Contacts of the helix formed by residues 326 - 336 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B HIS* 2.7 35.0 + - - +
323B THR 2.8 15.5 + - - +
324B VAL* 3.8 8.1 - - + +
325B THR* 1.3 75.5 - - - +
327B PRO* 1.3 72.6 - - - +
328B LYS* 3.2 14.4 + - - +
329B ARG* 3.0 32.0 + - + +
330B ILE* 2.9 25.1 + - - +
349B ILE* 4.7 4.1 - - - +
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Residues in contact with PRO 327 (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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325B THR 3.9 2.2 - - - +
326B ASN* 1.3 89.9 - - - +
328B LYS* 1.3 56.9 + - - +
330B ILE* 3.4 13.3 + - + +
331B ALA* 3.0 29.2 + - - +
349B ILE* 3.7 26.0 - - + -
354B GLU* 5.5 8.1 - - + +
358B ALA* 5.5 9.2 - - + -
361B ASP* 5.6 6.3 - - - +
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Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASN* 3.2 9.9 + - - +
327B PRO* 1.3 77.7 - - - +
329B ARG* 1.3 64.0 + - + +
331B ALA* 3.5 6.5 + - - +
332B THR* 3.0 28.3 + - - -
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Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B HIS* 3.4 44.4 + - + +
300B GLU* 2.6 33.1 + - - +
301B ASP* 3.1 20.4 + - - -
303B TRP* 3.7 23.5 - - - +
321B ARG 4.6 2.8 + - - -
322B LEU* 2.8 23.3 + - - +
323B THR* 3.4 25.7 - - - +
324B VAL* 5.3 1.0 - - - +
326B ASN* 3.0 27.7 + - + +
328B LYS* 1.3 74.5 - - + +
330B ILE* 1.3 57.2 + - - +
332B THR* 3.3 7.8 + - - -
333B ALA* 2.8 29.8 + - - +
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Residues in contact with ILE 330 (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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323B THR* 3.9 15.7 - - + -
325B THR 4.1 1.6 - - - -
326B ASN 2.9 30.3 + - - +
327B PRO* 3.6 9.9 - - + +
329B ARG* 1.3 73.4 - - - +
331B ALA* 1.3 59.8 + - - +
333B ALA* 3.2 1.6 + - - +
334B ILE* 2.8 49.8 + - + +
342B LEU* 3.7 39.7 - - + -
358B ALA* 3.8 23.6 - - + +
361B ASP* 5.1 5.4 - - + -
362B SER* 4.1 14.4 - - - +
367B TRP* 4.9 6.7 - - + -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B PRO 3.0 17.4 + - - +
328B LYS* 3.7 7.6 - - - +
329B ARG 3.4 0.2 - - - -
330B ILE* 1.3 77.2 - - - +
332B THR* 1.3 56.3 + - - +
334B ILE* 3.4 10.7 + - - +
335B GLU* 2.9 29.9 + - - +
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Residues in contact with THR 332 (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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303B TRP* 3.7 19.1 - - + +
328B LYS 3.0 14.8 + - - -
329B ARG* 3.4 10.7 - - - -
330B ILE 3.2 0.2 - - - -
331B ALA* 1.3 74.3 - - - +
333B ALA* 1.3 59.3 + - - +
335B GLU* 3.3 10.1 + - - +
336B LYS* 2.9 57.7 + - + +
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Residues in contact with ALA 333 (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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303B TRP* 3.5 21.1 - - + -
322B LEU* 4.1 7.9 - - + -
323B THR* 3.9 11.9 - - + -
329B ARG 2.8 17.0 + - - +
330B ILE 3.6 4.7 - - - +
332B THR* 1.3 76.2 - - - +
334B ILE* 1.3 59.8 + - - +
337B LYS* 3.2 3.3 + - - -
338B ALA* 3.0 30.0 + - + -
367B TRP* 3.6 25.8 - - + -
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Residues in contact with ILE 334 (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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330B ILE* 2.8 36.4 + - + +
331B ALA* 3.6 9.4 - - - +
333B ALA* 1.3 77.1 - - - +
335B GLU* 1.3 64.0 + - - +
337B LYS* 3.2 14.2 + - - +
361B ASP* 3.7 18.4 - - + +
362B SER* 4.5 3.4 - - - -
365B ALA* 3.6 31.4 - - + -
367B TRP* 3.6 29.4 + - + +
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Residues in contact with GLU 335 (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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331B ALA 2.9 17.2 + - - +
332B THR* 3.3 10.0 + - - +
334B ILE* 1.3 79.2 - - - +
336B LYS* 1.3 70.0 + - - +
337B LYS* 3.2 2.8 + - - +
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Residues in contact with LYS 336 (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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303B TRP* 3.5 52.5 - - + -
307B SER* 2.6 33.6 + - - +
332B THR* 2.9 30.7 + - + +
333B ALA 4.2 2.9 - - - +
335B GLU* 1.3 83.8 + - + +
337B LYS* 1.3 65.7 + - - +
338B ALA 4.4 1.8 - - - +
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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