Contacts of the helix formed by residues 575 - 592 (chain B) in PDB entry 4YHF
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 575 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B LEU* 3.5 16.6 - - - +
567B GLU* 5.1 2.3 + - - -
573B LYS 3.8 4.4 + - - -
574B PHE* 1.3 77.9 - - - +
576B SER* 1.3 62.5 + - - +
577B LYS* 3.0 25.0 + - - +
578B SER* 2.6 23.1 + - - -
579B ASP* 3.4 5.5 + - - +
638B ALA* 5.2 1.4 - - - +
719B EDO 3.2 24.2 - - - -
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Residues in contact with SER 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B GLU* 4.5 25.9 + - - -
518B LEU* 3.4 14.4 - - - +
575B SER* 1.3 75.7 - - - +
577B LYS* 1.3 71.6 + - - +
579B ASP* 3.2 9.4 + - - +
580B ILE* 3.0 28.6 + - - +
644B PHE* 4.2 3.0 - - - -
719B EDO 3.3 30.4 + - - -
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Residues in contact with LYS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B GLU* 5.8 0.2 + - - -
567B GLU* 4.8 0.2 - - - +
575B SER* 3.0 12.0 - - - +
576B SER* 1.3 88.6 + - - +
578B SER* 1.3 59.7 + - - +
579B ASP 3.3 0.2 - - - -
580B ILE* 3.5 8.7 - - + +
581B TRP 3.2 16.3 + - - -
638B ALA* 3.4 44.9 - - + +
639B ASP* 4.7 9.5 + - - +
641B ARG* 3.0 45.7 + - + +
642B PRO 3.3 20.6 + - - +
643B THR* 3.8 17.4 - - - +
719B EDO 5.5 3.1 - - - -
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Residues in contact with SER 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PRO* 3.8 14.1 - - - +
567B GLU* 4.6 2.2 + - - -
568B VAL* 3.6 29.2 - - - -
573B LYS 4.5 2.0 - - - -
574B PHE* 3.7 6.9 - - - -
575B SER* 2.6 36.0 + - - -
577B LYS* 1.3 76.1 - - - +
579B ASP* 1.3 65.3 + - - +
580B ILE 3.3 0.2 - - - -
581B TRP* 3.5 3.1 + - - +
582B ALA* 3.2 16.8 + - - +
641B ARG* 4.2 0.2 - - - +
717B EDO 3.6 23.4 + - - -
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Residues in contact with ASP 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B MET* 3.5 17.1 - - + +
517B PHE 4.5 1.2 - - - +
518B LEU* 3.6 12.3 - - - +
519B HIS* 2.8 27.7 + - - -
520B ARG* 3.2 24.8 + - - +
522B LEU* 4.3 5.8 + - - +
575B SER 3.4 8.5 + - - +
576B SER* 3.2 11.8 + - - +
578B SER* 1.3 79.0 + - - +
580B ILE* 1.3 64.2 + - - +
582B ALA* 3.3 6.8 + - - +
583B PHE* 3.0 23.2 + - - +
644B PHE* 3.6 16.4 - - + -
717B EDO 4.3 3.1 + - - -
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Residues in contact with ILE 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B GLU* 4.5 1.6 - - - +
576B SER* 3.0 20.3 + - - +
577B LYS* 3.5 15.7 - - + +
579B ASP* 1.3 76.5 - - - +
581B TRP* 1.3 63.8 + - - +
583B PHE* 3.1 5.1 + - - +
584B GLY 3.1 17.0 + - - -
633B CYS* 3.4 32.0 - - + +
641B ARG* 4.0 10.8 - - + -
642B PRO* 3.3 31.6 - - + +
643B THR* 3.7 3.6 - - - -
644B PHE* 3.4 48.9 - - + +
647B LEU* 3.9 5.4 - - + -
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Residues in contact with TRP 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ARG 4.8 2.0 + - - -
