Contacts of the helix formed by residues 326 - 336 (chain D) in PDB entry 2XH2
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 ASN 326 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D HIS* 3.3 30.3 + - - +
44D GLU* 5.2 0.8 - - - +
323D THR 2.9 14.8 + - - +
324D VAL* 3.9 14.1 - - + +
325D THR* 1.3 76.6 - - - +
327D PRO* 1.3 67.2 - - - +
328D LYS* 3.3 11.4 + - - +
329D ARG* 3.0 29.1 + - + +
330D ILE* 2.9 31.5 + - - +
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Residues in contact with PRO 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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325D THR 4.1 0.2 - - - -
326D ASN* 1.3 90.3 - - - +
328D LYS* 1.3 59.2 + - - +
330D ILE* 3.3 12.6 + - + +
331D ALA* 2.9 29.2 + - - +
349D ILE* 3.7 29.4 - - + -
354D GLU* 5.6 2.7 - - + +
357D LYS* 6.4 1.8 - - + +
358D ALA* 5.7 4.9 - - + -
361D ASP* 5.7 5.2 - - - +
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Residues in contact with LYS 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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326D ASN* 3.3 10.3 + - - +
327D PRO* 1.3 79.9 - - - +
329D ARG* 1.3 60.3 + - + +
331D ALA* 3.3 9.0 + - - +
332D THR* 3.0 30.5 + - - -
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Residues in contact with ARG 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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43D HIS* 3.4 56.0 + - + +
300D GLU* 2.7 30.3 + - - +
301D ASP* 3.1 15.0 + - - -
303D TRP* 3.5 29.0 - - + +
321D ALA 4.8 2.8 + - - -
322D LEU 2.7 26.5 + - - +
323D THR* 3.7 17.6 - - - +
324D VAL* 4.5 1.1 - - - -
326D ASN* 3.0 15.4 + - - +
328D LYS* 1.3 75.8 - - + +
330D ILE* 1.3 60.5 + - - +
332D THR* 3.3 9.2 + - - +
333D ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 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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323D THR* 4.0 15.9 - - + -
325D THR 4.1 2.0 - - - -
326D ASN 2.9 34.7 + - - +
327D PRO* 3.6 8.3 - - + +
329D ARG* 1.3 73.4 - - - +
331D ALA* 1.3 66.5 + - - +
333D ALA* 3.2 3.9 + - - +
334D ILE* 2.9 42.1 + - + +
342D LEU* 3.8 37.9 - - + -
358D ALA* 4.0 21.3 - - + +
361D ASP* 5.3 5.2 - - + -
362D SER* 4.0 17.0 - - - +
367D TRP* 4.8 7.4 - - + -
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Residues in contact with ALA 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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327D PRO 2.9 13.6 + - - +
328D LYS* 3.5 11.7 - - - +
330D ILE* 1.3 76.6 - - - +
332D THR* 1.3 55.6 + - - +
334D ILE* 3.3 12.5 + - - +
335D GLU* 3.0 29.5 + - - +
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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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303D TRP* 3.8 22.2 - - + +
328D LYS 3.0 15.2 + - - -
329D ARG* 3.5 10.1 - - - -
330D ILE 3.2 0.2 - - - -
331D ALA* 1.3 73.0 - - - +
333D ALA* 1.3 60.1 + - - +
335D GLU* 3.1 7.2 + - - +
336D LYS* 2.8 58.8 + - + +
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Residues in contact with ALA 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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303D TRP* 3.6 20.3 - - + -
322D LEU* 4.1 8.5 - - + -
323D THR* 4.1 11.2 - - + -
329D ARG 2.9 16.5 + - - +
330D ILE 3.6 2.2 - - - +
332D THR* 1.3 74.8 - - - +
334D ILE* 1.3 61.5 + - - +
337D LYS* 3.1 3.6 + - - -
338D ALA* 3.0 31.8 + - + +
367D TRP* 3.5 27.2 - - + -
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Residues in contact with ILE 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 ILE* 2.9 36.6 + - + +
331D ALA* 3.5 11.7 - - - +
333D ALA* 1.3 75.3 - - - +
335D GLU* 1.3 66.9 + - + +
337D LYS* 3.3 19.1 + - - +
361D ASP* 3.9 16.2 - - + +
362D SER* 4.5 3.6 - - - -
365D ALA* 3.7 31.0 - - + -
367D TRP* 3.6 29.9 + - + +
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Residues in contact with GLU 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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331D ALA 3.0 16.3 + - - +
332D THR* 3.1 6.9 + - - +
334D ILE* 1.3 79.4 - - + +
336D LYS* 1.3 80.9 + - - +
337D LYS* 3.1 17.1 + - - +
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Residues in contact with LYS 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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303D TRP* 3.7 44.8 - - + +
307D SER* 2.7 35.0 + - - +
332D THR* 2.8 35.5 + - + +
333D ALA 4.3 2.5 - - - +
335D GLU* 1.3 85.0 + - - +
337D LYS* 1.3 65.3 + - - +
338D ALA* 4.5 5.6 - - + +
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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