Contacts of the helix formed by residues 406 - 427 (chain A) in PDB entry 4GDY
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 SER 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLN* 5.0 0.9 - - - -
404A SER 3.6 2.7 + - - -
405A ALA* 1.3 74.3 - - - +
407A PRO* 1.4 70.2 - - - +
408A GLU* 3.6 17.9 + - - +
409A GLN* 2.8 56.8 + - - +
410A MET* 3.0 11.5 + - - +
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Residues in contact with PRO 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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329A GLN* 4.7 9.4 - - - +
332A ALA* 3.9 26.1 - - + +
336A ALA* 5.1 1.0 - - - +
405A ALA 4.6 1.6 - - - +
406A SER* 1.4 85.2 - - - +
408A GLU* 1.3 70.1 + - - +
410A MET* 3.5 16.2 - - - +
411A ASP* 3.3 22.2 + - - +
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A SER* 3.6 23.1 + - - +
407A PRO* 1.3 87.5 - - - +
409A GLN* 1.4 62.6 + - - +
410A MET 3.2 1.6 - - - -
411A ASP* 3.5 8.3 + - + +
412A VAL* 3.1 31.9 + - + +
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Residues in contact with GLN 409 (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 VAL* 5.0 11.8 - - - +
380A LEU* 4.7 2.9 - - + +
404A SER 5.1 1.4 + - - -
405A ALA* 3.7 20.4 - - + +
406A SER* 2.8 42.8 + - - +
408A GLU* 1.4 76.9 - - - +
410A MET* 1.4 56.3 + - - +
412A VAL* 3.6 5.6 + - - +
413A ALA* 3.1 30.6 + - - +
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Residues in contact with MET 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN* 3.6 19.5 - - - +
332A ALA* 3.8 14.1 - - - +
333A ILE* 3.7 37.9 - - + -
336A ALA* 4.0 14.6 - - + -
380A LEU* 4.9 5.8 - - + -
402A PHE* 3.6 29.6 - - + -
405A ALA* 3.4 32.3 - - + +
406A SER 3.0 13.4 + - - +
407A PRO* 3.5 9.2 - - - +
409A GLN* 1.4 72.6 - - - +
411A ASP* 1.4 58.3 + - - +
413A ALA* 3.4 4.8 + - - +
414A PHE* 2.9 36.0 + - + +
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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
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336A ALA* 4.0 14.0 - - + +
339A LYS* 2.9 38.1 + - - +
340A TRP* 3.3 25.3 + - - +
407A PRO 3.3 11.5 + - - +
408A GLU* 3.7 11.7 - - + +
409A GLN 3.5 0.4 - - - -
410A MET* 1.4 77.6 - - - +
412A VAL* 1.4 63.1 + - + +
415A GLN* 3.1 26.0 + - - +
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Residues in contact with VAL 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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408A GLU* 3.1 18.9 + - + +
409A GLN* 3.9 7.0 - - - +
410A MET 3.4 0.2 - - - -
411A ASP* 1.4 78.5 - - + +
413A ALA* 1.3 59.9 + - - +
415A GLN* 3.4 19.7 + - - +
416A VAL* 3.3 27.1 + - + +
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Residues in contact with ALA 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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378A GLY 5.6 1.3 - - - +
380A LEU* 3.8 27.6 - - + -
381A MET* 4.3 14.8 - - + +
409A GLN 3.1 18.6 + - - +
410A MET* 3.8 3.4 - - - +
411A ASP 3.4 0.2 - - - -
412A VAL* 1.3 72.8 - - - +
414A PHE* 1.4 62.3 + - - +
415A GLN 3.2 1.6 - - - -
416A VAL* 3.1 11.9 + - - +
417A LEU* 3.1 23.9 + - - +
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Residues in contact with PHE 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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333A ILE* 3.5 46.2 - - + -
336A ALA* 3.5 10.3 - - + -
337A ALA* 3.4 30.5 - - + -
340A TRP* 3.6 24.0 - - + +
341A LEU* 3.5 18.4 - - + +
356A LEU* 4.2 0.9 - - + -
358A ILE* 3.8 31.0 - - + -
380A LEU* 4.6 6.5 - - + -
381A MET* 4.1 19.1 - - + -
400A ALA* 4.3 4.9 - - + -
410A MET 2.9 19.0 + - - +
413A ALA* 1.4 72.5 - - - +
415A GLN* 1.3 58.6 + - - +
416A VAL 3.4 0.2 - - - -
417A LEU* 3.6 14.0 - - + +
418A ALA* 3.1 21.3 + - - +
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Residues in contact with GLN 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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340A TRP* 3.3 46.4 - - + -
411A ASP* 3.1 18.2 + - - +
412A VAL* 3.4 21.4 + - - +
414A PHE* 1.3 75.5 - - - +
416A VAL* 1.4 65.5 + - + +
418A ALA* 3.6 3.8 + - - +
419A GLN* 3.4 20.4 + - - +
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Residues in contact with VAL 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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412A VAL* 3.3 22.2 + - + +
413A ALA* 3.1 10.6 + - - +
415A GLN* 1.4 77.3 - - + +
417A LEU* 1.4 64.7 + - - +
419A GLN* 3.3 7.7 + - - +
420A LEU* 3.2 38.9 + - + +
