Contacts of the helix formed by residues 403 - 422 (chain A) in PDB entry 3GWX
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 VAL 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A GLY 4.1 17.3 - - - +
400A LEU* 4.3 19.4 + - + +
401A MET 3.5 8.9 - - - +
402A ASN* 1.3 71.0 - - - +
404A PRO* 1.3 74.1 - - + +
406A VAL* 4.3 7.2 - - - -
407A GLU* 2.7 56.5 + - + +
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Residues in contact with PRO 404 (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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401A MET 4.9 0.7 - - - +
402A ASN* 3.6 12.1 - - - +
403A VAL* 1.3 103.6 - - + +
405A ARG* 1.3 60.7 + - - +
407A GLU* 3.7 14.7 - - - +
408A ALA* 3.4 20.3 + - - +
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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
----------------------------------------------------------
305A SER* 5.3 4.0 + - - +
308A SER* 4.4 22.4 + - - -
309A LEU* 3.7 20.0 - - + -
402A ASN* 3.0 37.9 - - + +
404A PRO* 1.3 75.3 - - - +
406A VAL* 1.3 64.4 + - - +
408A ALA* 3.3 12.0 + - - +
409A ILE* 3.3 38.4 + - + +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 4.1 25.6 - - + -
317A LEU* 4.3 6.7 - - + -
393A LEU* 3.9 16.2 - - + -
394A CYS 3.6 33.0 - - - +
395A GLY* 3.6 2.9 - - - +
400A LEU* 3.8 28.9 - - + -
402A ASN 3.4 13.5 - - - +
403A VAL 3.1 5.3 + - - +
405A ARG* 1.3 74.1 - - - +
407A GLU* 1.3 66.4 + - - +
409A ILE* 2.9 20.3 + - - +
410A GLN* 2.9 11.4 + - - +
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY* 4.3 14.8 - - - +
396A ASP* 5.5 2.4 - - - +
403A VAL* 2.7 47.8 + - + +
404A PRO* 3.7 16.6 - - - +
406A VAL* 1.3 72.3 - - - +
408A ALA* 1.3 56.6 + - - +
410A GLN* 3.4 12.1 + - - +
411A ASP* 2.9 27.4 + - - +
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Residues in contact with ALA 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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404A PRO 3.4 10.6 + - - +
405A ARG* 3.3 19.2 + - - +
406A VAL 2.9 0.8 + - - -
407A GLU* 1.3 75.8 - - - +
409A ILE* 1.3 65.9 + - + +
411A ASP* 3.3 9.4 + - - +
412A THR* 3.2 24.8 + - - -
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Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 5.5 4.5 - - + -
303A ILE* 5.7 0.4 - - + -
305A SER* 3.5 47.1 - - - +
309A LEU* 4.8 5.2 - - + -
393A LEU* 3.4 41.3 - - + -
405A ARG* 3.3 42.4 + - + +
406A VAL* 2.9 8.9 + - - +
408A ALA* 1.3 72.1 - - - +
410A GLN* 1.3 67.0 + - - +
412A THR* 3.3 7.1 + - - -
413A ILE* 3.0 31.8 + - + +
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Residues in contact with GLN 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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390A ALA* 3.8 18.6 + - - +
393A LEU 3.0 22.8 + - - +
394A CYS* 4.0 14.2 - - - +
395A GLY* 3.5 16.0 + - - +
396A ASP* 4.8 5.4 + - - +
406A VAL 2.9 9.1 + - - +
407A GLU* 3.5 12.6 - - - +
409A ILE* 1.3 76.1 - - - +
411A ASP* 1.3 63.9 + - - +
413A ILE* 3.1 10.2 + - - +
414A LEU* 3.0 46.4 + - + +
439A MET* 4.6 9.7 - - - +
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Residues in contact with ASP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLU 2.9 14.8 + - - +
408A ALA* 3.5 12.3 - - - +
409A ILE 3.2 0.2 - - - -
410A GLN* 1.3 78.1 - - - +
412A THR* 1.3 58.5 + - - +
414A LEU* 3.5 6.5 + - - +
415A ARG* 2.8 72.2 + - - +
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Residues in contact with THR 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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211A LEU* 3.8 23.0 - - + +
214A PHE* 3.9 23.8 - - + -
408A ALA 3.2 12.2 + - - -
409A ILE* 3.3 11.2 + - - -
411A ASP* 1.3 79.6 + - - +
413A ILE* 1.3 57.8 + - - +
415A ARG* 3.3 9.6 + - - +
416A ALA* 2.8 27.9 + - - +
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Residues in contact with ILE 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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214A PHE* 3.7 22.7 - - + -
218A ILE* 4.6 3.8 - - + -
