Contacts of the helix formed by residues 369 - 389 (chain A) in PDB entry 3WOO
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 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A LEU* 3.8 28.9 - - - +
365A GLN* 3.9 6.4 + - - -
366A GLY 2.8 11.7 + - - -
368A LYS* 1.3 78.9 - - - +
370A GLN* 1.3 64.2 + - - +
371A PRO* 3.4 2.7 - - - -
372A ALA* 3.3 9.2 + - - +
373A LEU* 3.2 28.4 + - - +
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Residues in contact with GLN 370 (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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366A GLY 3.9 3.4 + - - +
367A ALA* 3.0 21.8 + - - +
369A GLY* 1.3 76.7 - - - +
371A PRO* 1.3 72.0 - - + +
373A LEU* 3.2 22.2 + - - +
374A ASP* 2.9 57.9 + - - +
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Residues in contact with PRO 371 (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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367A ALA 3.6 8.5 - - - +
368A LYS* 3.7 11.4 - - - +
369A GLY 3.5 3.6 - - - -
370A GLN* 1.3 94.7 - - + +
372A ALA* 1.3 55.4 + - - +
374A ASP* 3.4 9.6 + - + +
375A ALA* 3.0 27.7 + - - +
555A VAL* 3.7 16.2 - - + +
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 3.6 26.0 - - + -
369A GLY* 3.3 7.1 + - - +
370A GLN 3.2 0.8 - - - -
371A PRO* 1.3 77.1 - - - +
373A LEU* 1.3 59.6 - - - +
375A ALA* 3.2 4.5 + - - +
376A HIS* 2.9 28.6 + - - +
555A VAL* 3.7 17.4 - - + +
556A TYR* 3.7 5.7 - - + -
559A ALA* 3.7 22.2 - - + -
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 3.9 31.6 - - + +
362A LEU* 3.8 19.5 - - + +
363A LYS* 4.2 27.8 - - + +
366A GLY 6.0 0.4 - - - +
369A GLY 3.2 19.1 + - - +
370A GLN* 3.2 31.8 + - - +
372A ALA* 1.3 75.1 - - - +
374A ASP* 1.3 63.7 + - - +
376A HIS* 3.2 8.5 + - - +
377A ALA* 3.1 21.3 + - - +
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Residues in contact with ASP 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLN* 2.9 50.1 + - - +
371A PRO* 3.5 8.4 - - + +
373A LEU* 1.3 74.1 - - - +
375A ALA* 1.3 61.3 + - - +
377A ALA* 3.3 8.3 + - - +
378A LYS* 2.9 28.2 + - - +
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO 3.0 17.4 + - - +
372A ALA 3.5 5.8 - - - +
374A ASP* 1.3 76.2 - - - +
376A HIS* 1.3 58.9 + - - +
378A LYS* 3.1 2.7 + - - +
379A LEU* 2.8 35.8 + - - +
552A ALA* 3.5 34.8 - - - +
555A VAL* 4.1 6.5 - - + -
556A TYR* 4.0 13.5 - - + +
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Residues in contact with HIS 376 (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 18.4 - - + +
355A GLU* 2.8 28.3 + - - +
359A LEU* 3.9 27.8 - - + +
372A ALA 2.9 13.8 + - - +
373A LEU 3.5 9.5 + - - +
374A ASP 3.2 0.2 - - - -
375A ALA* 1.3 78.7 - - - +
377A ALA* 1.3 63.3 + - - +
379A LEU* 3.3 5.9 + - - +
380A LEU* 3.0 42.6 + - + +
556A TYR* 3.5 40.3 - + + -
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Residues in contact with ALA 377 (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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373A LEU 3.1 12.8 + - - +
374A ASP* 3.7 10.1 - - - +
376A HIS* 1.3 79.8 + - - +
378A LYS* 1.3 62.1 + - - +
380A LEU* 3.5 7.7 + - - +
381A ASP* 3.0 23.2 + - - +
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Residues in contact with LYS 378 (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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374A ASP 2.9 16.5 + - - +
375A ALA* 3.1 4.9 + - - +
377A ALA* 1.3 76.3 - - - +
379A LEU* 1.3 63.9 + - - +
381A ASP* 3.2 13.0 + - + +
382A LEU* 3.0 45.9 + - + +
385A GLN* 5.9 0.6 + - - -
548A GLU* 3.5 34.2 + - + +
551A ALA* 6.3 1.6 - - + -
552A ALA* 3.9 20.2 - - + -
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Residues in contact with LEU 379 (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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281A LEU* 4.0 26.0 - - + -
284A GLU* 5.0 3.0 - - - +
375A ALA 2.8 20.4 + - - +
376A HIS* 3.7 4.3 - - - +
378A LYS* 1.3 77.4 - - - +
380A LEU* 1.3 56.7 + - - +
382A LEU* 3.2 11.6 + - + +
383A LEU* 3.0 28.1 + - - +
549A ASN* 3.1 28.0 - - - +
