Contacts of the helix formed by residues 401 - 420 (chain A) in PDB entry 4BWM
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 GLU 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A VAL* 3.9 2.7 - - - -
323A ALA* 5.9 0.7 - - - +
334A ARG* 3.0 37.8 + - - -
399A THR* 3.4 3.0 + - - -
400A GLU* 1.3 79.2 - - - +
402A ALA* 1.3 70.6 + - - +
403A GLY 2.9 20.3 + - - -
404A GLU* 2.9 48.8 + - - +
405A ARG* 3.0 24.4 + - - +
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLY* 3.5 30.6 - - - +
309A PHE* 4.1 2.5 - - - +
310A VAL* 3.5 11.0 - - + +
323A ALA* 3.8 36.6 - - + +
324A LEU 4.0 0.4 - - - +
325A ALA* 3.8 10.5 - - + -
401A GLU* 1.3 77.7 + - - +
403A GLY* 1.3 57.4 + - - +
405A ARG* 3.3 2.6 + - - -
406A ALA* 2.9 26.0 + - - +
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Residues in contact with GLY 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ALA* 3.7 16.7 - - - +
332A VAL* 3.7 20.9 - - - +
334A ARG* 3.9 4.7 - - - -
401A GLU* 2.9 18.5 + - - -
402A ALA* 1.3 77.0 - - - +
404A GLU* 1.3 58.3 + - - +
406A ALA* 3.2 4.3 + - - +
407A ALA* 3.0 27.8 + - - +
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG* 5.3 1.8 - - - +
397A GLU 5.2 3.6 - - - +
399A THR* 2.7 47.9 + - + +
401A GLU* 2.9 29.6 + - - +
403A GLY* 1.3 73.9 - - - +
405A ARG* 1.3 59.7 + - - +
407A ALA* 3.5 6.9 + - - +
408A LEU* 2.9 29.5 + - - +
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLY* 4.1 9.9 - - - -
309A PHE* 2.9 28.8 + - - +
310A VAL* 3.7 24.7 - - - +
311A LEU 4.6 2.4 - - - +
351A LEU* 4.5 1.2 - - - +
352A LEU* 6.1 0.2 - - - +
398A TRP* 3.3 54.5 - - + +
399A THR* 2.7 32.9 + - - +
400A GLU* 3.1 27.7 + - - +
401A GLU 3.0 19.3 + - - +
402A ALA 3.7 4.7 - - - +
404A GLU* 1.3 74.8 - - - +
406A ALA* 1.3 59.5 + - - +
408A LEU* 3.7 7.2 - - - +
409A SER* 3.0 32.8 + - - +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 3.4 22.7 - - - +
307A VAL 3.8 3.8 - - - -
308A GLY* 3.4 20.6 - - - +
325A ALA 3.9 4.3 - - - +
326A ALA 3.9 5.4 - - - -
327A ALA* 3.7 20.1 - - + +
332A VAL* 5.3 0.4 - - + -
402A ALA 2.9 11.5 + - - +
403A GLY* 3.2 9.4 + - - +
405A ARG* 1.3 75.5 - - - +
407A ALA* 1.3 63.4 + - - +
409A SER* 3.3 4.5 + - - -
410A GLU 3.1 17.8 + - - -
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Residues in contact with ALA 407 (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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295A GLU* 5.7 4.5 - - - +
327A ALA* 3.7 14.5 - - + +
330A GLY* 5.6 8.5 - - - +
332A VAL* 5.9 2.9 - - + -
403A GLY 3.0 15.7 + - - +
404A GLU* 3.7 7.6 - - - +
406A ALA* 1.3 77.8 - - - +
408A LEU* 1.3 57.4 + - - +
410A GLU* 3.3 7.8 + - - +
411A ARG* 3.0 28.5 + - - +
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Residues in contact with LEU 408 (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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351A LEU* 3.9 17.5 - - + -
387A PRO 5.3 0.2 - - - +
391A ALA* 4.1 9.2 - - + -
395A GLY 3.7 19.1 - - - +
396A GLY* 3.9 15.3 - - - -
397A GLU 3.5 28.5 - - - +
398A TRP* 3.9 17.0 - - + +
404A GLU 2.9 19.0 + - - +
405A ARG* 3.7 5.2 - - - +
407A ALA* 1.3 73.7 - - - +
409A SER* 1.3 55.5 + - - +
411A ARG* 3.2 9.1 + - + +
412A LEU* 2.8 57.6 + - + +
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 4.0 8.5 - - - -
307A VAL 3.6 7.0 + - - -
308A GLY* 5.3 0.2 - - - -
350A GLY* 3.8 12.8 - - - -
351A LEU* 3.0 45.9 + - - +
373A PRO* 3.5 5.9 - - - +
405A ARG* 3.0 15.5 + - - +
406A ALA 3.4 9.4 - - - -
407A ALA 3.3 0.2 - - - -
408A LEU* 1.3 74.8 - - - +
410A GLU* 1.3 58.2 + - - +
413A PHE* 2.9 32.1 + - - +
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Residues in contact with GLU 410 (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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306A PHE* 3.6 32.9 - - + -
327A ALA* 4.0 7.0 - - - +
328A ARG* 3.5 18.3 + - - -
329A GLY* 2.8 25.9 + - - -
330A GLY* 3.1 25.7 + - - -
406A ALA 3.1 9.7 + - - +
407A ALA* 3.5 9.2 - - - +
408A LEU 3.3 0.2 - - - -
409A SER* 1.3 79.1 - - - +
411A ARG* 1.3 63.2 + - - +
413A PHE* 3.4 2.8 + - - +
414A ALA* 3.2 23.4 + - + +
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY 5.4 8.5 - - - +
396A GLY* 5.9 2.7 - - - -
407A ALA 3.0 17.0 + - - +
408A LEU* 3.2 13.4 + - + +
410A GLU* 1.3 77.2 - - - +
412A LEU* 1.3 60.6 + - + +
414A ALA* 3.4 6.5 + - - +
