Contacts of the helix formed by residues 559 - 579 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A ILE 4.3 0.4 + - - -
558A LEU* 1.3 76.4 - - - +
560A LEU* 1.3 63.7 + - - +
561A GLN* 4.1 10.6 - - - +
562A SER* 2.6 35.0 + - - -
563A LYS* 3.2 18.3 + - - +
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Residues in contact with LEU 560 (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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559A ASP* 1.3 74.4 - - - +
561A GLN* 1.3 64.0 + - - +
563A LYS* 3.2 14.1 + - + +
564A LEU* 3.0 45.5 + - + +
659A LEU* 4.1 26.0 - - + -
691A PRO* 4.2 21.3 - - + -
694A ILE* 4.6 5.4 - - + -
726A ILE* 5.4 10.8 - - + -
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Residues in contact with GLN 561 (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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559A ASP* 3.2 11.4 + - - +
560A LEU* 1.3 78.7 - - - +
562A SER* 1.3 63.4 + - - +
564A LEU* 3.1 4.8 + - - +
565A ILE* 3.0 42.3 + - + +
723A LEU* 4.0 25.1 + - + +
726A ILE* 4.9 14.7 - - + +
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Residues in contact with SER 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A LEU* 4.2 22.9 - - - -
559A ASP* 2.6 28.9 + - - -
561A GLN* 1.3 76.4 - - - +
563A LYS* 1.3 62.2 + - - +
565A ILE* 3.6 11.3 + - - +
566A ILE* 3.3 30.0 + - - +
600A GLY* 4.7 1.9 - - - +
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Residues in contact with LYS 563 (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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551A LEU* 5.9 1.6 - - - -
558A LEU* 3.6 39.9 + - + +
559A ASP 3.2 12.2 + - - +
560A LEU* 3.2 25.0 + - + +
562A SER* 1.3 77.3 - - - +
564A LEU* 1.3 60.6 + - + +
566A ILE* 3.3 6.0 + - - +
567A ALA* 2.9 28.2 + - - +
658A ILE* 3.4 40.8 - - + +
659A LEU* 2.9 34.0 + - + +
660A THR 5.5 0.8 - - - -
661A GLY 5.9 0.2 - - - +
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Residues in contact with LEU 564 (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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560A LEU* 3.0 43.1 + - + +
561A GLN 3.1 3.6 + - - +
563A LYS* 1.3 76.0 - - + +
565A ILE* 1.3 55.9 + - - +
567A ALA* 3.7 5.2 - - + +
568A VAL* 2.8 42.4 + - + +
655A LEU* 5.3 4.5 - - + -
659A LEU* 5.9 1.8 - - + -
694A ILE* 3.9 25.4 - - + -
719A LEU* 3.9 24.2 - - + +
722A CYS* 3.9 29.2 - - + +
723A LEU* 3.9 23.6 - - + -
726A ILE* 4.8 3.8 - - + -
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Residues in contact with ILE 565 (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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561A GLN* 3.0 42.8 + - + +
562A SER* 3.9 9.0 - - - +
564A LEU* 1.3 74.6 - - - +
566A ILE* 1.3 67.6 + - - +
568A VAL* 3.8 4.7 - - - +
569A ASP* 2.9 25.8 + - - +
600A GLY 3.7 17.0 - - - +
601A HIS* 3.6 34.3 - - + +
723A LEU* 4.2 17.0 - - + -
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Residues in contact with ILE 566 (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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547A LEU* 4.3 13.5 - - + -
550A LEU* 5.8 0.2 - - + -
558A LEU* 3.9 23.6 - - + -
562A SER* 3.3 15.7 + - - +
563A LYS* 3.3 8.4 + - - +
565A ILE* 1.3 79.6 - - - +
567A ALA* 1.3 64.9 + - - +
569A ASP* 3.0 1.6 + - - +
570A VAL* 3.0 23.2 + - + +
594A ILE* 4.3 10.8 - - + -
596A LEU* 4.1 28.0 - - + -
600A GLY* 3.7 17.7 - - - +
602A ALA* 4.0 20.6 - - + -
658A ILE* 4.1 18.4 - - + -
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Residues in contact with ALA 567 (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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563A LYS 2.9 16.9 + - - +
564A LEU* 3.7 9.0 - - + +
566A ILE* 1.3 76.8 - - - +
568A VAL* 1.3 56.6 + - - +
570A VAL* 3.4 1.9 + - - -
571A ALA* 3.0 19.9 + - - +
651A TYR* 2.7 35.3 + - + +
655A LEU* 3.7 24.5 - - + -
658A ILE* 4.4 11.6 - - + +
719A LEU* 3.9 7.9 - - + -
