Contacts of the helix formed by residues 575 - 592 (chain B) in PDB entry 4DN5
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 ALA 575 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B HIS* 3.5 48.4 + - + -
512B LEU* 4.0 10.5 - - - -
541B LEU* 3.9 18.6 - - + +
574B ASP* 1.3 77.9 - - - +
576B LYS* 1.3 64.0 + - + +
577B VAL 3.2 3.7 + - - -
578B ASP* 3.6 7.3 + - - +
579B VAL* 4.2 4.2 + - - +
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Residues in contact with LYS 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLU* 4.4 0.2 - - - +
574B ASP* 3.0 30.7 + - - +
575B ALA* 1.3 79.9 - - + +
577B VAL* 1.3 63.7 + - - +
578B ASP 3.3 0.2 - - - -
579B VAL* 3.0 24.4 - - + +
580B TRP 3.5 3.3 + - - -
638B PRO* 3.1 28.2 + - + +
639B ILE* 4.4 8.3 + - - +
641B ARG* 3.2 48.5 + - - +
642B VAL 3.9 10.1 - - - +
643B SER* 4.4 20.0 - - - +
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Residues in contact with VAL 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B LEU* 4.2 15.5 - - + -
514B GLY* 5.5 7.0 - - - +
557B PRO* 6.1 4.9 - - + -
562B HIS 5.7 0.2 - - - +
563B MET* 6.2 0.2 - - - -
564B ALA* 4.4 9.5 - - + +
566B GLU* 4.1 12.8 - - - +
567B VAL* 3.8 32.5 - - + -
573B CYS* 4.2 14.1 - - + -
574B ASP 3.3 17.5 - - - +
576B LYS* 1.3 78.1 - - - +
578B ASP* 1.3 68.2 + - - +
580B TRP* 3.4 6.4 + - - +
581B SER* 3.3 26.2 + - - +
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Residues in contact with ASP 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 3.8 10.5 - - + +
506B LEU* 5.6 0.2 - - - +
507B HIS* 2.8 36.9 + - + +
512B LEU* 3.4 12.9 - - - +
513B HIS* 2.9 31.9 + - - +
514B GLY* 3.3 21.8 + - - -
516B VAL* 3.5 22.2 - - + +
575B ALA 3.6 1.2 + - - +
576B LYS 3.3 0.8 - - - -
577B VAL* 1.3 80.2 - - - +
579B VAL* 1.3 58.2 + - - +
581B SER 3.4 0.5 + - - -
582B SER* 2.9 29.1 + - - -
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Residues in contact with VAL 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B LEU* 4.4 10.1 - - + -
503B LEU* 5.2 1.6 - - + -
507B HIS* 5.0 2.2 - - + -
575B ALA 4.2 5.8 + - - +
576B LYS* 3.0 30.0 - - + +
578B ASP* 1.3 73.0 - - - +
580B TRP* 1.3 63.0 + - - +
582B SER* 2.6 21.2 + - - -
583B CYS* 3.3 15.2 + - - -
633B GLY* 4.2 3.2 - - - +
641B ARG* 3.6 12.1 - - + -
642B VAL 3.3 19.7 - - - +
643B SER* 3.8 4.0 - - - +
644B ALA* 3.6 40.2 - - + +
647B LEU* 4.3 10.1 - - + +
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Residues in contact with TRP 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B THR 4.9 0.8 + - - -
562B HIS 3.3 20.6 - - - -
563B MET 3.1 20.0 + - - -
564B ALA* 3.8 14.1 - - + -
565B PRO* 3.7 29.8 - - + -
576B LYS 4.1 1.1 - - - +
577B VAL 3.4 8.9 + - - +
578B ASP 3.3 0.2 - - - -
579B VAL* 1.3 82.1 - - - +
581B SER* 1.3 56.6 + - - +
583B CYS* 2.9 20.8 + - - +
584B CYS* 3.0 26.4 + - - -
596B TRP* 4.1 15.7 - + - -
