Contacts of the helix formed by residues 328 - 346 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A SER* 3.3 9.5 + - - -
327A ALA* 1.3 77.6 - - - +
329A THR* 1.3 61.4 + - - -
331A GLU* 3.3 10.1 - - - -
332A ASP* 2.8 35.6 + - - -
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Residues in contact with THR 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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328A GLY* 1.3 71.6 - - - -
330A GLN* 1.3 70.4 + - - +
332A ASP* 3.3 2.8 + - - +
333A ALA* 3.0 23.6 + - - +
356A PRO* 5.3 0.9 - - - +
358A TYR* 3.6 31.7 + - + +
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Residues in contact with GLN 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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328A GLY 3.4 0.2 - - - -
329A THR* 1.3 82.8 + - - +
331A GLU* 1.3 71.0 + - + +
333A ALA* 3.3 8.3 + - + +
334A ALA* 3.1 21.9 + - + +
337A ARG* 5.0 0.9 + - - -
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 3.0 39.6 - - + +
328A GLY* 3.3 12.9 - - - -
329A THR 4.0 0.2 + - - -
330A GLN* 1.3 81.5 + - + +
332A ASP* 1.3 60.7 + - - +
334A ALA* 3.2 7.1 + - - +
335A SER* 2.8 33.5 + - - +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A MET* 3.7 22.6 - - + +
325A GLU 4.5 1.0 - - - +
326A SER* 2.6 24.9 + - - -
327A ALA* 2.9 25.5 + - - +
328A GLY 2.8 19.6 + - - +
329A THR 3.6 1.6 - - - +
331A GLU* 1.3 71.9 - - - +
333A ALA* 1.3 66.9 + - - +
335A SER* 3.2 8.6 + - - -
336A LEU* 3.0 27.9 + - - +
356A PRO* 4.1 6.5 - - + -
358A TYR* 2.6 33.1 + - - +
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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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329A THR 3.0 14.4 + - - +
330A GLN* 3.6 12.3 - - + +
331A GLU 3.3 0.2 - - - -
332A ASP* 1.3 79.8 - - - +
334A ALA* 1.3 60.0 + - - +
336A LEU* 3.5 4.4 + - - +
337A ARG* 3.4 45.3 + - - +
356A PRO* 4.2 14.3 - - + +
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Residues in contact with ALA 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 GLN* 3.1 14.5 + - + +
331A GLU* 3.6 10.8 - - - +
333A ALA* 1.3 75.4 - - - +
335A SER* 1.3 64.1 + - - +
337A ARG* 3.2 29.3 + - - +
338A VAL* 3.2 19.5 + - + +
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Residues in contact with SER 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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215A MET* 5.9 0.2 - - - -
306A ALA* 3.3 23.4 + - - +
307A LYS 5.6 0.5 + - - -
308A LEU* 3.6 26.0 - - - +
327A ALA* 5.6 3.1 - - - +
331A GLU* 2.8 21.2 + - - +
332A ASP* 3.2 9.9 + - - -
334A ALA* 1.3 76.7 - - - +
336A LEU* 1.3 60.5 + - - +
338A VAL* 3.3 5.8 + - - -
339A PHE* 3.0 23.2 + - - +
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Residues in contact with LEU 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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215A MET* 4.0 13.9 - - + -
217A PHE* 3.7 46.4 - - + -
308A LEU* 4.7 4.0 - - + -
332A ASP 3.0 18.6 + - - +
333A ALA* 3.8 5.8 - - - +
334A ALA 3.2 0.2 - - - -
335A SER* 1.3 79.9 - - - +
337A ARG* 1.3 60.2 + - + +
339A PHE* 3.5 5.2 - - + +
340A THR* 2.9 31.5 + - - -
354A PRO* 3.8 26.3 - - + +
355A GLN 3.8 3.8 - - - -
356A PRO* 3.5 36.6 - - + -
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Residues in contact with ARG 337 (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 GLN 5.0 0.8 + - - -
333A ALA* 3.4 26.6 + - - +
334A ALA* 3.2 37.7 + - - +
336A LEU* 1.3 74.7 - - + +
338A VAL* 1.3 61.5 + - + +
340A THR* 3.3 7.9 + - - -
341A GLU* 2.8 41.2 + - + +
55B ASP* 3.7 24.3 + - - -
57B LEU* 4.3 29.6 - - + +
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Residues in contact with VAL 338 (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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305A ALA* 3.5 29.4 - - + +
306A ALA* 3.5 9.4 - - + +
334A ALA* 3.2 16.0 + - + +
335A SER* 3.3 9.6 + - - +
337A ARG* 1.3 74.4 - - + +
339A PHE* 1.3 65.5 + - - +
341A GLU* 3.1 24.2 + - - +
342A ALA* 3.0 22.6 + - + +
345A ARG* 5.3 0.6 + - - +
