Contacts of the helix formed by residues 374 - 397 (chain A) in PDB entry 5AVL
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 ASP 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.7 7.2 - - + +
285A ASP* 3.0 13.9 + - - +
372A VAL* 4.1 3.8 - - - -
373A GLN* 1.3 79.2 - - + +
375A GLN* 1.3 65.5 + - - +
376A LEU* 3.2 9.7 + - - +
377A GLN* 3.1 39.2 + - + +
378A VAL* 2.9 23.7 + - - +
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Residues in contact with GLN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ALA* 3.2 42.4 + - + +
368A ASP* 4.8 4.0 - - - +
369A ARG 5.5 1.4 + - - -
372A VAL* 3.9 23.7 - - + +
373A GLN 3.1 5.8 + - - +
374A ASP* 1.3 74.8 - - - +
376A LEU* 1.3 52.1 + - - +
378A VAL* 3.1 1.1 + - - -
379A GLU* 2.7 35.0 + - - +
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASP* 3.2 7.5 - - - +
375A GLN* 1.3 77.3 - - - +
377A GLN* 1.3 58.2 + - - +
379A GLU* 3.4 12.6 + - + +
380A ARG* 2.8 76.9 + - + +
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Residues in contact with GLN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLY* 5.7 0.9 - - - +
281A LEU* 3.9 17.7 - - + -
374A ASP* 3.1 31.5 + - + +
376A LEU* 1.3 79.2 - - - +
378A VAL* 1.3 63.6 - - - +
380A ARG* 4.2 21.1 - - - +
381A LEU* 3.0 54.5 + - + +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.8 30.7 - - + -
285A ASP* 5.1 2.9 - - - +
289A LEU* 4.0 10.5 - - + -
365A PHE* 3.6 18.2 - - + +
366A SER 3.6 9.6 - - - +
367A ALA* 3.5 31.0 - - + +
372A VAL* 4.0 13.5 - - + -
374A ASP 2.9 19.1 + - - +
375A GLN 3.6 3.4 - - - +
377A GLN* 1.3 77.8 - - - +
379A GLU* 1.3 55.7 + - - +
381A LEU* 3.4 8.6 - - - +
382A GLN* 2.9 26.5 + - - +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ALA* 3.8 15.0 - - + +
375A GLN 2.7 21.6 + - - +
376A LEU* 3.7 12.7 - - + +
378A VAL* 1.3 71.8 - - - +
380A ARG* 1.3 63.1 + - + +
382A GLN* 3.0 23.5 + - - +
383A HIS* 3.1 42.3 + - + +
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Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 2.8 65.4 + - + +
377A GLN* 3.9 22.0 - - - +
379A GLU* 1.3 71.5 - - + +
381A LEU* 1.3 62.1 + - - +
383A HIS* 3.2 19.5 + - - +
384A THR* 3.3 18.6 + - - +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO 4.1 7.6 - - - +
277A GLY* 4.0 32.1 - - - +
281A LEU* 4.5 6.3 - - + -
365A PHE* 3.7 35.7 - - + -
377A GLN* 3.0 47.4 + - + +
378A VAL* 3.4 4.0 - - - +
380A ARG* 1.3 75.8 - - - +
382A GLN* 1.3 63.2 + - - +
384A THR* 3.0 28.9 + - + +
385A TYR* 3.1 13.8 - - + -
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Residues in contact with GLN 382 (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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362A ILE* 2.6 50.6 + - + +
363A SER* 4.9 0.2 - - - +
365A PHE* 2.9 29.1 + - - +
366A SER* 3.4 16.2 + - - +
367A ALA 4.9 2.3 + - - -
378A VAL 2.9 11.3 + - - +
379A GLU* 3.0 14.0 + - - +
381A LEU* 1.3 72.4 - - - +
383A HIS* 1.3 68.6 + - + +
385A TYR* 3.2 8.7 + - - +
386A VAL* 2.9 33.0 + - + +
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Residues in contact with HIS 383 (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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379A GLU* 3.1 47.0 + - + +
380A ARG* 3.7 10.1 - - - +
381A LEU 3.2 0.4 - - - -
382A GLN* 1.3 86.8 + - + +
384A THR* 1.3 60.3 + - - +
386A VAL* 3.7 13.8 - - + +
387A GLU* 2.8 38.1 + - + +
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Residues in contact with THR 384 (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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210A GLN* 4.9 1.9 - - - +
213A MET* 4.4 7.3 - - - +
380A ARG 3.3 17.9 - - - +
381A LEU* 3.0 18.0 + - + +
383A HIS* 1.3 77.8 - - + +
385A TYR* 1.3 71.9 + - - +
387A GLU* 3.6 11.9 + - - +
388A ALA* 3.0 28.2 + - - +
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Residues in contact with TYR 385 (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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213A MET* 3.5 36.8 - - + -
217A LEU* 4.3 6.1 - - + -
275A LEU* 3.6 6.3 - - + -
276A PRO* 2.6 47.7 + - + +
358A LEU* 4.0 14.6 - - + +
361A ALA* 3.9 21.1 - - + -
362A ILE* 3.9 17.6 - - + +
365A PHE* 3.4 33.4 - + - -
381A LEU* 3.1 27.8 - - + -
382A GLN* 3.2 8.1 + - - +
384A THR* 1.3 85.3 + - - +
386A VAL* 1.3 59.5 + - - +
388A ALA* 3.7 4.5 - - - +
389A LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.8 30.3 - - + -
382A GLN* 2.9 27.0 + - + +
383A HIS* 3.2 15.2 + - + +
385A TYR* 1.3 75.5 - - - +
387A GLU* 1.3 56.9 + - + +
389A LEU* 3.2 5.8 + - - +
390A HIS* 2.9 26.4 + - - +
404A PHE* 3.7 24.6 - - + -
