Contacts of the helix formed by residues 559 - 579 (chain B) in PDB entry 4YFI
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 ASP 559 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557B ILE 4.2 1.0 + - - -
558B LEU* 1.3 76.3 - - - +
560B LEU* 1.3 62.0 + - - +
561B GLN* 3.3 13.6 + - + +
562B SER* 2.7 51.0 + - - -
563B LYS* 3.3 10.9 + - - +
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Residues in contact with LEU 560 (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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558B LEU 4.0 0.8 + - - -
559B ASP* 1.3 72.8 - - - +
561B GLN* 1.3 60.8 + - - +
563B LYS* 3.4 10.9 + - + +
564B LEU* 3.1 32.6 + - + +
659B LEU* 4.0 26.7 - - + -
691B PRO* 5.1 13.9 - - + -
694B ILE* 5.1 4.7 - - + -
726B ILE* 3.3 39.3 - - + -
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Residues in contact with GLN 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ASP* 3.2 10.5 - - - +
560B LEU* 1.3 79.4 - - - +
562B SER* 1.3 56.6 + - - +
564B LEU* 3.4 2.4 + - - +
565B ILE* 3.0 44.6 + - - +
723B LEU* 4.0 16.3 - - + +
726B ILE* 4.3 18.6 - - + +
727B GLU* 3.2 39.6 + - + +
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Residues in contact with SER 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B LEU* 4.0 24.2 - - - +
559B ASP* 2.7 41.2 + - - -
561B GLN* 1.3 69.6 - - - +
563B LYS* 1.3 64.9 + - - +
565B ILE* 3.5 10.9 + - - +
566B ILE* 3.3 30.2 + - - +
600B GLY* 4.7 1.8 - - - +
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Residues in contact with LYS 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 6.1 0.7 - - - -
558B LEU* 3.5 39.8 + - + +
559B ASP 3.3 10.5 + - - +
560B LEU* 3.5 16.4 - - + +
562B SER* 1.3 77.9 - - - +
564B LEU* 1.3 58.7 + - - +
566B ILE* 3.4 8.9 + - - +
567B ALA* 3.0 27.5 + - - +
658B ILE* 3.5 38.4 - - + +
659B LEU* 2.9 41.4 + - + +
660B THR 5.3 1.2 - - - -
661B GLY* 6.1 0.4 - - - -
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Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B LEU* 3.1 28.7 + - + +
561B GLN 4.0 0.2 - - - +
563B LYS* 1.3 76.6 - - - +
565B ILE* 1.3 59.8 - - - +
567B ALA* 3.9 6.2 - - + +
568B VAL* 2.8 37.4 + - + +
655B LEU* 5.2 1.8 - - + -
659B LEU* 5.0 5.2 - - + -
694B ILE* 3.9 24.7 - - + -
719B LEU* 4.1 23.8 - - + +
722B CYS* 4.1 17.7 - - + +
723B LEU* 3.8 22.2 - - + +
726B ILE* 3.3 35.4 - - + -
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Residues in contact with ILE 565 (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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561B GLN* 3.0 44.1 + - - +
562B SER* 3.8 7.9 - - - +
564B LEU* 1.3 77.1 - - - +
566B ILE* 1.3 58.0 + - - +
568B VAL* 3.8 4.5 - - - +
569B ASP* 2.9 31.8 + - - +
599B ASP 5.9 0.4 - - - +
600B GLY 3.4 24.0 - - - +
601B HIS* 4.0 31.2 - - + +
723B LEU* 4.1 18.4 - - + -
727B GLU* 5.4 1.1 - - - +
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Residues in contact with ILE 566 (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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547B LEU* 3.9 27.1 - - + -
550B LEU* 5.4 2.7 - - + -
558B LEU* 4.4 19.1 - - + -
562B SER* 3.3 15.6 + - - +
563B LYS* 3.5 8.3 - - - +