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Residues in contact with PHE 339 (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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217A PHE* 3.9 28.0 - + + -
219A TYR* 3.6 28.7 - + - -
299A ALA* 3.5 26.5 - - + -
302A ALA* 3.6 24.0 - - + +
303A CYS* 3.8 15.9 - - - -
306A ALA* 3.6 10.0 - - + +
308A LEU* 4.4 5.2 - - + -
320A LEU* 4.1 19.5 - - + -
322A VAL* 4.8 2.2 - - + -
335A SER 3.0 13.8 + - - +
336A LEU* 3.5 12.1 - - - +
338A VAL* 1.3 77.1 - - - +
340A THR* 1.3 64.8 + - - +
342A ALA* 3.3 2.9 + - - +
343A MET* 3.0 49.2 + - + +
354A PRO* 5.1 0.9 - - + -
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Residues in contact with THR 340 (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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219A TYR* 3.7 8.8 - - - +
336A LEU 2.9 18.1 + - - -
337A ARG* 3.6 7.8 - - - -
338A VAL 3.2 0.2 - - - -
339A PHE* 1.3 81.0 - - - +
341A GLU* 1.3 53.8 + - - +
343A MET* 3.3 1.6 + - - +
344A THR* 2.8 39.8 + - - +
350A PRO* 3.6 35.7 - - + -
353A PRO* 5.9 0.4 - - + -
354A PRO* 3.3 26.2 - - + +
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Residues in contact with GLU 341 (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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337A ARG* 2.8 32.7 + - - +
338A VAL* 3.1 26.1 + - - +
340A THR* 1.3 75.9 - - + +
342A ALA* 1.3 57.6 + - - +
344A THR* 3.2 8.8 + - - -
345A ARG* 3.0 43.2 + - - +
57B LEU* 6.1 1.0 - - - +
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Residues in contact with ALA 342 (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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302A ALA* 3.8 17.9 - - + -
305A ALA* 3.9 15.3 - - + -
338A VAL 3.0 11.0 + - - +
339A PHE 3.7 7.2 - - - +
341A GLU* 1.3 74.0 - - - +
343A MET* 1.3 66.8 + - - +
345A ARG* 3.0 32.8 + - - +
346A TYR* 2.9 33.6 + - + -
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Residues in contact with MET 343 (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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219A TYR* 3.4 43.5 - - + +
221A THR* 4.4 3.1 - - - +
224A PHE* 6.0 1.3 - - + -
295A CYS* 4.9 7.9 - - - +
298A LYS* 3.5 40.4 - - + +
299A ALA* 3.7 17.0 - - + +
302A ALA* 3.8 3.1 - - + -
320A LEU* 4.7 3.8 - - + -
339A PHE* 3.0 39.1 + - + +
340A THR 3.6 0.9 - - - +
342A ALA* 1.3 74.9 - - - +
344A THR* 1.3 60.3 + - - +
346A TYR* 3.2 12.3 + - - +
347A SER 3.3 1.0 + - - -
348A ALA* 2.9 42.1 + - + +
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Residues in contact with THR 344 (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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57A LEU 5.3 1.9 - - - +
340A THR* 2.8 31.8 + - - +
341A GLU* 3.4 8.3 - - - -
343A MET* 1.3 77.1 - - - +
345A ARG* 1.3 63.7 + - + +
347A SER* 2.9 15.1 + - - -
348A ALA 3.8 0.5 + - - -
349A PRO* 3.7 33.7 - - + +
350A PRO* 4.0 2.3 - - - +
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Residues in contact with ARG 345 (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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57A LEU 4.1 3.5 - - - +
58A GLN* 3.5 3.8 - - - -
59A VAL* 2.9 51.7 + - + +
61A ASP* 3.1 28.3 + - - +
305A ALA* 4.5 7.3 - - - +
338A VAL* 5.3 0.4 + - - +
341A GLU* 3.0 22.8 + - - +
342A ALA* 3.4 43.2 - - - +
344A THR* 1.3 76.2 - - + +
346A TYR* 1.3 64.7 + - + +
347A SER 3.0 4.9 + - - -
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Residues in contact with TYR 346 (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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58A GLN* 2.8 22.0 + - - +
59A VAL 3.6 16.6 - - - -
60A LEU* 4.3 9.2 - - + -
61A ASP* 2.6 42.1 + - - -
63A HIS* 3.9 5.4 - - - +
64A TYR* 4.0 9.9 - + + -
298A LYS* 3.0 60.8 + - + -
301A ALA* 3.5 27.0 + - + +
302A ALA 3.9 5.2 - - - -
305A ALA* 4.8 1.0 - - - +
342A ALA* 2.9 31.1 + - + +
343A MET* 3.5 8.1 - - - +
344A THR 3.2 0.4 - - - -
345A ARG* 1.3 81.3 + - + +
347A SER* 1.3 66.1 + - - +
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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