408A LEU* 4.4 14.4 - - + -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PRO* 5.5 0.5 - - - +
210A GLN* 3.9 12.9 - - - +
383A HIS* 2.8 25.0 + - + +
384A THR* 3.7 12.2 - - - +
386A VAL* 1.3 74.2 - - + +
388A ALA* 1.3 55.4 + - - +
390A HIS* 3.1 9.7 + - + +
391A ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.0 0.3 - - - +
210A GLN* 3.7 20.6 + - + -
213A MET* 3.7 25.4 - - + -
214A ILE* 3.9 17.9 - - + +
358A LEU* 4.2 6.5 - - + -
384A THR 3.0 17.8 + - - +
385A TYR* 3.3 5.3 + - - +
387A GLU* 1.3 76.1 - - - +
389A LEU* 1.3 58.0 + - - +
391A ALA* 3.4 2.1 + - - +
392A TYR* 2.9 29.5 + - - +
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Residues in contact with LEU 389 (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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355A GLU* 4.3 20.4 - - + +
358A LEU* 3.7 31.3 - - + +
359A LEU* 4.2 13.2 - - + -
362A ILE* 3.9 20.9 - - + -
385A TYR 2.9 13.9 + - - +
386A VAL 3.4 8.1 - - - +
388A ALA* 1.3 73.4 - - - +
390A HIS* 1.3 66.4 + - - +
392A TYR* 3.0 3.0 + - + +
393A VAL* 2.9 45.5 + - + +
404A PHE* 4.1 15.3 - - + -
407A MET* 4.4 11.7 - - + -
408A LEU* 4.2 11.7 - - + -
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PRO* 3.7 30.4 - - + +
386A VAL 2.9 13.3 + - - +
387A GLU* 3.1 13.1 + - + +
389A LEU* 1.3 77.6 - - - +
391A ALA* 1.3 61.9 + - - +
393A VAL* 3.4 2.3 + - - +
394A SER* 3.0 31.4 + - - -
401A ARG* 6.0 3.6 - - - +
404A PHE* 3.5 50.2 - + + +
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Residues in contact with ALA 391 (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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204A PRO* 3.4 30.9 - - + +
205A GLN 4.1 3.6 - - - +
206A LEU* 3.8 31.0 - - + -
210A GLN* 4.2 6.5 - - - +
387A GLU 2.9 16.2 + - - +
390A HIS* 1.3 77.0 - - - +
392A TYR* 1.3 61.8 + - - +
394A SER* 3.3 14.5 + - - -
395A ILE* 3.5 14.0 + - - +
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Residues in contact with TYR 392 (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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206A LEU* 4.0 13.8 - - + +
211A LEU* 6.6 0.2 - - + -
214A ILE* 4.1 25.8 - - + -
352A ASN* 3.3 29.5 + - - -
354A ALA* 3.2 30.5 - - + +
355A GLU* 3.7 26.5 - - + -
358A LEU* 4.7 1.6 - - + -
388A ALA 2.9 17.7 + - - +
389A LEU* 3.4 8.5 - - + +
391A ALA* 1.3 72.5 - - - +
393A VAL* 1.3 58.6 + - + +
394A SER 3.0 4.7 - - - -
395A ILE* 2.9 27.1 + - + +
396A HIS* 3.0 20.6 + - + +
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Residues in contact with VAL 393 (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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355A GLU* 4.1 7.0 - - + +
389A LEU* 2.9 33.0 + - + +
390A HIS 3.9 3.6 - - - +
392A TYR* 1.3 77.0 - - + +
394A SER* 1.3 55.8 + - - +
396A HIS* 4.2 7.4 - - - -
397A HIS* 2.7 43.1 + - + +
400A ASP 5.2 1.3 - - - +
403A MET* 3.7 17.5 - - + -
404A PHE* 3.7 32.3 - - + +
407A MET* 3.8 28.5 - - + -
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PRO* 4.1 21.5 - - - +
390A HIS* 3.0 26.7 + - - -
391A ALA 3.4 11.7 - - - -
392A TYR 3.0 0.8 - - - -
393A VAL* 1.3 80.4 - - - +
395A ILE* 1.3 58.7 + - - +
397A HIS 4.8 2.9 - - - -
398A PRO* 3.4 26.9 - - - +
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Residues in contact with ILE 395 (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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204A PRO 6.1 0.2 - - - +
206A LEU* 3.8 42.6 - - + +
391A ALA 3.5 8.7 + - - +
392A TYR* 2.9 10.7 + - + +
394A SER* 1.3 77.7 - - - +
396A HIS* 1.3 66.4 + - - +
398A PRO* 3.5 14.0 - - - +
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Residues in contact with HIS 396 (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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350A GLN 4.5 10.3 - - - -
352A ASN* 3.1 27.8 + - + -
355A GLU* 2.4 39.0 + - - +
392A TYR* 3.0 23.3 + + + +
393A VAL* 4.1 1.8 - - - +
395A ILE* 1.3 79.5 - - - +
397A HIS* 1.3 82.0 + + + +
398A PRO* 3.6 5.7 - - - +
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU 4.9 5.8 + - - -
350A GLN* 5.3 1.5 + - + -
355A GLU* 3.9 4.4 + - - -
393A VAL* 2.7 37.6 + - + +
394A SER* 4.5 1.4 - - - +
396A HIS* 1.3 111.3 + + - +
398A PRO* 1.3 65.5 - - - +
399A HIS 3.0 5.4 + - - -
400A ASP* 3.1 22.4 + - + +
401A ARG* 5.3 0.2 - - - -
403A MET* 3.7 45.8 - - + +
407A MET* 4.4 1.4 - - + +
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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
------------------------------------------------------------
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