Contacts of the helix formed by residues 328 - 346 (chain B) in PDB entry 2AX1
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 GLY 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B SER* 3.1 12.9 + - - -
327B ALA* 1.3 78.2 - - - +
329B THR* 1.3 56.5 + - - -
330B GLN 3.4 2.2 - - - -
331B GLU* 3.3 8.9 + - - -
332B ASP* 2.8 36.0 + - - -
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Residues in contact with THR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B SER* 5.4 0.2 - - - +
328B GLY* 1.3 72.1 - - - -
330B GLN* 1.3 68.5 + - - +
331B GLU* 4.0 0.2 + - - -
332B ASP* 3.6 1.7 + - - +
333B ALA* 3.2 21.8 + - - +
356B PRO* 5.7 0.5 - - - +
358B TYR* 3.7 38.5 + - + +
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Residues in contact with GLN 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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328B GLY 3.4 0.4 - - - -
329B THR* 1.3 78.1 + - - +
331B GLU* 1.3 74.8 + - - +
333B ALA* 3.2 7.1 + - - +
334B ALA* 3.1 23.0 + - - +
337B ARG* 5.0 1.0 + - - -
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Residues in contact with GLU 331 (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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327B ALA* 3.0 41.1 - - + +
328B GLY* 3.4 12.3 - - - +
330B GLN* 1.3 85.1 + - - +
332B ASP* 1.3 56.9 + - - +
334B ALA* 3.4 5.3 + - - +
335B SER* 2.8 32.1 + - - -
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 3.5 22.0 - - + +
325B GLU 4.6 1.0 - - - +
326B SER* 2.6 25.1 + - - -
327B ALA* 2.9 24.9 + - - +
328B GLY 2.8 21.5 + - - +
329B THR 3.8 1.1 - - - +
331B GLU* 1.3 73.7 - - - +
333B ALA* 1.3 56.6 + - - +
335B SER* 2.7 21.8 + - - -
336B LEU* 2.9 20.4 + - - +
356B PRO* 4.4 5.6 - - + -
358B TYR* 2.6 34.3 + - - +
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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
----------------------------------------------------------
329B THR 3.2 11.7 + - - +
330B GLN* 3.2 10.5 + - - +
332B ASP* 1.3 79.8 - - - +
334B ALA* 1.3 62.3 + - - +
336B LEU* 3.4 4.2 + - - +
337B ARG* 3.3 45.6 + - - +
356B PRO* 4.3 16.5 - - + +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLN 3.1 13.5 + - - +
331B GLU* 3.8 5.8 - - - +
333B ALA* 1.3 77.7 - - - +
335B SER* 1.3 63.6 + - - +
337B ARG* 2.9 32.2 + - - +
338B VAL* 3.1 18.4 + - + +
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 4.7 1.0 - - - +
306B ALA* 3.3 21.7 - - - +
308B LEU* 3.4 27.1 - - - +
327B ALA* 6.5 1.1 - - - -
331B GLU 2.8 13.8 + - - -
332B ASP* 2.7 25.6 + - - -
334B ALA* 1.3 77.8 - - - +
336B LEU* 1.3 58.4 + - - +
338B VAL* 3.2 7.9 + - - +
339B PHE* 3.0 23.0 + - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 3.5 30.5 - - + -
217B PHE* 3.8 29.4 - - + -
308B LEU* 5.1 3.6 - - + -
332B ASP 2.9 15.5 + - - +
333B ALA 3.7 5.8 - - - +
334B ALA 3.2 0.2 - - - -
335B SER* 1.3 77.7 + - - +
337B ARG* 1.3 62.1 + - + +
339B PHE* 3.3 6.9 + - + +
340B THR* 3.0 32.9 + - - -
354B PRO* 3.6 34.4 - - + +
355B GLN 3.9 1.1 - - - -
356B PRO* 3.5 35.9 - - + -
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Residues in contact with ARG 337 (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 GLN 5.0 0.8 + - - -
333B ALA* 3.3 26.0 + - - +
334B ALA* 2.9 32.6 + - - +
336B LEU* 1.3 77.4 - - + +
338B VAL* 1.3 61.1 + - + +
340B THR* 3.4 7.2 + - - -
341B GLU* 3.0 40.6 + - - +
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA* 3.6 27.8 - - + +
306B ALA* 3.8 8.5 - - + +
334B ALA* 3.1 16.9 + - + +
335B SER* 3.6 9.4 - - - +
337B ARG* 1.3 74.0 - - + +
339B PHE* 1.3 67.0 + - - +
341B GLU* 3.1 19.1 + - + +
342B ALA* 2.9 21.5 + - + +
345B ARG* 5.3 2.2 + - - +
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Residues in contact with PHE 339 (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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217B PHE* 3.8 26.9 - + + -