564B LEU 3.2 0.2 - - - -
565B ILE* 1.3 78.6 - - - +
567B ALA* 1.3 58.2 + - - +
569B ASP* 3.3 3.1 + - - +
570B VAL* 2.9 34.3 + - + +
594B ILE* 4.6 0.7 - - + -
596B LEU* 3.7 25.4 - - + -
600B GLY* 3.7 17.0 - - - +
602B ALA* 4.1 17.0 - - + -
658B ILE* 4.0 20.4 - - + -
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Residues in contact with ALA 567 (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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563B LYS 3.0 14.2 + - - +
564B LEU* 3.3 7.4 + - + +
566B ILE* 1.3 80.5 - - - +
568B VAL* 1.3 56.9 + - - +
570B VAL* 3.4 3.9 + - - -
571B ALA* 2.9 18.5 + - - +
651B TYR* 2.7 32.5 + - - +
655B LEU* 3.6 23.8 - - + -
658B ILE* 4.1 16.2 - - + -
719B LEU* 4.1 5.4 - - + -
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Residues in contact with VAL 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B LEU* 2.8 24.0 + - + +
565B ILE* 3.8 4.7 - - - +
567B ALA* 1.3 74.7 - - - +
569B ASP* 1.3 64.3 + - - +
571B ALA* 3.2 6.9 + - - +
572B LYS* 2.8 49.6 + - + +
716B VAL* 5.0 3.1 - - + +
719B LEU* 3.4 42.6 - - + +
720B GLU* 4.1 23.1 - - + +
723B LEU* 5.0 9.0 - - + -
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Residues in contact with ASP 569 (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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520B CYS* 3.2 30.2 - - - +
565B ILE* 2.9 20.3 + - - +
566B ILE 3.6 4.7 - - - +
568B VAL* 1.3 79.5 - - - +
570B VAL* 1.3 62.9 + - - +
572B LYS* 3.4 9.5 + - - +
573B GLY 3.1 18.0 + - - -
601B HIS* 2.7 37.4 + - - +
602B ALA* 2.8 40.5 + - + +
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ILE* 2.9 24.4 + - + +
567B ALA* 3.8 5.8 - - - +
569B ASP* 1.3 77.3 - - - +
571B ALA* 1.3 62.4 + - - +
572B LYS 3.2 0.3 + - - -
573B GLY* 3.2 2.4 + - - -
574B MET* 3.0 28.8 + - + +
589B LEU* 4.3 8.1 - - + -
594B ILE* 3.5 48.9 - - + -
602B ALA* 4.4 4.9 - - + -
603B VAL 5.2 1.1 - - - +
604B VAL* 4.1 22.9 - - + +
651B TYR* 3.7 25.6 - - + -
658B ILE* 5.8 1.1 - - + -
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Residues in contact with ALA 571 (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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567B ALA 2.9 18.3 + - - +
568B VAL* 3.2 7.2 + - - +
570B VAL* 1.3 76.0 - - - +
572B LYS* 1.3 57.1 + - - +
574B MET 3.5 0.2 + - - -
575B GLU* 2.9 23.4 + - - +
651B TYR* 3.8 13.9 - - + +
712B PHE* 3.7 15.0 - - + -
715B VAL* 3.9 18.2 - - + -
716B VAL* 3.4 25.7 - - + +
719B LEU* 4.4 2.0 - - + -
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Residues in contact with LYS 572 (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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518B HIS* 4.0 13.1 + - + +
520B CYS* 4.1 17.0 - - - -
568B VAL* 2.8 30.1 + - + +
569B ASP* 3.6 10.6 + - - +
571B ALA* 1.3 74.7 - - - +
573B GLY* 1.3 60.6 + - - +
574B MET 3.2 0.2 - - - -
575B GLU* 3.3 8.1 + - - +
576B TYR* 2.9 29.8 + - - +
716B VAL* 3.9 19.3 - - + -
720B GLU* 3.1 28.2 + - - +
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Residues in contact with GLY 573 (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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518B HIS* 4.3 2.7 - - - -