608B ILE* 4.5 0.9 - - + -
613B PRO* 4.7 3.6 - - + -
614B PRO* 3.7 27.4 - - + -
633B GLY 3.6 9.4 + - - -
634B LEU* 3.2 50.4 - - + +
636B LYS* 4.4 6.1 - - + -
641B ARG* 3.7 26.5 - - - +
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Residues in contact with SER 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B GLY 5.7 1.2 + - - -
515B ASP* 6.0 0.5 - - - -
516B VAL* 3.3 38.6 + - - +
562B HIS* 2.7 44.9 + - - +
577B VAL* 3.3 16.2 + - - +
578B ASP 3.4 1.3 + - - -
580B TRP* 1.3 78.0 - - - +
582B SER* 1.3 58.1 + - - +
584B CYS* 3.2 2.0 + - - -
585B MET* 2.9 24.6 + - - +
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Residues in contact with SER 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LEU* 3.8 27.1 - - - +
500B LEU* 4.2 6.5 - - - +
503B LEU* 4.3 12.1 - - - -
516B VAL* 4.1 14.3 - - - +
578B ASP 2.9 13.4 + - - -
579B VAL* 2.6 28.4 + - - -
581B SER* 1.3 76.2 - - - +
583B CYS* 1.3 52.0 + - - +
585B MET* 3.2 13.0 - - - +
586B MET* 2.7 31.7 + - - +
647B LEU* 4.3 3.6 - - - +
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Residues in contact with CYS 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LEU* 5.3 4.9 - - - -
579B VAL 3.7 11.0 - - - +
580B TRP 2.9 9.8 + - - +
582B SER* 1.3 79.3 + - - +
584B CYS* 1.3 60.2 + - - +
586B MET* 3.3 8.6 - - - +
587B LEU* 2.9 33.5 + - - +
629B ALA 4.3 0.7 - - - -
630B ILE* 3.8 33.9 - - + +
633B GLY* 3.9 13.5 - - - -
634B LEU* 3.9 19.5 - - + -
647B LEU* 4.1 15.5 - - - -
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Residues in contact with CYS 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B THR 3.9 14.4 - - - -
562B HIS* 3.6 20.2 - - + +
580B TRP* 3.0 48.9 + - - -
581B SER 3.4 8.3 - - - +
583B CYS* 1.3 74.1 - - - +
585B MET* 1.3 60.1 + - - +
587B LEU* 3.2 7.4 + - - +
588B HIS* 2.8 27.2 + - - +
595B PRO* 3.6 26.2 - - + +
596B TRP* 5.2 1.3 - - - -
614B PRO* 5.5 0.9 - - - -
634B LEU* 4.4 6.1 - - - -
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Residues in contact with MET 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LEU* 4.3 5.2 - - + -
495B TYR 5.2 0.2 - - - +
496B LEU* 4.4 10.8 - - + -
499B ALA* 4.1 26.0 - - + -
516B VAL* 4.7 5.4 - - + -
517B LYS* 3.3 31.0 - - - +
518B ALA* 3.4 24.5 - - + +
521B VAL* 3.8 12.1 - - + -
532B LEU* 6.2 0.4 - - + -
562B HIS* 3.6 10.9 + - - +
581B SER 2.9 13.4 + - - +
582B SER* 3.2 22.9 - - - +
584B CYS* 1.3 73.2 - - - +
586B MET* 1.3 54.2 + - - +
588B HIS* 3.0 7.1 + - - +
589B MET* 2.8 55.9 + - + +
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Residues in contact with MET 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B GLU 5.5 0.2 - - - +
492B ALA* 3.4 39.7 - - + +
493B LEU* 4.0 11.7 - - + +
496B LEU* 3.4 33.0 - - + -
582B SER 2.7 18.1 + - - +
583B CYS* 3.3 15.7 - - - +
585B MET* 1.3 72.4 - - - +
587B LEU* 1.3 61.4 + - - +
