Contacts of the helix formed by residues 420 - 439 (chain A) in PDB entry 5DKG
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 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A VAL 3.3 1.2 + - - -
419A GLU* 1.3 71.8 - - - +
421A MET* 1.3 59.4 + - - +
423A GLU* 3.1 27.7 + - - +
424A ILE* 3.2 23.9 + - - +
520A LYS* 5.2 0.7 - - - -
524A HIS* 3.8 25.4 + - - -
601A 5C7 3.9 7.9 - - - +
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Residues in contact with MET 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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342A MET* 3.5 32.3 - - + -
343A MET* 3.8 15.7 - - - -
346A LEU* 4.2 4.9 - - + -
415A GLY* 3.3 32.5 - - - +
418A VAL* 3.2 28.1 + - + +
419A GLU 3.3 1.8 + - - -
420A GLY* 1.3 75.8 - - - +
422A VAL* 1.3 56.2 + - - +
424A ILE* 3.1 7.2 - - - +
425A PHE* 2.7 68.6 + - + +
601A 5C7 3.6 25.3 - - + +
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Residues in contact with VAL 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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412A ARG* 3.4 42.8 - - + +
415A GLY 3.8 2.2 - - - +
416A LYS* 3.7 45.8 - - + +
418A VAL 4.4 1.7 + - - +
421A MET* 1.3 76.0 - - - +
423A GLU* 1.3 67.9 + - - +
425A PHE* 3.3 6.6 + - - +
426A ASP* 2.9 31.9 + - - +
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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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420A GLY* 3.1 32.9 + - - +
422A VAL* 1.3 85.7 + - + +
424A ILE* 1.3 60.8 + - - +
426A ASP* 3.4 7.4 + - - +
427A MET* 3.3 28.8 + - + +
520A LYS* 3.9 24.0 - - - +
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Residues in contact with ILE 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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388A MET* 4.1 16.8 - - + -
420A GLY 3.2 12.9 + - - +
421A MET 3.1 11.7 - - - +
423A GLU* 1.3 77.4 - - - +
425A PHE* 1.3 76.5 + - + +
427A MET* 3.5 22.1 + - + +
428A LEU* 3.1 34.0 + - + +
517A MET* 3.4 29.8 - - + +
520A LYS* 4.1 7.2 - - + -
521A GLY* 3.7 19.3 - - - +
601A 5C7 3.7 36.1 - - + -
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Residues in contact with PHE 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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342A MET* 5.4 0.2 - - - -
346A LEU* 4.9 0.9 - - + -
402A LEU* 3.5 17.3 - - + -
404A PHE* 3.7 36.1 - + - -
410A LEU* 4.1 18.2 - - + -
411A ASP 3.5 26.9 - - - -
412A ARG* 3.9 19.1 - - + -
414A GLN 4.9 1.3 - - - -
415A GLY* 4.3 7.4 - - - -
421A MET* 2.7 55.1 + - + +
422A VAL* 3.6 6.5 - - - +
424A ILE* 1.3 87.1 - - + +
426A ASP* 1.3 57.8 + - - +
428A LEU* 3.2 4.7 + - + +
429A LEU* 2.8 36.4 + - + +
601A 5C7 4.7 3.6 - + + -
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Residues in contact with ASP 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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412A ARG* 2.8 52.1 + - - +
422A VAL* 2.9 23.0 + - - +
423A GLU* 3.8 8.2 - - - +
424A ILE 3.4 0.2 - - - -
425A PHE* 1.3 76.2 - - - +
427A MET* 1.3 58.1 + - + +
429A LEU* 3.4 8.4 + - - +
430A ALA* 2.8 29.8 + - - +
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Residues in contact with MET 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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423A GLU* 3.3 21.4 + - + +
424A ILE* 3.6 25.8 - - + +
425A PHE 3.2 0.2 - - - -
426A ASP* 1.3 75.4 - - + +
428A LEU* 1.3 56.8 + - - +
430A ALA* 3.3 5.3 + - - +
431A THR* 2.7 36.6 + - - -
513A HIS* 3.5 21.3 + - + +
516A HIS* 4.1 18.6 - - - -
517A MET* 3.5 25.1 - - + -
520A LYS* 3.5 30.5 - - + -
459B TYR 4.9 4.9 - - - +
460B THR* 5.4 9.2 - - - -
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Residues in contact with LEU 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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388A MET* 3.8 26.9 - - + +
391A LEU* 3.9 22.0 - - + -
392A VAL* 3.7 18.2 - - + +
402A LEU* 3.9 24.2 - - + -
424A ILE* 3.1 25.2 + - + +
425A PHE* 3.5 7.2 - - + +
427A MET* 1.3 77.2 - - - +
429A LEU* 1.3 58.3 + - - +
431A THR* 3.1 4.7 + - - -
432A SER* 2.9 28.6 + - - -
517A MET* 3.5 24.5 - - + -
601A 5C7 3.9 18.6 - - + -
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Residues in contact with LEU 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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400A GLY* 3.5 42.4 - - - +
401A LYS* 3.5 22.0 - - - +
402A LEU* 3.7 14.4 - - + -
410A LEU 5.3 0.2 - - - +
411A ASP 5.2 0.4 - - - -
412A ARG* 4.1 31.0 - - + +
425A PHE* 2.8 24.8 + - + +
426A ASP* 3.6 9.4 - - - +
428A LEU* 1.3 76.3 - - - +
430A ALA* 1.3 56.6 + - - +
