Contacts of the helix formed by residues 326 - 336 (chain A) in PDB entry 2XGZ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A HIS* 4.8 6.5 + - - +
323A THR 2.9 14.4 + - - +
324A VAL* 3.6 16.8 - - + +
325A THR* 1.3 77.1 - - - +
327A PRO* 1.4 69.7 - - - +
328A LYS* 3.1 23.3 + - - +
329A ARG* 2.9 28.1 + - + +
330A ILE* 2.9 15.7 + - - +
349A ILE* 3.7 20.7 - - + +
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Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A THR 3.7 9.0 - - - +
326A ASN* 1.4 87.4 - - - +
328A LYS* 1.3 55.1 + - - +
330A ILE* 3.7 11.0 - - + +
331A ALA* 2.9 30.0 + - - +
349A ILE* 4.5 8.3 - - + -
354A GLU* 3.9 24.7 - - + +
357A LYS* 4.0 21.3 - - + +
358A ALA* 4.1 6.3 - - + +
361A ASP* 3.8 21.4 - - - +
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Residues in contact with LYS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ASN* 3.0 14.9 + - - +
327A PRO* 1.3 78.5 - - - +
329A ARG* 1.3 63.5 + - + +
331A ALA* 3.6 7.5 - - - +
332A THR* 3.3 21.7 + - - -
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.3 34.2 + - - -
300A GLU 3.1 21.0 + - - -
301A ASP* 2.5 23.2 + - - -
303A TRP* 3.7 24.7 - - + +
322A LEU 2.6 33.6 + - - +
323A THR* 3.4 23.8 - - - +
324A VAL* 3.8 18.4 - - + -
326A ASN* 2.9 14.8 + - + +
328A LYS* 1.3 75.9 - - + +
330A ILE* 1.3 60.2 + - - +
332A THR* 3.1 10.8 + - - -
333A ALA* 2.9 27.5 + - - +
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Residues in contact with ILE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A THR* 3.9 25.1 - - + -
326A ASN 2.9 24.1 + - - +
327A PRO* 3.7 5.2 - - + +
329A ARG* 1.3 74.0 - - - +
331A ALA* 1.3 60.3 + - - +
333A ALA* 3.2 1.1 + - - +
334A ILE* 2.8 55.0 + - + +
342A LEU* 3.8 22.9 - - + -
358A ALA* 3.5 35.9 - - + +
361A ASP* 4.6 6.3 - - + -
362A SER* 3.8 19.3 - - - +
367A TRP* 4.5 7.4 - - + -
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A PRO 2.9 18.2 + - - +
328A LYS* 3.6 9.6 - - - +
330A ILE* 1.3 76.3 - - - +
332A THR* 1.3 61.0 + - - +
334A ILE* 3.4 9.7 + - - +
335A GLU* 3.0 24.1 + - - +
361A ASP* 6.3 0.2 - - - +
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Residues in contact with THR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A TRP* 3.7 23.6 - - + +
328A LYS 3.3 12.0 + - - -
329A ARG* 3.1 11.0 + - - -
331A ALA* 1.3 74.3 - - - +
333A ALA* 1.3 65.7 + - - +
335A GLU* 3.3 5.2 + - - +
336A LYS* 3.0 54.8 + - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A TRP* 3.5 19.9 - - + -
322A LEU* 4.3 6.7 - - + -
323A THR* 3.8 12.3 - - + -
329A ARG 2.9 16.0 + - - +
330A ILE 3.6 2.0 - - - +
332A THR* 1.3 75.3 - - - +
334A ILE* 1.3 62.4 + - - +
337A LYS* 3.1 4.0 + - - -
338A ALA* 3.0 30.3 + - + -
367A TRP* 3.5 29.3 - - + -
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Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ILE* 2.8 39.2 + - + +
331A ALA* 3.7 8.3 - - - +
333A ALA* 1.3 77.2 - - - +
335A GLU* 1.3 64.3 + - - +
337A LYS* 3.1 21.1 + - - +
361A ASP* 3.8 14.4 - - + +
362A SER* 4.7 2.2 - - - -
365A ALA* 3.5 35.4 - - + -
367A TRP* 3.8 22.2 - - + +
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ALA 3.0 17.6 + - - +
332A THR* 3.7 6.5 - - + +
334A ILE* 1.3 78.5 - - - +
336A LYS* 1.3 63.4 + - + +
337A LYS* 3.4 12.6 + - - +
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A TRP* 3.7 48.5 - - + -
307A SER* 2.7 34.3 + - - +
332A THR* 3.0 41.0 + - + +
333A ALA 4.2 2.5 - - - +
335A GLU* 1.3 78.0 - - + +
337A LYS* 1.3 65.9 + - - +
338A ALA 4.5 1.6 - - - +
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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