Contacts of the helix formed by residues 423 - 443 (chain A) in PDB entry 4YOZ
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 PRO 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A PHE* 3.6 35.4 - - + +
419A CYS* 4.4 5.8 - - + -
421A ARG 3.3 10.7 - - - +
422A ASN* 1.3 88.5 - - - +
424A VAL* 1.3 63.9 + - - +
425A GLU 3.0 3.5 + - - -
426A ASN* 3.0 14.0 + - + +
427A ILE* 2.9 35.5 + - + +
492A LEU* 3.8 34.1 - - + +
493A GLU* 5.4 2.5 - - + -
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO* 4.3 15.3 - - + -
413A ILE* 5.5 4.7 - - + -
416A PHE* 3.5 30.7 - - + -
422A ASN* 2.9 32.4 + - - +
423A PRO* 1.3 79.2 - - - +
425A GLU* 1.3 74.2 + - + +
427A ILE* 3.7 3.6 + - - +
428A MET* 3.2 36.3 + - + +
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASN 4.5 3.3 + - - +
423A PRO 3.2 0.6 - - - -
424A VAL* 1.3 89.4 - - + +
426A ASN* 1.3 67.6 + - - +
428A MET* 3.2 30.7 + - - +
429A LYS* 3.0 41.4 + - - +
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Residues in contact with ASN 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASN 5.3 2.9 + - - -
423A PRO* 3.0 14.7 + - + +
425A GLU* 1.3 79.9 - - - +
427A ILE* 1.3 65.2 + - + +
429A LYS* 3.4 20.3 + - - +
430A ILE* 3.1 32.4 + - + +
493A GLU* 6.2 1.6 - - - +
495A ASP* 5.6 3.8 - - - +
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A PHE* 3.5 31.6 - - + -
423A PRO* 2.9 32.5 + - + +
424A VAL* 3.9 4.3 - - - +
426A ASN* 1.3 76.5 - - + +
428A MET* 1.3 65.4 + - - +
430A ILE* 3.2 11.0 + - - +
431A LEU* 3.0 21.8 + - + +
468A TYR* 3.2 33.0 - - + +
469A TYR* 4.1 15.9 - - + +
472A LEU* 4.2 2.0 - - + -
492A LEU* 4.5 0.7 - - + +
498A HIS* 3.6 37.7 - - + +
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Residues in contact with MET 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO* 5.7 4.5 - - + -
424A VAL* 3.2 23.6 + - + +
425A GLU* 3.2 33.4 - - - +
427A ILE* 1.3 79.7 - - - +
429A LYS* 1.3 57.2 + - + +
431A LEU* 3.3 5.2 + - - +
432A LYS* 2.9 30.0 + - - +
469A TYR* 4.0 19.1 - - - +
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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
----------------------------------------------------------
425A GLU* 3.0 25.9 + - - +
426A ASN* 3.6 22.6 + - - +
427A ILE 3.2 0.2 - - - -
428A MET* 1.3 77.6 - - + +
430A ILE* 1.3 57.0 + - + +
432A LYS* 3.2 10.7 + - + +
433A GLY* 2.8 27.0 + - - -
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Residues in contact with ILE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASN* 3.1 19.8 + - + +
427A ILE* 3.2 8.7 + - + +
429A LYS* 1.3 76.3 - - + +
431A LEU* 1.3 61.8 + - + +
433A GLY* 3.2 1.9 + - - +
434A ILE* 2.8 42.6 + - + +
495A ASP* 3.7 35.0 - - + +
498A HIS* 4.1 26.9 - - + -
499A ARG* 3.8 29.8 - - + +
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Residues in contact with LEU 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 ILE 3.0 17.7 + - - +
428A MET* 3.7 7.0 - - - +
430A ILE* 1.3 82.4 - - + +
432A LYS* 1.3 57.7 + - - +
434A ILE* 3.9 3.4 - - - +
435A GLY* 2.8 27.5 + - - -
461A LEU* 5.2 0.9 - - - +
465A GLU* 3.9 33.4 - - + +
468A TYR* 3.8 26.0 - - + -
469A TYR* 3.4 39.9 - - + +
498A HIS 5.2 0.2 - - - +
502A MET* 3.6 35.8 - - + +
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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
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428A MET 2.9 17.7 + - - +
429A LYS* 3.5 11.4 - - + +
431A LEU* 1.3 75.6 - - - +
433A GLY* 1.3 64.7 + - - +
435A GLY* 3.9 0.6 - - - -
436A GLU* 3.1 29.0 + - + +
465A GLU* 5.6 0.2 - - - -
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Residues in contact with GLY 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 2.8 15.1 + - - -
430A ILE* 3.7 2.9 - - - -
432A LYS* 1.3 77.2 - - - +
434A ILE* 1.3 59.8 + - - +
436A GLU* 3.4 6.5 + - - +
437A THR* 3.1 28.9 + - - -
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Residues in contact with ILE 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 ILE* 2.8 38.6 + - + +
431A LEU 3.9 3.1 - - - +
433A GLY* 1.3 72.2 - - - +
435A GLY* 1.3 59.3 + - - +
437A THR* 3.5 0.6 + - - -
438A PHE* 2.9 28.8 + - - +