552A ALA* 3.7 26.2 - - + +
553A ARG* 3.9 26.0 + - - +
556A TYR* 3.7 28.7 - - + -
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.9 13.8 - - + +
283A ALA* 3.5 32.3 - - + -
355A GLU* 5.8 1.3 - - - +
376A HIS* 3.0 35.4 + - + +
377A ALA* 3.7 8.3 - - - +
378A LYS 3.2 0.2 - - - -
379A LEU* 1.3 78.6 - - - +
381A ASP* 1.3 61.4 + - - +
383A LEU* 3.4 8.7 + - + +
384A GLU* 3.1 31.1 + - + +
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Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA 3.0 15.3 + - - +
378A LYS* 3.2 17.6 + - + +
380A LEU* 1.3 75.3 - - - +
382A LEU* 1.3 61.3 + - - +
384A GLU* 3.2 11.0 + - - +
385A GLN* 2.8 52.6 + - - +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 3.0 31.6 + - + +
379A LEU* 3.2 14.8 + - + +
381A ASP* 1.3 77.7 - - - +
383A LEU* 1.3 61.7 + - - +
385A GLN* 3.3 20.7 + - - +
386A SER* 3.0 22.2 + - - -
545A ARG* 3.7 29.7 - - + +
548A GLU* 3.5 35.2 - - + +
549A ASN* 3.6 35.9 - - + +
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Residues in contact with LEU 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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281A LEU* 5.5 1.1 - - + -
283A ALA* 3.2 41.1 - - + -
284A GLU* 3.6 26.0 - - + +
287A ASN* 3.1 29.4 - - + +
379A LEU 3.0 13.1 + - - +
380A LEU* 3.5 14.4 - - + +
382A LEU* 1.3 77.0 - - - +
384A GLU* 1.3 67.1 + - - +
386A SER* 3.2 13.0 - - - -
387A LYS* 3.0 22.6 + - + +
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Residues in contact with GLU 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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283A ALA* 5.8 1.6 - - - +
287A ASN* 5.4 0.7 + - - -
380A LEU* 3.1 23.9 + - + +
381A ASP* 3.2 14.8 + - - +
383A LEU* 1.3 82.1 - - + +
385A GLN* 1.3 65.1 + - + +
387A LYS* 3.3 34.2 + - - +
388A ALA* 3.2 21.8 + - - +
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Residues in contact with GLN 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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378A LYS* 5.9 0.5 + - - -
381A ASP* 2.8 39.1 + - - +
382A LEU* 3.5 21.5 - - - +
383A LEU 3.3 0.2 - - - -
384A GLU* 1.3 77.9 - - - +
386A SER* 1.3 62.7 + - - +
388A ALA* 3.4 15.1 + - - +
389A THR* 4.1 6.6 + - - +
545A ARG* 3.7 37.5 + - - +
548A GLU* 4.7 6.8 + - - +
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Residues in contact with SER 386 (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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382A LEU 3.0 13.0 + - - -
383A LEU* 3.2 19.7 - - - -
385A GLN* 1.3 75.1 - - - +
387A LYS* 1.3 65.1 + - - -
388A ALA 3.4 0.5 + - - -
389A THR* 3.4 13.8 + - - -
390A ARG* 3.4 13.7 + - - +
393A ASP* 4.6 2.1 - - - +
545A ARG* 3.6 26.8 + - - +
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Residues in contact with LYS 387 (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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287A ASN* 3.6 29.0 + - - +
383A LEU* 3.0 16.3 + - + +
384A GLU* 3.5 33.3 + - - +
386A SER* 1.3 76.9 - - - +
388A ALA* 1.3 63.9 + - - +
389A THR 3.0 1.6 + - - -
390A ARG* 3.1 60.2 + - - +
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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
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384A GLU 3.2 11.2 + - - +
385A GLN* 3.7 12.8 - - - +
386A SER 3.2 1.0 - - - -
387A LYS* 1.3 77.0 - - - +
389A THR* 1.3 57.8 + - + +
390A ARG 3.6 0.2 - - - -
470A ASP* 5.2 0.7 - - - +
471A GLN* 2.7 27.9 - - - +
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Residues in contact with THR 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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385A GLN 4.3 6.3 + - - +
386A SER* 3.4 7.2 + - - -
387A LYS 3.1 0.6 - - - -
388A ALA* 1.3 90.6 - - + +
390A ARG* 1.3 55.4 + - - +
391A ASP 3.3 2.6 + - - -
392A ARG* 3.4 36.4 + - - +
393A ASP* 2.7 48.7 + - - -
470A ASP 5.9 0.9 - - - +
471A GLN* 3.5 11.2 - - - +
541A GLU* 5.0 3.3 + - - +
545A ARG* 5.0 5.1 + - - +
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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