219B TYR* 3.6 33.0 - + - -
299B ALA* 3.6 36.8 - - + -
302B ALA* 3.6 24.1 - - + +
303B CYS* 3.7 16.4 - - - -
306B ALA* 3.7 10.7 - - + +
308B LEU* 4.2 10.8 - - + -
320B LEU* 4.2 7.0 - - + -
322B VAL* 5.0 1.3 - - + -
335B SER 3.0 13.4 + - - +
336B LEU* 3.3 13.4 + - - +
338B VAL* 1.3 75.8 - - - +
340B THR* 1.3 59.9 + - - +
342B ALA* 3.2 4.9 + - - +
343B MET* 2.9 43.8 + - + +
354B PRO* 5.1 1.1 - - + -
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Residues in contact with THR 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 3.8 8.8 + - - +
336B LEU 3.0 16.8 + - - -
337B ARG* 3.6 7.8 - - - -
339B PHE* 1.3 76.8 - - - +
341B GLU* 1.3 61.4 + - + +
343B MET* 3.3 1.9 + - - +
344B THR* 2.8 35.9 + - - +
350B PRO* 3.6 33.7 - - + -
353B PRO* 5.9 0.9 - - + -
354B PRO* 3.3 28.2 - - + +
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG* 3.0 28.3 + - + +
338B VAL* 3.1 22.3 + - + +
340B THR* 1.3 75.9 - - + +
342B ALA* 1.3 63.6 + - - +
344B THR* 3.3 7.6 + - - -
345B ARG* 3.0 38.1 + - + +
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Residues in contact with ALA 342 (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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302B ALA* 3.7 18.2 - - + -
305B ALA* 3.8 16.2 - - + -
338B VAL 2.9 12.7 + - - +
339B PHE 3.5 7.9 - - - +
341B GLU* 1.3 74.5 - - - +
343B MET* 1.3 65.0 + - - +
345B ARG* 3.1 31.5 + - - +
346B TYR* 3.0 31.9 + - + -
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Residues in contact with MET 343 (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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219B TYR* 3.4 44.4 - - + +
221B THR* 4.3 3.8 - - - +
224B PHE* 5.9 1.1 - - + -
295B CYS* 4.8 8.3 - - - +
298B LYS* 3.6 37.2 - - + +
299B ALA* 3.6 21.1 - - + +
302B ALA* 3.8 2.9 - - + -
320B LEU* 4.7 3.4 - - + -
339B PHE* 2.9 38.0 + - + +
340B THR 3.7 0.9 - - - +
342B ALA* 1.3 75.3 - - - +
344B THR* 1.3 62.9 + - - +
346B TYR* 3.1 12.1 + - - +
347B SER 3.2 0.7 + - - -
348B ALA* 3.0 40.7 + - + +
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Residues in contact with THR 344 (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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57B LEU 4.1 4.7 - - - +
340B THR* 2.8 24.6 + - - +
341B GLU* 3.5 8.4 - - - -
342B ALA 3.1 0.2 - - - -
343B MET* 1.3 77.8 - - - +
345B ARG* 1.3 57.1 + - + +
347B SER* 2.9 20.6 + - - -
348B ALA 4.0 0.2 + - - -
349B PRO* 3.8 33.3 - - + +
350B PRO* 3.9 7.4 - - - +
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Residues in contact with ARG 345 (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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57B LEU 3.8 1.5 - - - +
58B GLN* 3.4 4.3 - - - -
59B VAL* 2.9 54.9 + - + +
61B ASP* 3.2 26.8 + - - +
305B ALA* 4.4 8.3 - - - +
338B VAL* 5.3 1.8 + - - +
341B GLU* 3.0 23.5 + - - +
342B ALA* 3.1 40.1 + - - +
344B THR* 1.3 77.1 - - + +
346B TYR* 1.3 63.5 + - + +
347B SER 3.2 3.6 + - - -
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Residues in contact with TYR 346 (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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58B GLN* 2.9 14.5 + - - +
59B VAL 3.7 15.9 - - - -
60B LEU* 4.4 2.9 - - + -
61B ASP* 2.7 42.8 + - - -
63B HIS* 3.9 5.4 - - - +
64B TYR* 4.0 18.4 - + + -
298B LYS* 2.9 67.5 + - + -
301B ALA* 3.6 23.7 + - + +
302B ALA* 3.8 6.7 - - - -
305B ALA* 4.7 1.2 - - - +
342B ALA* 3.0 33.3 + - + +
343B MET* 3.6 8.3 - - - +
344B THR 3.1 0.6 - - - -
345B ARG* 1.3 79.4 + - + +
347B SER* 1.3 67.0 + - - +
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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
------------------------------------------------------------
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