589B MET* 3.4 7.7 + - + +
590B LEU* 3.3 34.6 + - + +
626B THR* 5.4 5.4 - - + -
630B ILE* 3.8 33.7 - - + -
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B CYS 2.9 19.8 + - - +
584B CYS* 3.2 9.6 + - - +
586B MET* 1.3 76.3 - - - +
588B HIS* 1.3 56.7 + - - +
590B LEU* 4.8 2.9 - - + +
591B ASN* 3.0 42.4 + - - +
593B CYS 4.1 2.0 - - - +
595B PRO* 3.9 30.3 - - + -
614B PRO* 4.0 15.7 - - + +
617B GLU* 4.0 9.2 - - + +
618B ILE* 3.8 42.6 - - + +
619B PRO* 5.3 1.6 - - + -
630B ILE* 4.3 9.6 - - + -
634B LEU* 3.8 20.4 - - + -
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Residues in contact with HIS 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LYS* 4.9 3.6 + - - -
478B GLY* 4.7 3.4 - - - -
481B VAL* 3.4 31.2 - - + +
518B ALA* 3.6 25.4 + - + +
519B ASP* 5.9 1.3 - - - -
562B HIS* 5.2 3.2 - - - +
584B CYS 2.8 14.1 + - - +
585B MET* 3.4 11.4 - - - +
587B LEU* 1.3 74.7 - - - +
589B MET* 1.3 59.6 + - - +
592B GLY* 3.0 30.7 + - - -
593B CYS* 3.3 36.3 + - - +
594B HIS* 3.7 32.1 + + + +
595B PRO* 4.7 0.4 - - + +
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Residues in contact with MET 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LEU* 3.6 25.4 - - + -
481B VAL* 4.0 15.4 - - + +
486B CYS* 3.5 4.5 - - - +
487B LEU* 2.7 49.2 + - + +
492B ALA* 3.3 44.2 - - + +
495B TYR* 4.3 2.9 - - - -
496B LEU* 4.4 7.6 - - + +
518B ALA* 5.5 1.8 - - + -
585B MET* 2.8 49.5 + - + +
586B MET* 3.4 21.3 + - + +
588B HIS* 1.3 74.6 - - - +
590B LEU* 1.3 54.5 + - - +
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Residues in contact with LEU 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B CYS* 3.2 23.7 - - - +
487B LEU 3.7 19.1 - - - +
489B GLU* 4.3 21.3 - - + +
492B ALA* 3.8 18.2 - - + -
586B MET* 3.3 28.5 + - + +
587B LEU* 4.2 4.9 - - + +
589B MET* 1.3 76.4 - - - +
591B ASN* 1.3 61.6 + - - +
592B GLY 3.3 0.4 - - - -
619B PRO* 4.0 33.4 - - + +
622B CYS* 4.5 10.8 - - - -
626B THR* 5.1 4.7 - - + -
630B ILE* 4.3 19.5 - - + -
673B ARG 5.5 0.2 + - - -
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Residues in contact with ASN 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B CYS* 4.1 1.6 - - - -
587B LEU* 3.0 31.8 + - - +
590B LEU* 1.3 77.2 - - - +
592B GLY* 1.3 58.6 + - - +
593B CYS* 3.1 23.2 + - - +
617B GLU* 2.8 34.4 + - - +
619B PRO* 4.0 14.8 - - - +
672B PRO* 3.4 1.9 - - - +
673B ARG* 2.8 67.0 + - + +
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Residues in contact with GLY 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A LYS* 5.7 0.9 + - - -
481B VAL* 5.4 3.1 - - - +
485B GLY 3.3 26.5 - - - +
486B CYS* 3.7 4.0 - - - +
588B HIS* 3.0 27.1 + - - -
590B LEU 3.3 2.8 + - - -
591B ASN* 1.3 76.5 - - - +
593B CYS* 1.3 59.4 + - - +
672B PRO* 3.9 8.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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