Contacts of the helix formed by residues 412 - 434 (chain A) in PDB entry 1GUX
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 LYS 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A PRO* 5.5 2.9 - - + -
401A ILE* 4.6 32.1 - - + +
404A PHE* 3.9 26.9 - - + +
405A ASN* 5.4 4.9 - - - +
410A ASN* 3.0 20.9 + - - +
411A PRO* 1.3 79.4 - - - +
413A GLU* 1.3 57.9 + - - +
415A ILE* 3.7 2.6 - - - +
416A LEU* 3.0 56.7 + - + +
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Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASN* 4.6 7.3 + - - +
411A PRO 3.4 0.4 - - - -
412A LYS* 1.3 77.0 - - - +
414A SER* 1.3 65.6 + - - +
416A LEU* 3.9 7.9 - - - +
417A LYS* 2.9 30.1 + - - +
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASN 5.0 0.3 + - - -
411A PRO* 2.9 25.0 + - - +
413A GLU* 1.3 81.6 - - - +
415A ILE* 1.3 61.2 + - - +
417A LYS* 3.7 5.9 - - - +
418A ARG* 2.8 42.1 + - - +
478A ASN* 5.1 2.9 + - - -
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A PHE* 3.5 38.4 - - + -
411A PRO* 2.9 37.4 + - + +
412A LYS* 3.7 4.9 - - - +
414A SER* 1.3 77.9 + - - +
416A LEU* 1.3 57.6 + - + +
418A ARG* 3.3 15.0 + - - +
419A VAL* 3.0 29.3 + - - +
453A TYR* 4.0 12.5 + - + +
454A TYR* 4.0 28.9 - - + +
457A MET* 5.1 0.4 - - + -
477A LEU* 5.1 0.4 - - + -
483A HIS* 3.6 33.4 - - + +
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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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395A GLN* 3.2 41.1 + - - +
396A PRO* 3.7 22.0 - - + -
404A PHE* 5.9 0.4 - - + -
412A LYS* 3.0 51.5 + - + +
413A GLU* 3.9 6.7 - - - +
415A ILE* 1.3 74.3 - - + +
417A LYS* 1.3 60.6 - - - +
419A VAL* 3.3 6.9 + - - +
420A LYS* 3.0 28.2 + - - +
454A TYR* 3.7 5.8 - - - +
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Residues in contact with LYS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLU 2.9 20.0 + - - +
414A SER* 3.7 6.7 - - - +
416A LEU* 1.3 74.7 - - - +
418A ARG* 1.3 54.3 + - - +
420A LYS* 3.1 8.3 + - + +
421A ASP* 2.8 66.6 + - - +
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Residues in contact with ARG 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 SER* 2.8 27.3 + - - +
415A ILE* 3.6 26.6 + - - +
417A LYS* 1.3 75.9 - - - +
419A VAL* 1.3 67.5 + - + +
421A ASP* 3.1 6.5 + - - -
422A ILE* 2.8 44.3 + - + +
453A TYR* 4.5 5.3 + - + -
480A ASN* 3.8 28.9 + - - +
483A HIS* 3.2 51.4 - - - +
484A MET* 3.6 30.3 - - + +
487A LEU* 5.1 6.3 - - + -
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Residues in contact with VAL 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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394A ASP 5.5 0.7 - - - +
395A GLN* 4.8 7.2 - - - +
415A ILE 3.0 16.3 + - - +
416A LEU* 3.5 9.0 - - - +
418A ARG* 1.3 76.2 - - + +
420A LYS* 1.3 63.5 + - - +
422A ILE* 4.9 0.2 - - - -
423A GLY* 3.0 14.2 + - - -
446A TYR* 2.7 28.1 + - + -
450A VAL* 3.8 33.2 - - + -
453A TYR* 4.1 17.3 - - + -
454A TYR* 3.3 30.1 - - + +
487A LEU* 5.5 4.9 - - + -
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Residues in contact with LYS 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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416A LEU 3.0 14.0 + - - +
417A LYS* 3.1 11.0 + - + +
419A VAL* 1.3 84.7 - - - +
421A ASP* 1.3 63.1 + - - +
423A GLY* 3.6 9.5 - - - -
424A TYR* 3.1 66.6 + - + +
427A LYS* 2.9 31.7 - - - +
446A TYR* 4.8 1.9 - - - -
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Residues in contact with ASP 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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417A LYS* 2.8 61.7 + - - +
418A ARG* 3.8 5.7 - - - +
420A LYS* 1.3 74.0 - - - +
422A ILE* 1.3 67.2 + - + +
424A TYR* 3.2 18.4 + - - +
425A ILE* 3.1 30.9 + - + +
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Residues in contact with ILE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ARG* 2.8 33.7 + - + +
421A ASP* 1.3 75.9 - - + +
423A GLY* 1.3 56.6 + - - +
425A ILE* 3.1 21.6 + - + -
426A PHE* 2.7 34.3 + - + +
446A TYR* 3.5 16.2 - - + +
484A MET* 4.0 26.5 - - + -
487A LEU* 3.8 16.6 - - + -
521A LEU* 3.4 39.0 - - + +
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Residues in contact with GLY 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 VAL 3.0 10.1 + - - -
420A LYS* 3.6 14.6 - - - -
421A ASP 3.2 0.2 - - - -
422A ILE* 1.3 74.0 - - - +
424A TYR* 1.3 63.8 + - - +
427A LYS* 3.0 34.5 + - - +
446A TYR* 3.2 32.9 + - - -