432A SER* 3.2 7.0 + - - -
433A SER* 2.9 30.2 + - - -
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Residues in contact with ALA 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 ASP 2.8 17.2 + - - +
427A MET* 3.6 6.1 - - - +
429A LEU* 1.3 75.9 - - - +
431A THR* 1.3 57.5 + - - +
433A SER* 3.5 7.0 + - - -
434A ARG* 3.0 27.9 + - - +
459B TYR* 3.9 30.9 - - + +
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Residues in contact with THR 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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392A VAL* 3.8 22.2 - - + -
427A MET 2.7 19.5 + - - -
428A LEU 3.1 8.2 + - - -
430A ALA* 1.3 74.3 - - - +
432A SER* 1.3 60.1 + - - +
434A ARG* 3.2 7.7 + - - +
435A PHE* 2.9 34.0 + - + +
510A ILE* 4.0 26.2 - - + -
513A HIS* 3.1 22.1 + - + -
514A ILE* 4.6 5.6 - - + -
517A MET* 3.4 12.3 - - + +
459B TYR* 5.6 2.2 - - - -
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Residues in contact with SER 432 (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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392A VAL* 3.3 23.7 + - - +
395A SER* 3.3 37.7 + - - -
396A MET* 3.4 5.8 + - - +
398A HIS 5.2 0.2 + - - -
399A PRO* 6.1 0.2 - - - +
401A LYS 5.6 0.2 - - - -
402A LEU* 5.3 1.6 - - - -
428A LEU 2.9 12.4 + - - -
429A LEU* 3.6 13.2 - - - -
431A THR* 1.3 77.1 - - - +
433A SER* 1.3 57.3 + - - +
435A PHE* 3.3 4.2 + - - +
436A ARG* 2.9 28.9 + - - +
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Residues in contact with SER 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 LEU 2.9 17.0 + - - -
430A ALA* 3.8 7.6 - - - -
432A SER* 1.3 75.4 - - - +
434A ARG* 1.3 58.2 + - - +
436A ARG* 3.2 10.7 + - - +
437A MET* 2.9 42.1 + - - +
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Residues in contact with ARG 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 ALA 3.0 14.8 + - - +
431A THR* 3.3 13.0 - - - +
433A SER* 1.3 73.3 - - - +
435A PHE* 1.3 64.1 + - - +
437A MET* 3.2 13.7 + - - +
438A MET* 3.1 55.8 + - - +
506A GLN* 4.0 25.7 + - - +
510A ILE* 3.6 23.3 - - + +
459B TYR* 3.6 35.8 + - + -
476B HIS* 3.6 39.3 + - - +
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Residues in contact with PHE 435 (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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389A ILE* 4.1 24.9 - - + -
392A VAL* 3.4 30.1 - - + -
393A TRP* 4.8 5.2 - - - -
396A MET* 3.7 17.8 - - + +
431A THR* 2.9 13.3 + - + +
432A SER 3.6 7.4 - - - +
434A ARG* 1.3 75.2 - - - +
436A ARG* 1.3 61.8 + - - +
438A MET* 3.3 4.5 + - - -
439A ASN 3.1 17.8 + - - -
440A LEU* 3.1 45.5 + - + -
445A PHE* 5.5 0.2 - + - -
448A LEU* 4.3 19.5 - - + -
507A LEU* 4.7 4.3 - - + -
510A ILE* 3.7 44.9 - - + -
511A LEU* 5.7 0.4 - - + -
514A ILE* 4.6 2.5 - - + -
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Residues in contact with ARG 436 (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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396A MET* 3.2 41.8 + - + +
397A GLU* 5.2 7.5 + - - +
399A PRO* 3.9 30.1 - - - +
432A SER 2.9 16.6 + - - +
433A SER* 3.5 11.8 + - - +
434A ARG 3.1 0.4 - - - -
435A PHE* 1.3 78.1 - - - +
437A MET* 1.3 90.3 + - - +
439A ASN* 3.4 17.2 + - - +
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Residues in contact with MET 437 (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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433A SER* 2.9 27.9 + - - +
434A ARG* 3.2 14.1 + - - +
436A ARG* 1.3 112.0 - - - +
438A MET* 1.3 61.7 + - + +
439A ASN* 3.2 11.2 + - - -
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Residues in contact with MET 438 (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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434A ARG* 3.1 43.1 + - - +
435A PHE* 3.9 6.5 - - - +
436A ARG 3.3 0.2 - - - -
437A MET* 1.3 75.5 - - - +
439A ASN* 1.3 66.8 + - - +
440A LEU* 4.5 3.4 - - + +
503A ARG* 2.8 47.8 + - + +
506A GLN* 3.3 35.0 - - + +
507A LEU* 3.6 26.7 - - + -
510A ILE* 3.7 30.1 - - - -
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Residues in contact with ASN 439 (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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396A MET* 4.9 4.0 - - - -
435A PHE 3.1 4.8 + - - -
436A ARG 3.4 10.7 + - - +
437A MET 3.2 16.4 + - - -
438A MET* 1.3 79.0 + - - +
440A LEU* 1.3 61.8 + - - +
441A GLN* 2.9 27.8 + - - +
503A ARG* 3.3 7.8 + - - -
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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
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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