Contacts of the helix formed by residues 369 - 389 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU* 3.9 36.3 - - - +
363B LYS* 6.0 0.4 - - - -
365B GLN* 3.7 9.3 + - - -
366B GLY 3.2 7.9 + - - -
367B ALA 3.1 0.2 + - - -
368B LYS* 1.3 77.7 - - - +
370B GLN* 1.3 60.6 + - - +
371B PRO* 3.6 2.0 - - - -
372B ALA* 3.9 7.8 + - - +
373B LEU* 3.5 21.3 + - - +
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Residues in contact with GLN 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLY 3.5 9.3 + - - +
367B ALA* 3.3 16.4 - - - +
369B GLY* 1.3 76.7 - - - +
371B PRO* 1.3 75.1 - - + +
373B LEU* 3.1 22.1 + - - +
374B ASP* 3.0 41.0 + - - +
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Residues in contact with PRO 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA 3.7 4.5 - - - +
368B LYS 3.4 15.5 - - - +
369B GLY 3.6 0.7 - - - -
370B GLN* 1.3 94.2 - - + +
372B ALA* 1.3 63.3 + - - +
374B ASP* 2.9 24.5 + - + +
375B ALA* 3.0 13.2 + - - +
555B VAL* 3.9 16.1 - - + +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU* 3.6 31.4 - - + -
369B GLY* 4.0 4.5 - - - +
370B GLN 3.3 0.4 - - - -
371B PRO* 1.3 80.5 - - - +
373B LEU* 1.3 63.1 + - - +
375B ALA* 3.4 5.3 + - - +
376B HIS* 3.1 18.4 + - - +
555B VAL* 3.8 17.1 - - + +
556B TYR* 3.7 10.7 - - + +
559B ALA* 3.8 20.4 - - + -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 4.4 21.8 - - + +
362B LEU* 4.4 9.2 - - + +
363B LYS* 3.7 48.9 - - + +
369B GLY 3.5 9.4 + - - +
370B GLN* 3.1 22.1 + - - +
372B ALA* 1.3 79.9 - - - +
374B ASP* 1.3 63.0 + - - +
376B HIS* 3.6 9.1 + - + +
377B ALA* 3.3 19.7 + - + +
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Residues in contact with ASP 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B GLN* 3.0 44.3 + - - +
371B PRO* 2.9 14.9 + - + +
373B LEU* 1.3 75.4 - - - +
375B ALA* 1.3 56.7 + - - +
377B ALA* 2.8 29.8 + - - +
378B LYS* 2.8 15.0 + - - +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PRO 3.0 10.0 + - - +
372B ALA 3.4 9.4 - - - +
374B ASP* 1.3 74.4 - - - +
376B HIS* 1.3 62.7 + - - +
378B LYS* 3.0 3.7 + - - +
379B LEU* 2.9 30.7 + - - +
552B ALA* 3.3 38.4 - - - +
555B VAL* 4.1 7.6 - - + -
556B TYR* 3.8 14.6 - - + +
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Residues in contact with HIS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 4.1 10.4 - - + +
355B GLU* 2.7 31.5 + - - -
359B LEU* 3.8 28.1 - - + +
372B ALA 3.1 9.0 + - - +
373B LEU* 3.6 13.9 + - + +
374B ASP 3.2 0.2 - - - -
375B ALA* 1.3 74.8 - - - +
377B ALA* 1.3 65.3 + - - +
379B LEU* 3.5 4.6 + - - +
380B LEU* 3.1 54.3 + - + +
556B TYR* 3.3 49.9 - + + -
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 3.3 11.5 + - + +
374B ASP* 2.8 19.8 + - - +
376B HIS* 1.3 80.4 + - - +
378B LYS* 1.3 61.9 + - - +
380B LEU* 3.5 8.0 + - - +
381B ASP* 3.3 19.9 + - - +
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASP 2.8 11.1 + - - +
375B ALA* 3.3 9.6 - - - +
377B ALA* 1.3 75.9 - - - +
379B LEU* 1.3 55.7 + - - +
381B ASP* 2.8 40.4 + - - +
382B LEU* 2.8 32.8 + - + +
548B GLU* 3.3 34.0 + - + +
551B ALA* 6.3 0.2 - - + -
552B ALA* 3.6 24.5 - - + -
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.7 31.0 - - + -
284B GLU* 5.1 2.8 - - - +
375B ALA 2.9 22.5 + - - +
376B HIS* 3.8 0.9 - - - +
378B LYS* 1.3 70.4 - - - +
380B LEU* 1.3 57.6 + - - +
382B LEU* 3.3 7.7 + - + +
383B LEU* 2.9 29.1 + - - +
549B ASN* 3.1 27.1 - - - +