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Residues in contact with TYR 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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420A LYS* 3.1 56.6 + - + +
421A ASP* 3.4 16.4 - - - +
422A ILE 3.2 0.4 - - - -
423A GLY* 1.3 75.1 - - - +
425A ILE* 1.3 63.5 + - + +
427A LYS* 4.1 7.9 - - + +
428A GLU* 3.2 29.7 + - - +
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASP* 3.1 20.6 + - + +
422A ILE* 3.1 27.8 + - + +
424A TYR* 1.3 79.0 - - + +
426A PHE* 1.3 58.1 + - - +
428A GLU* 3.1 14.2 - - - +
429A LYS* 2.9 55.6 + - + +
520A VAL* 3.6 24.9 - - + +
522A ASN* 5.7 7.6 - - - +
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ILE* 2.7 23.7 + - + +
423A GLY 3.9 0.7 - - - +
425A ILE* 1.3 73.6 - - - +
427A LYS* 1.3 56.1 + - - +
429A LYS* 3.2 1.6 + - - +
430A PHE* 2.7 59.8 + + + +
442A GLY* 3.5 21.1 - - - -
445A ARG* 4.4 1.6 - - + -
446A TYR* 3.8 36.6 - + + -
491A LEU* 4.4 10.8 - - + -
495A MET* 3.1 35.4 - - + -
516A TRP* 3.6 19.0 - + - -
517A ILE* 4.1 21.3 - - + -
520A VAL* 4.0 17.9 - - + +
521A LEU* 5.1 0.7 - - + -
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Residues in contact with LYS 427 (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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420A LYS* 2.9 31.9 - - - +
423A GLY* 3.0 22.4 + - - +
424A TYR* 4.1 7.9 - - + +
426A PHE* 1.3 77.0 - - + +
428A GLU* 1.3 67.8 + - - +
430A PHE* 3.9 4.0 - - - +
431A ALA* 3.0 26.5 + - - +
438A CYS* 4.7 9.8 - - + -
439A VAL 5.1 5.7 + - - +
442A GLY* 4.3 5.2 - - - +
443A SER* 3.2 50.4 + - - +
446A TYR* 4.1 16.3 - - - -
447A LYS* 5.8 4.4 - - - +
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Residues in contact with GLU 428 (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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424A TYR* 3.2 18.3 + - - +
425A ILE* 3.1 24.0 - - - +
427A LYS* 1.3 79.2 - - - +
429A LYS* 1.3 94.7 + - - +
431A ALA* 3.4 2.4 + - - +
432A LYS* 3.1 40.5 + - - +
438A CYS* 4.2 18.7 - - - -
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Residues in contact with LYS 429 (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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425A ILE* 2.9 37.5 + - + +
426A PHE 3.8 2.7 - - - +
428A GLU* 1.3 106.5 + - - +
430A PHE* 1.3 64.3 + - - +
432A LYS* 2.7 40.8 + - + +
433A ALA* 3.0 24.1 + - - +
516A TRP* 4.2 7.2 + - + +
520A VAL* 4.3 27.4 - - + -
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Residues in contact with PHE 430 (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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426A PHE* 2.7 47.5 + + + +
427A LYS* 3.9 4.0 - - - +
429A LYS* 1.3 72.5 - - - +
431A ALA* 1.3 55.1 + - - +
433A ALA* 3.2 4.7 + - + +
434A VAL* 2.8 59.1 + - + +
439A VAL* 3.9 16.6 - - + -
441A ILE* 3.9 19.3 - - + -
442A GLY* 3.3 30.7 - - - -
445A ARG* 4.0 33.0 - - - -
495A MET* 4.6 2.5 - - - -
516A TRP* 4.1 16.1 - + + -
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Residues in contact with ALA 431 (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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427A LYS 3.0 14.0 + - - +
428A GLU 3.7 4.0 - - - +
430A PHE* 1.3 78.9 - - - +
432A LYS* 1.3 59.9 + - + +
435A GLY* 2.4 43.7 + - - +
437A GLY* 5.0 0.8 + - - -
438A CYS* 3.2 44.9 - - - +
439A VAL* 3.8 5.4 - - - +
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Residues in contact with LYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 3.1 29.4 + - - +
429A LYS* 2.7 54.0 - - + +
431A ALA* 1.3 78.4 - - - +
433A ALA* 1.3 68.5 + - - +
434A VAL 4.4 0.2 - - - -
435A GLY* 3.9 3.1 + - - -
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Residues in contact with ALA 433 (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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429A LYS 3.0 11.0 + - - +
430A PHE* 3.4 11.9 - - + +
432A LYS* 1.3 85.9 - - - +
434A VAL* 1.3 67.5 + - + +
516A TRP* 4.7 16.6 - - + +
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Residues in contact with VAL 434 (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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430A PHE* 2.8 50.6 + - + +
433A ALA* 1.3 79.9 - - + +
435A GLY* 1.3 60.8 + - - +
439A VAL* 5.5 5.4 - - + -
441A ILE* 6.3 3.1 - - + -
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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
------------------------------------------------------------
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