563B TRP 3.3 23.1 + - - -
564B SER 3.4 21.1 + - - +
565B PRO* 3.5 23.6 - - + -
566B PRO* 3.6 20.2 - - + -
577B LYS 3.2 11.0 + - - +
578B SER 3.7 7.6 - - - +
579B ASP 3.3 0.2 - - - -
580B ILE* 1.3 77.8 - - - +
582B ALA* 1.3 62.1 + - - +
584B GLY 3.0 10.7 + - - -
585B VAL* 3.2 23.0 + - + +
598B TYR* 4.7 4.6 + - - -
610B ILE* 4.2 23.1 - - + -
615B ARG* 3.6 29.8 - - - -
633B CYS 3.4 14.1 + - - +
634B TRP* 3.3 49.6 + + + -
635B HIS 3.9 4.0 - - - -
641B ARG* 3.7 7.6 - - - +
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Residues in contact with ALA 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LEU* 3.6 29.3 - - + +
563B TRP* 3.5 24.4 - - + +
578B SER 3.2 10.4 + - - +
579B ASP* 3.7 8.3 - - - +
581B TRP* 1.3 80.5 - - - +
583B PHE* 1.3 59.2 + - - +
585B VAL* 3.1 8.8 + - - +
586B LEU* 2.8 27.2 + - - +
717B EDO 3.8 11.0 - - - +
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Residues in contact with PHE 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B CYS* 3.8 20.2 - - - -
505B VAL* 3.9 22.4 - - + -
506B CYS* 3.8 30.5 - - + -
522B LEU* 3.8 12.1 - - + +
579B ASP 3.0 13.3 + - - +
580B ILE 3.1 8.5 + - - +
582B ALA* 1.3 75.8 - - - +
584B GLY* 1.3 60.1 + - - +
586B LEU* 3.1 8.0 + - + +
587B MET* 2.9 60.9 + - + +
590B ILE* 6.5 0.4 - - + -
633B CYS* 4.2 2.5 - - - -
644B PHE* 3.6 19.1 - + + -
647B LEU* 3.7 29.2 - - + -
651B ILE* 4.1 10.1 - - + -
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Residues in contact with GLY 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B ILE 3.1 6.7 + - - -
581B TRP 3.0 9.9 + - - -
583B PHE* 1.3 79.5 - - - +
585B VAL* 1.3 60.5 + - - +
587B MET* 3.2 6.5 + - - +
588B TRP* 3.2 16.3 + - - +
630B MET* 3.9 10.8 - - - +
633B CYS* 3.8 18.6 - - - -
634B TRP* 3.4 22.6 - - - -
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Residues in contact with VAL 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ARG 3.7 18.8 - - - +
563B TRP* 3.5 29.2 - - + +
581B TRP* 3.2 30.5 + - + +
582B ALA 3.1 8.1 + - - +
584B GLY* 1.3 75.8 - - - +
586B LEU* 1.3 57.3 + - - +
588B TRP* 3.2 5.6 + - - +
589B GLU* 3.0 26.0 + - - +
597B PRO* 3.8 18.8 - - + -
598B TYR* 4.7 2.0 - - - +
616B LEU* 4.1 14.4 - - + -
634B TRP* 3.7 17.0 - - + +
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 4.0 13.9 - - + -
505B VAL* 3.6 39.9 - - + -
522B LEU* 4.0 20.0 - - + -
523B ALA* 4.0 3.1 - - - -
524B ALA* 3.5 39.7 - - + +
527B CYS* 4.1 6.5 - - - -
563B TRP* 4.7 0.4 - - - -
582B ALA 2.8 13.2 + - - +
583B PHE* 3.1 13.9 + - + +
585B VAL* 1.3 74.7 - - - +
587B MET* 1.3 64.4 + - - +
589B GLU* 3.2 8.9 + - - +
590B ILE* 3.0 29.0 + - + +
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Residues in contact with MET 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B LEU* 5.4 2.5 - - + -
502B CYS* 3.7 33.0 - - + -
583B PHE* 2.9 49.2 + - + +