552B ALA* 3.9 16.8 - - + +
553B ARG* 3.8 42.1 + - - +
556B TYR* 3.8 27.6 - - + -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.8 14.3 - - + +
283B ALA* 3.8 28.7 - - + -
355B GLU* 5.2 3.1 - - - +
376B HIS* 3.1 40.2 + - + +
377B ALA* 3.6 8.1 - - - +
378B LYS 3.2 0.2 - - - -
379B LEU* 1.3 77.3 - - - +
381B ASP* 1.3 57.3 + - - +
383B LEU* 3.4 7.9 + - + +
384B GLU* 3.1 31.7 + - + +
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Residues in contact with ASP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ALA 3.3 9.7 + - - +
378B LYS* 2.8 26.0 + - - +
380B LEU* 1.3 77.3 - - - +
382B LEU* 1.3 65.8 + - - +
384B GLU* 3.1 18.0 + - - +
385B GLN* 3.1 30.5 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS* 2.8 29.3 + - + +
379B LEU* 3.5 10.5 - - + +
381B ASP* 1.3 77.5 - - - +
383B LEU* 1.3 62.6 + - - +
385B GLN* 3.2 29.7 - - - +
386B SER* 3.0 21.4 + - - -
545B ARG* 3.8 17.5 - - + +
548B GLU* 3.5 32.5 - - + +
549B ASN* 3.4 54.1 - - - +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 5.6 1.1 - - + -
283B ALA* 3.3 47.1 - - + +
284B GLU* 3.7 22.9 - - + +
287B ASN* 4.0 30.3 - - + +
379B LEU 2.9 14.0 + - - +
380B LEU* 3.5 13.7 - - + +
381B ASP 3.2 0.2 - - - -
382B LEU* 1.3 76.6 - - - +
384B GLU* 1.3 61.4 + - + +
386B SER* 2.9 13.4 + - - +
387B LYS* 2.9 27.5 + - + +
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Residues in contact with GLU 384 (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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287B ASN* 5.2 1.6 + - - -
380B LEU* 3.1 16.8 + - + +
381B ASP* 3.1 13.6 + - - +
383B LEU* 1.3 77.5 - - + +
385B GLN* 1.3 56.3 + - - +
387B LYS* 3.3 35.8 + - - +
388B ALA* 3.0 28.2 + - - +
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Residues in contact with GLN 385 (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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381B ASP* 3.1 27.3 + - - +
382B LEU* 3.2 29.1 - - - +
384B GLU* 1.3 75.1 - - - +
386B SER* 1.3 67.0 + - - +
388B ALA* 3.3 19.9 + - - +
389B THR* 4.0 5.9 + - - +
545B ARG* 3.7 36.4 + - - +
548B GLU* 4.9 6.6 + - - +
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU 3.0 7.9 + - - -
383B LEU* 2.9 24.8 + - - +
385B GLN* 1.3 78.2 - - - +
387B LYS* 1.3 60.7 + - - +
388B ALA 3.3 1.0 + - - -
389B THR* 3.4 13.3 + - - -
390B ARG* 3.4 14.1 + - - +
393B ASP* 4.4 2.1 - - - +
545B ARG* 3.7 29.6 - - - +
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Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASN* 3.6 21.7 - - - +
383B LEU* 2.9 18.0 + - + +
384B GLU* 3.4 32.9 + - - +
385B GLN 3.1 0.2 - - - -
386B SER* 1.3 78.1 + - - +
388B ALA* 1.3 62.0 + - - +
389B THR 3.1 1.4 + - - -
390B ARG* 3.2 63.5 + - - +
391B ASP* 5.0 0.7 - - - +
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B GLU 3.0 13.0 + - - +
385B GLN* 3.3 14.7 + - - +
387B LYS* 1.3 75.8 - - - +
389B THR* 1.3 64.5 + - + +
470B ASP* 5.3 1.9 - - - +
471B GLN* 3.6 16.6 + - - +
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLN 4.0 5.6 + - - +
386B SER* 3.6 7.4 + - - -
387B LYS 3.1 0.6 - - - -
388B ALA* 1.3 83.7 - - + +
390B ARG* 1.3 65.6 + - - +
391B ASP 3.3 2.7 - - - -
392B ARG* 3.1 39.3 + - + +
393B ASP* 2.8 43.6 + - - -
470B ASP 6.0 1.8 - - - +
471B GLN* 3.5 11.0 - - - +
545B ARG* 4.7 5.5 + - - -
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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