520B CYS* 3.6 22.5 - - - +
521B VAL* 3.7 18.5 - - - +
569B ASP 3.1 8.1 + - - -
570B VAL 3.7 2.9 - - - -
572B LYS* 1.3 78.1 - - - +
574B MET* 1.3 58.7 + - - +
576B TYR* 3.3 4.5 - - - +
577B LEU* 3.0 32.2 + - - +
604B VAL* 4.8 1.8 - - - -
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Residues in contact with MET 574 (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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570B VAL* 3.0 23.2 + - + +
573B GLY* 1.3 73.3 - - - +
575B GLU* 1.3 66.1 + - - +
577B LEU* 3.2 19.1 + - + +
578B HIS* 3.0 37.0 + - + +
586B HIS* 4.2 9.2 - - + -
589B LEU* 3.9 25.8 - - + -
604B VAL* 4.2 15.5 - - + -
647B ASP* 3.4 42.8 - - + +
712B PHE* 3.6 35.7 - - + -
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Residues in contact with GLU 575 (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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571B ALA 2.9 18.4 + - - +
572B LYS* 3.6 8.9 - - - +
574B MET* 1.3 76.6 - - - +
576B TYR* 1.3 65.7 + - - +
578B HIS* 3.3 1.0 + - - -
579B ASN* 3.2 42.9 + - + +
712B PHE* 3.8 15.8 - - + +
713B SER* 3.2 34.9 - - - +
716B VAL* 3.7 21.3 - - + +
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Residues in contact with TYR 576 (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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515B GLN 3.3 12.0 + - - -
516B LEU* 4.3 17.3 - - + -
517B ASN* 2.8 46.2 + - - +
518B HIS* 3.5 40.2 - + + +
521B VAL* 4.0 13.9 - - + -
572B LYS 2.9 13.4 + - - +
573B GLY 3.3 7.2 - - - +
574B MET 3.2 0.2 - - - -
575B GLU* 1.3 78.5 - - - +
577B LEU* 1.3 70.3 + - + +
579B ASN* 3.2 9.7 + - - +
580B LEU* 3.4 36.7 + - + +
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Residues in contact with LEU 577 (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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516B LEU* 3.5 31.9 - - + -
521B VAL* 4.4 5.6 - - + -
573B GLY 3.0 19.5 + - - +
574B MET* 3.2 29.3 + - + +
576B TYR* 1.3 85.7 - - + +
578B HIS* 1.3 65.1 + - + +
579B ASN 3.2 1.4 + - - -
580B LEU* 3.5 13.7 + - + +
584B ILE* 3.1 48.1 + - + +
586B HIS* 4.6 7.6 - - + -
604B VAL* 4.7 2.2 - - + -
607B PHE* 3.6 31.6 - - + -
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Residues in contact with HIS 578 (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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574B MET* 3.0 18.2 + - + +
575B GLU* 3.3 4.9 + - - +
577B LEU* 1.3 79.0 - - + +
579B ASN* 1.3 66.2 + - - +
580B LEU 3.6 0.4 - - - -
583B PRO* 3.6 22.8 - - - +
584B ILE 3.3 19.1 - - - -
644B ILE* 3.1 60.8 - - + +
647B ASP* 3.0 23.0 + - + +
648B VAL* 4.6 1.7 - - + +
711B GLU* 5.4 3.5 + - - +
712B PHE* 3.4 40.7 + + + +
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Residues in contact with ASN 579 (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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575B GLU* 3.2 39.7 + - + +
576B TYR* 3.2 4.0 + - - +
577B LEU 3.2 0.4 - - - -
578B HIS* 1.3 87.0 - - - +
580B LEU* 1.3 66.7 + - - +
581B THR 3.9 0.2 + - - -
712B PHE* 5.9 0.8 - - - +
713B SER* 5.1 8.3 - - - +
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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