499A ARG* 3.9 24.7 - - + +
502A MET* 3.7 42.6 - - + -
506A LEU* 3.9 10.5 - - + -
526A LEU* 3.7 39.9 - - + +
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Residues in contact with GLY 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU 2.8 19.2 + - - -
432A LYS* 3.9 1.3 - - - -
434A ILE* 1.3 78.1 - - - +
436A GLU* 1.3 60.3 + - - +
438A PHE* 3.7 2.0 - - - +
439A CYS* 3.1 30.4 + - - -
461A LEU* 3.5 31.8 - - - +
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Residues in contact with GLU 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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432A LYS* 3.1 22.5 + - + +
433A GLY* 3.8 6.1 - - - +
434A ILE 3.3 0.2 - - - -
435A GLY* 1.3 72.5 - - - +
437A THR* 1.3 62.2 + - - +
439A CYS* 3.3 6.7 + - - +
440A GLN* 3.0 58.2 + - + +
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Residues in contact with THR 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 GLY 3.1 17.0 + - - -
434A ILE* 4.0 3.1 - - - -
436A GLU* 1.3 76.4 - - - +
438A PHE* 1.3 62.2 + - - +
440A GLN* 3.3 14.6 + - - +
441A HIS* 3.1 37.4 + - + +
525A VAL* 3.3 28.9 - - + +
526A LEU* 4.3 8.3 - - + -
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Residues in contact with PHE 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 ILE 2.9 19.0 + - - +
435A GLY* 3.7 4.5 - - - +
437A THR* 1.3 77.1 - - - +
439A CYS* 1.3 67.9 + - - +
441A HIS* 3.9 1.4 - - - +
442A TYR* 2.9 55.6 + + - +
457A ALA* 3.3 33.2 - - + -
460A ARG* 4.0 17.7 - - + -
461A LEU* 4.3 13.2 - - + -
506A LEU* 4.3 23.1 - - + -
510A LEU* 4.5 12.6 - - + -
521A TRP* 3.8 28.2 - + - -
522A ILE* 4.0 12.1 - - + -
525A VAL* 4.3 8.5 - - - -
526A LEU* 4.5 4.4 - - + +
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Residues in contact with CYS 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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435A GLY 3.1 22.3 + - - +
436A GLU* 3.7 6.3 - - - +
438A PHE* 1.3 83.2 - - - +
440A GLN* 1.3 54.1 + - + +
442A TYR* 4.2 5.4 - - - -
443A THR* 2.7 39.4 + - - +
454A ILE* 3.7 27.6 - - + -
457A ALA* 4.0 14.1 - - - -
458A VAL* 4.4 11.2 - - - -
461A LEU* 4.5 9.6 - - - -
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Residues in contact with GLN 440 (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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436A GLU* 3.0 46.0 + - + +
437A THR* 3.6 19.1 + - - +
438A PHE 3.3 0.2 - - - -
439A CYS* 1.3 77.1 - - + +
441A HIS* 1.3 64.4 + - + +
443A THR* 3.5 3.9 + - - -
444A GLN* 3.2 46.4 + - - +
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Residues in contact with HIS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A THR* 3.1 34.0 + - + +
438A PHE 4.0 0.7 - - - +
440A GLN* 1.3 82.7 - - + +
442A TYR* 1.3 65.6 + - - +
444A GLN* 3.1 21.8 - - - +
446A THR* 5.7 8.3 - - - +
449A GLN* 6.1 0.9 - - - +
517A ARG* 5.1 0.9 + - - -
521A TRP* 4.0 10.8 + - + +
524A GLU 5.8 0.2 - - - -
525A VAL* 3.6 51.8 + - + +
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Residues in contact with TYR 442 (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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438A PHE* 2.9 45.1 + + + +
439A CYS 3.8 3.4 - - - +
441A HIS* 1.3 79.1 - - - +
443A THR* 1.3 59.3 + - + +
444A GLN 3.3 0.9 + - - -
451A GLY* 3.6 1.6 - - - -
452A SER* 3.1 41.4 + - - -
453A HIS 3.5 14.8 - - - -
456A PHE* 3.4 19.3 - - - +
457A ALA* 3.3 30.7 - - + -
460A ARG* 4.4 19.1 + - + +
510A LEU* 4.7 6.3 - - + -
515A SER* 5.7 0.2 - - - -
517A ARG* 3.0 60.1 + - - +
521A TRP* 4.2 3.3 - - + -
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Residues in contact with THR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A CYS 2.7 23.2 + - - +
440A GLN* 3.5 7.6 + - - -
442A TYR* 1.3 80.4 - - + +
444A GLN* 1.3 63.9 + - - +
451A GLY* 4.1 8.4 - - - -
452A SER 3.1 23.4 + - - +
453A HIS 4.1 0.2 - - - -
454A ILE* 3.7 38.8 - - + +
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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
------------------------------------------------------------
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