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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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341A LEU* 3.9 28.5 - - + -
358A ILE* 5.0 2.2 - - + -
369A LEU* 4.5 12.3 - - + -
370A ILE* 6.3 2.0 - - + -
381A MET* 3.7 31.4 - - + -
398A LEU* 4.2 25.1 - - + -
413A ALA 3.1 13.2 + - - +
414A PHE* 3.6 17.7 - - + +
415A GLN 3.4 0.2 - - - -
416A VAL* 1.4 75.2 - - - +
418A ALA* 1.4 56.2 + - - +
420A LEU* 3.2 10.8 + - + +
421A ILE* 3.0 53.3 + - + +
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Residues in contact with ALA 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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340A TRP* 3.8 32.8 - - + +
341A LEU* 5.5 2.0 - - - +
344A LEU* 3.9 15.3 - - + +
414A PHE 3.1 14.2 + - - +
415A GLN* 3.7 7.4 - - - +
416A VAL 3.4 0.4 - - - -
417A LEU* 1.4 78.2 - - - +
419A GLN* 1.3 55.9 + - - +
421A ILE* 3.6 5.1 + - - +
422A LYS* 3.1 42.9 + - - +
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Residues in contact with GLN 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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415A GLN 3.4 9.8 + - - +
416A VAL* 3.3 10.8 + - - +
418A ALA* 1.3 74.6 - - - +
420A LEU* 1.4 63.3 + - - +
422A LYS* 3.3 13.5 + - + +
423A GLU* 2.8 55.7 + - + +
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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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369A LEU* 3.7 35.4 - - + +
370A ILE* 5.2 7.2 - - - +
416A VAL* 3.2 32.2 + - + +
417A LEU* 3.6 11.4 - - + +
419A GLN* 1.4 75.2 - - + +
421A ILE* 1.4 63.7 + - - +
423A GLU* 3.3 26.8 + - - +
424A SER* 3.3 24.8 + - - -
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Residues in contact with ILE 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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341A LEU* 5.3 6.3 - - + -
344A LEU* 3.7 34.5 - - + +
345A ALA* 5.4 2.2 - - + -
360A VAL* 3.8 38.4 - - + -
363A ILE* 4.1 1.9 - - + +
369A LEU* 4.0 19.7 - - + -
417A LEU* 3.0 44.5 + - + +
418A ALA* 3.7 6.5 - - - +
420A LEU* 1.4 75.0 - - - +
422A LYS* 1.3 60.5 + - - +
423A GLU 3.3 0.2 + - - -
424A SER* 3.4 4.3 + - - -
425A LEU* 3.2 43.4 + - + +
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Residues in contact with LYS 422 (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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340A TRP* 5.4 4.6 + - - -
344A LEU* 4.3 24.8 - - + +
418A ALA* 3.1 31.9 + - - +
419A GLN* 3.4 14.8 - - + +
421A ILE* 1.3 76.2 - - - +
423A GLU* 1.4 59.7 + - + +
425A LEU* 3.7 10.1 + - + +
426A LEU* 3.5 28.8 + - + +
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Residues in contact with GLU 423 (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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419A GLN* 2.8 52.6 + - + +
420A LEU* 3.4 26.6 + - - +
421A ILE 3.3 0.2 - - - -
422A LYS* 1.4 74.4 - - + +
424A SER* 1.4 63.3 + - - +
426A LEU* 3.3 25.9 + - + +
427A VAL* 3.8 7.1 + - - +
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Residues in contact with SER 424 (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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363A ILE* 3.6 26.5 - - - -
368A GLU* 4.0 11.9 + - - -
369A LEU* 3.2 23.6 - - - +
420A LEU 3.3 5.3 + - - -
421A ILE 3.8 3.1 - - - -
423A GLU* 1.4 74.8 - - - +
425A LEU* 1.3 64.3 + - - +
427A VAL* 3.3 29.9 - - - +
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Residues in contact with LEU 425 (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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344A LEU* 4.4 15.5 - - + +
362A GLY* 3.8 24.9 - - - +
363A ILE* 3.8 18.4 - - + -
421A ILE* 3.2 36.1 + - + +
422A LYS* 4.0 8.3 - - + +
423A GLU 3.3 0.4 - - - -
424A SER* 1.3 75.7 - - - +
426A LEU* 1.3 59.5 + - - +
427A VAL 3.4 4.8 + - - +
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Residues in contact with LEU 426 (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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422A LYS* 3.5 16.7 + - + +
423A GLU* 3.3 16.3 + - + +
424A SER 3.2 0.4 - - - -
425A LEU* 1.3 80.6 - - - +
427A VAL* 1.3 59.0 + - + +
428A PRO* 4.0 6.1 - - - +
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU 3.8 5.1 + - - +
424A SER* 3.3 26.7 - - - +
425A LEU 3.4 4.4 - - - +
426A LEU* 1.3 78.6 - - - +
428A PRO* 1.4 77.1 - - + +
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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