 1.6 - - - -
327B ARG* 2.8 28.1 + - - -
402B SAH 3.8 16.2 + - - -
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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