584B GLY* 3.2 8.0 + - - +
586B LEU* 1.3 75.4 - - - +
588B TRP* 1.3 57.3 + - - +
590B ILE* 3.3 1.9 + - + +
591B TYR* 2.9 35.3 + - + -
626B VAL* 3.9 29.6 - - + +
629B ILE* 4.1 17.5 - - + -
630B MET* 3.8 36.8 - - + -
633B CYS* 5.3 0.2 - - - -
651B ILE* 5.1 5.2 - - + -
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Residues in contact with TRP 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B GLY 3.2 9.1 + - - +
585B VAL 3.3 8.3 - - - +
586B LEU 3.2 0.4 - - - -
587B MET* 1.3 77.7 - - - +
589B GLU* 1.3 66.7 + - - +
591B TYR* 3.8 0.7 - - - +
592B SER* 2.8 43.7 + - - -
595B LYS* 3.3 37.5 - - + -
597B PRO* 3.6 24.7 - - + -
616B LEU* 3.5 32.3 - - + +
617B TYR* 2.9 43.7 + + - +
619B PRO* 3.6 18.1 - - + +
630B MET* 4.0 15.7 - - - +
634B TRP* 4.5 0.7 - - + -
721B EDO 3.4 42.6 - - - -
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Residues in contact with GLU 589 (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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483B LEU* 4.2 13.0 - - + +
486B LEU* 3.8 3.4 - - + +
524B ALA* 2.9 45.5 + - + +
525B ARG 4.7 1.6 + - - -
563B TRP* 3.0 38.0 + - - -
585B VAL 3.0 13.6 + - - +
586B LEU* 3.2 14.4 + - + +
588B TRP* 1.3 79.1 - - + +
590B ILE* 1.3 59.7 + - - +
592B SER* 3.2 9.0 + - - -
594B GLY* 2.8 32.8 + - - -
595B LYS 4.2 14.1 - - - +
597B PRO* 4.3 13.0 - - + +
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Residues in contact with ILE 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 4.3 21.3 - - + -
486B LEU* 4.0 11.3 - - + +
498B LEU* 3.7 42.0 - - + +
501B MET* 4.2 23.8 - - + +
502B CYS* 3.6 24.9 - - - +
505B VAL* 5.2 1.8 - - + -
583B PHE* 6.5 0.2 - - + -
586B LEU* 3.0 35.6 + - + +
587B MET* 3.5 6.3 - - - +
589B GLU* 1.3 76.7 - - - +
591B TYR* 1.3 64.5 + - + +
592B SER 3.1 0.2 - - - -
593B LEU* 2.9 29.1 + - - +
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Residues in contact with TYR 591 (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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495B THR 4.0 4.5 + - - -
498B LEU* 3.8 29.2 - - + -
499B LEU* 3.3 36.4 + - - +
502B CYS* 3.8 23.1 - - - -
587B MET* 2.9 27.4 + - + +
590B ILE* 1.3 79.7 - - + +
592B SER* 1.3 55.7 + - - +
593B LEU* 3.3 2.6 + - - -
619B PRO* 3.7 28.3 - - + +
621B LEU* 3.6 40.0 + - - +
622B ALA* 3.8 10.3 - - + -
626B VAL* 3.5 28.7 - - + +
630B MET* 4.2 4.7 - - + -
710B NA 3.6 18.7 - - - -
723B SO4 4.5 1.7 + - - -
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Residues in contact with SER 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B TRP* 2.8 39.1 + - - -
589B GLU* 3.2 10.2 + - - -
591B TYR* 1.3 76.2 - - - +
593B LEU* 1.3 70.9 + - - +
595B LYS* 3.3 52.3 + - - +
617B TYR* 5.7 0.2 - - - -
619B PRO* 4.4 8.3 - - - -
723B SO4 4.5 7.2 - - - -
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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