Contacts of the helix formed by residues 324 - 336 (chain D) in PDB entry 6AH0
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 HIS 324 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320D VAL 3.2 10.6 + - - -
321D LEU* 3.2 8.6 + - - -
322D ARG 3.1 0.6 - - - -
323D GLN* 1.3 76.8 - - - +
325D ARG* 1.3 62.5 + - - +
326D MET 3.3 2.9 - - - -
327D MET* 3.1 6.2 + - - +
328D ILE* 2.8 22.7 + - - -
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Residues in contact with ARG 325 (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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293D LEU* 5.2 13.6 - - - +
321D LEU 3.0 12.9 + - - -
322D ARG* 3.1 12.6 + - - +
323D GLN 3.5 1.6 + - - -
324D HIS* 1.3 77.0 - - - +
326D MET* 1.3 62.5 + - - +
328D ILE* 4.6 0.9 - - - +
329D LEU* 3.0 21.8 + - - -
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Residues in contact with MET 326 (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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324D HIS 3.3 1.2 - - - -
325D ARG* 1.3 74.7 - - - +
327D MET* 1.3 62.9 + - - +
330D TYR* 3.0 23.6 + - - -
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Residues in contact with MET 327 (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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324D HIS* 3.1 7.4 + - - +
326D MET* 1.3 75.1 - - - +
328D ILE* 1.3 61.8 + - - +
331D CYS* 2.9 25.9 + - - +
332D THR 4.1 0.3 + - - -
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Residues in contact with ILE 328 (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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324D HIS 2.8 18.9 + - - -
325D ARG* 4.0 0.9 - - - +
327D MET* 1.3 73.3 - - - +
329D LEU* 1.3 61.8 + - - +
332D THR* 3.2 20.1 + - - -
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Residues in contact with LEU 329 (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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290D LEU* 5.8 4.0 - - - +
293D LEU* 5.5 11.6 - - - +
294D LYS* 5.8 0.9 - - - +
325D ARG 3.0 15.7 + - - -
326D MET* 5.4 0.2 - - - +
328D ILE* 1.3 77.3 - - - +
330D TYR* 1.3 61.5 + - - +
332D THR* 4.1 0.2 - - - -
333D LEU* 3.2 17.7 + - - -
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Residues in contact with TYR 330 (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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326D MET 3.0 14.9 + - - -
329D LEU* 1.3 76.4 - - - +
331D CYS* 1.3 57.9 + - - +
333D LEU* 3.4 2.1 + - - +
334D LEU* 2.9 26.0 + - - -
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Residues in contact with CYS 331 (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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264D ASP 5.2 3.6 + - - +
326D MET 4.3 0.2 + - - -
327D MET* 2.9 17.1 + - - +
330D TYR* 1.3 73.3 - - - +
332D THR* 1.3 60.2 + - - +
334D LEU* 4.3 1.6 - - - +
335D ALA* 2.9 27.1 + - - +
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Residues in contact with THR 332 (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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264D ASP 4.7 12.8 - - - -
265D ALA* 4.7 8.9 - - - +
327D MET 4.1 0.4 + - - -
328D ILE 3.2 17.3 + - - -
329D LEU 4.1 0.2 - - - -
331D CYS* 1.3 77.6 - - - +
333D LEU* 1.3 61.3 + - - +
335D ALA* 3.4 0.9 + - - -
336D SER* 3.2 18.2 + - - -
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Residues in contact with LEU 333 (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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329D LEU 3.2 13.9 + - - -
330D TYR 3.7 2.5 - - - -
331D CYS 3.3 0.2 - - - -
332D THR* 1.3 76.4 - - - +
334D LEU* 1.3 62.0 + - - +
336D SER* 3.2 12.0 + - - -
337D ALA* 3.3 10.2 + - - -
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Residues in contact with LEU 334 (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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330D TYR 2.9 16.2 + - - -
331D CYS* 3.9 1.8 - - - +
333D LEU* 1.3 75.2 - - - +
335D ALA* 1.3 62.9 + - - +
337D ALA* 3.0 20.1 + - - +
343D LYS* 5.9 5.3 - - - +
346D ILE* 6.4 2.0 - - - +
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Residues in contact with ALA 335 (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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264D ASP* 5.3 2.5 - - - +
265D ALA* 4.9 17.3 + - - +
331D CYS 2.9 19.1 + - - -
332D THR 3.9 1.3 - - - -
333D LEU 3.3 0.2 - - - -
334D LEU* 1.3 76.5 - - - +
336D SER* 1.3 59.3 + - - +
337D ALA 3.7 2.8 + - - +
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Residues in contact with SER 336 (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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265D ALA* 5.0 4.0 - - - +
332D THR 3.2 9.2 + - - -
333D LEU* 3.2 8.8 + - - +
334D LEU 3.1 1.2 - - - -
335D ALA* 1.3 77.4 - - - +
337D ALA* 1.3 57.8 + - - +
338D GLN 3.7 2.6 + - - -
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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