415A ASN* 3.1 28.6 + - + +
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Residues in contact with LEU 412 (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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351A LEU* 4.0 19.1 - - + -
373A PRO* 3.9 15.5 - - + -
387A PRO 5.3 0.7 - - - +
390A VAL* 4.1 25.1 - - + +
391A ALA* 4.5 6.3 - - + +
394A TYR* 4.0 25.4 - - + +
395A GLY 3.7 17.9 - - - +
408A LEU* 2.8 49.3 + - + +
409A SER 4.0 0.7 - - - +
411A ARG* 1.3 73.9 - - + +
413A PHE* 1.3 65.1 + - - +
415A ASN* 4.3 5.4 - - - +
416A LEU* 2.9 33.0 + - + +
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Residues in contact with PHE 413 (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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306A PHE* 3.6 26.9 - + + -
349A ARG* 3.8 11.9 - - - -
371A ASP* 3.4 45.5 - - + -
373A PRO* 3.9 14.8 - - + +
376A LEU* 3.7 24.4 - - + +
409A SER 2.9 19.7 + - - +
410A GLU 3.8 1.6 - - - +
411A ARG 3.4 0.2 - - - -
412A LEU* 1.3 75.4 - - - +
414A ALA* 1.3 63.0 + - - +
417A TRP* 2.8 69.4 + + + +
430A TYR* 4.2 2.2 - - - -
1838A FMT 4.6 3.1 - - - -
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Residues in contact with ALA 414 (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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410A GLU* 3.2 14.6 + - + +
411A ARG* 3.8 6.3 - - - +
413A PHE* 1.3 86.0 - - + +
415A ASN* 1.3 63.1 + - - +
417A TRP* 4.0 2.9 - - - +
418A GLY* 3.1 19.2 + - - -
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Residues in contact with ASN 415 (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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394A TYR* 3.0 37.4 + - - +
411A ARG* 3.1 20.5 + - + +
412A LEU* 3.7 8.8 - - + +
414A ALA* 1.3 79.1 - - - +
416A LEU* 1.3 59.1 + - + +
418A GLY* 3.2 1.9 + - - -
419A ARG* 2.8 54.9 + - - +
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Residues in contact with LEU 416 (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 PRO* 3.3 33.9 - - + +
376A LEU* 3.9 18.4 - - + -
377A ALA* 3.7 15.7 - - + +
380A LEU* 3.6 23.0 - - + +
390A VAL* 4.2 10.3 - - + -
394A TYR* 3.8 37.2 - - + -
412A LEU* 2.9 27.0 + - + +
415A ASN* 1.3 72.5 - - + +
417A TRP* 1.3 66.0 + - - +
419A ARG* 3.1 8.3 + - - +
420A LEU* 3.1 25.8 + - - +
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Residues in contact with TRP 417 (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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371A ASP* 5.3 0.4 - - - -
376A LEU* 3.9 15.6 - - + +
413A PHE* 2.8 55.1 + + + +
414A ALA* 4.0 3.8 - - - +
416A LEU* 1.3 73.5 - - - +
418A GLY* 1.3 63.3 + - - +
420A LEU* 3.2 15.0 + - + +
421A GLU* 3.4 18.8 + - + +
427A LEU* 3.8 27.3 - - + +
430A TYR* 3.8 27.4 - + - -
431A ARG* 3.3 36.1 - - - -
435A ARG* 5.8 1.3 - - - -
1837A FMT 3.9 9.5 + - - -
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Residues in contact with GLY 418 (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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414A ALA 3.1 14.8 + - - -
415A ASN 3.6 4.5 - - - -
417A TRP* 1.3 78.8 - - - +
419A ARG* 1.3 60.5 + - - +
421A GLU* 3.2 36.4 + - - +
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Residues in contact with ARG 419 (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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380A LEU* 4.0 21.4 - - + +
393A ARG 5.7 0.6 + - - -
394A TYR* 3.5 41.9 + - - +
415A ASN* 2.8 39.1 + - - +
416A LEU* 3.1 13.4 + - - +
418A GLY* 1.3 76.0 - - - +
420A LEU* 1.3 58.7 + - - +
421A GLU 3.4 2.6 + - - +
423A GLU* 4.5 6.9 - - - +
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Residues in contact with LEU 420 (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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376A LEU* 3.6 44.9 - - + +
379A LEU* 5.0 5.4 - - + -
380A LEU* 3.7 29.2 - - + +
416A LEU 3.1 18.3 + - - +
417A TRP* 3.2 7.4 + - - +
418A GLY 3.1 0.6 - - - -
419A ARG* 1.3 77.5 - - - +
421A GLU* 1.3 65.2 + - - +
422A GLY 3.2 0.5 + - - -
423A GLU* 2.9 25.9 + - + +
426A LEU* 3.9 34.1 - - + +
427A LEU* 3.8 28.3 - - + +
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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
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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