386A LEU* 3.5 35.1 - - + +
389A ALA* 3.7 16.4 - - + +
390A ALA* 3.9 13.2 - - + +
393A LEU* 3.3 44.9 - - + -
409A ILE* 3.0 20.5 + - + +
410A GLN* 3.6 7.0 - - - +
412A THR* 1.3 77.0 - - - +
414A LEU* 1.3 51.5 + - - +
416A ALA* 3.1 3.3 + - - +
417A LEU* 2.6 36.5 + - + +
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Residues in contact with LEU 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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390A ALA* 4.3 14.8 - - + -
410A GLN* 3.0 43.8 + - + +
411A ASP* 4.0 5.4 - - - +
413A ILE* 1.3 75.5 - - - +
415A ARG* 1.3 57.5 + - - +
417A LEU* 3.2 12.7 - - + +
418A GLU* 2.8 24.8 + - - +
432A PHE* 3.4 23.9 - - + -
436A LEU* 3.7 31.2 - - + -
439A MET* 4.3 13.9 - - - -
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Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.2 8.5 - - + -
411A ASP* 2.8 55.3 + - - +
412A THR* 3.4 10.1 - - - +
414A LEU* 1.3 74.7 - - - +
416A ALA* 1.3 62.4 + - - +
418A GLU* 3.4 7.4 + - - +
419A PHE* 3.0 51.1 + - + -
432A PHE* 5.8 0.2 - - - -
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.9 28.6 - - + +
214A PHE* 3.8 23.6 - - + -
215A SER* 4.5 4.2 + - - -
386A LEU* 4.3 10.8 - - + -
412A THR 2.8 17.4 + - - +
413A ILE 3.5 4.0 - - - +
415A ARG* 1.3 72.4 - - - +
417A LEU* 1.3 61.2 + - - +
419A PHE* 3.2 2.6 + - - +
420A HIS* 2.8 32.6 + - - +
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Residues in contact with LEU 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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383A ASP* 4.2 10.1 - - - +
386A LEU* 3.4 39.2 - - + +
387A PHE* 4.2 11.0 - - + +
390A ALA* 5.7 0.9 - - + -
413A ILE* 2.6 22.5 + - + +
414A LEU* 3.2 20.0 - - + +
416A ALA* 1.3 74.6 - - - +
418A GLU* 1.3 60.4 + - - +
420A HIS* 3.6 0.9 - - - +
421A LEU* 3.1 48.4 + - + +
432A PHE* 3.4 27.8 - - + +
435A LEU* 4.7 15.9 - - + -
436A LEU* 6.1 0.7 - - + -
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Residues in contact with GLU 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 LEU 2.8 14.0 + - - +
415A ARG* 3.4 7.6 + - - +
416A ALA 3.3 0.2 - - - -
417A LEU* 1.3 73.3 - - - +
419A PHE* 1.3 72.6 + - + +
421A LEU* 3.4 5.3 + - - +
422A GLN* 3.1 32.8 + - + +
432A PHE* 3.3 57.4 - - + +
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Residues in contact with PHE 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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208A VAL* 3.5 35.4 - - + +
211A LEU* 3.2 28.5 - - + -
212A LYS* 6.6 0.7 - - + -
415A ARG* 3.0 40.7 + - + +
416A ALA* 3.8 4.7 - - - +
418A GLU* 1.3 84.3 - - + +
420A HIS* 1.3 62.0 + - - +
422A GLN* 3.0 36.4 - - + +
423A ALA* 3.5 6.8 + - - +
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Residues in contact with HIS 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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215A SER* 4.0 12.3 - - - +
382A SER* 3.0 34.6 + - - -
383A ASP* 3.0 29.3 + - - -
386A LEU* 3.4 26.4 - - + +
416A ALA 2.8 17.0 + - - +
417A LEU 3.6 2.5 - - - +
419A PHE* 1.3 74.1 - - - +
421A LEU* 1.3 61.5 + - - +
422A GLN 3.0 5.6 + - - -
423A ALA* 3.3 9.5 + - - +
424A ASN* 3.3 28.3 + - + +
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Residues in contact with LEU 421 (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 LEU* 4.4 4.7 - - + -
383A ASP* 4.0 16.6 - - + +
417A LEU* 3.1 45.1 + - + +
418A GLU* 3.8 5.8 - - + +
419A PHE 3.3 0.2 - - - -
420A HIS* 1.3 74.4 - - - +
422A GLN* 1.3 66.0 + - - +
425A HIS* 3.4 48.3 + - + +
426A PRO* 5.1 0.2 - - - +
431A LEU* 3.8 23.3 - - + -
432A PHE* 3.7 39.9 - - + +
435A LEU* 4.2 3.4 - - + -
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Residues in contact with GLN 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 3.1 28.4 + - + +
419A PHE* 3.0 30.8 + - + +
421A LEU* 1.3 83.3 - - - +
423A ALA* 1.3 57.3 + - + +
424A ASN 3.3 3.6 + - - -
426A PRO* 3.7 21.0 - - - +
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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