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Residues in contact with VAL 568 (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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564A LEU* 2.8 29.4 + - - +
565A ILE* 3.8 5.4 - - - +
567A ALA* 1.3 70.6 - - - +
569A ASP* 1.3 63.4 + - - +
571A ALA* 3.2 2.7 + - - +
572A LYS* 2.9 53.2 + - + +
716A VAL* 4.8 5.8 - - + -
719A LEU* 3.2 37.5 - - + -
720A GLU* 4.5 13.7 - - + -
723A LEU* 4.0 20.0 - - + -
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Residues in contact with ASP 569 (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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520A CYS* 3.3 30.5 - - - +
565A ILE* 2.9 21.1 + - - +
566A ILE 3.6 3.1 - - - +
568A VAL* 1.3 74.3 - - - +
570A VAL* 1.3 67.0 + - - +
572A LYS* 3.3 10.0 + - - +
573A GLY 3.0 17.8 + - - -
601A HIS* 2.8 37.0 + - - -
602A ALA* 3.2 37.2 + - + +
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Residues in contact with VAL 570 (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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520A CYS 5.4 0.4 - - - -
566A ILE* 3.0 22.5 + - + +
567A ALA* 3.7 7.9 - - - +
569A ASP* 1.3 75.5 - - - +
571A ALA* 1.3 65.3 + - - +
573A GLY* 3.2 2.4 + - - -
574A MET* 3.0 33.0 + - + +
589A LEU* 4.4 12.1 - - + -
594A ILE* 3.5 42.2 - - + -
602A ALA* 4.5 3.8 - - + -
603A VAL 5.6 1.1 - - - -
604A VAL* 4.0 22.4 - - + +
651A TYR* 3.6 25.6 - - + -
658A ILE* 5.7 1.6 - - + -
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Residues in contact with ALA 571 (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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567A ALA 3.0 18.8 + - - +
568A VAL* 3.5 8.1 - - - +
569A ASP 3.2 0.2 - - - -
570A VAL* 1.3 76.5 - - - +
572A LYS* 1.3 57.6 + - - +
574A MET* 3.2 3.1 + - - +
575A GLU* 2.8 29.3 + - - +
651A TYR* 4.0 2.9 - - - +
712A PHE* 3.8 17.1 - - + -
715A VAL* 3.9 24.7 - - + -
716A VAL* 3.5 18.7 - - + +
719A LEU* 4.3 2.0 - - + -
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Residues in contact with LYS 572 (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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518A HIS* 4.1 13.9 + - + +
520A CYS* 4.0 16.8 - - - -
568A VAL* 2.9 35.9 + - + +
569A ASP* 3.7 9.4 + - - +
570A VAL 3.3 0.2 - - - -
571A ALA* 1.3 74.9 - - - +
573A GLY* 1.3 59.8 + - - +
575A GLU* 3.2 9.5 + - - +
576A TYR* 2.9 30.0 + - - +
716A VAL* 3.6 19.3 - - + +
720A GLU* 3.5 25.8 + - - -
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Residues in contact with GLY 573 (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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518A HIS* 4.5 0.7 - - - -
520A CYS* 3.7 28.6 - - - +
521A VAL* 3.7 10.9 - - - +
569A ASP 3.0 11.1 + - - -
570A VAL 3.2 3.6 + - - -
572A LYS* 1.3 74.5 - - - +
574A MET* 1.3 60.0 + - - +
576A TYR* 3.3 8.1 + - - +
577A LEU* 3.2 29.6 + - - +
604A VAL* 4.7 1.6 - - - -
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Residues in contact with MET 574 (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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570A VAL* 3.0 17.4 + - + +
571A ALA 3.6 4.7 - - - +
573A GLY* 1.3 74.5 - - - +
575A GLU* 1.3 59.5 + - - +
576A TYR 3.2 0.2 - - - -
577A LEU* 3.3 18.2 + - + +
578A HIS* 2.9 41.9 + - + +
586A HIS* 3.8 12.8 - - + +
589A LEU* 4.1 20.6 - - + -
604A VAL* 4.1 20.2 - - - -
647A ASP* 3.3 42.6 - - + +
712A PHE* 3.5 32.8 - - + -
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Residues in contact with GLU 575 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571A ALA 2.8 17.8 + - - +
572A LYS* 3.4 14.1 - - - +
574A MET* 1.3 72.6 - - - +
576A TYR* 1.3 62.8 + - - +
578A HIS* 3.4 0.8 + - - -
579A ASN* 2.8 46.8 + - + +
712A PHE* 3.8 15.4 - - + +
713A SER* 3.2 32.3 - - - +
716A VAL* 3.6 22.5 - - + +
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Residues in contact with TYR 576 (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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515A GLN 3.5 10.7 + - - -
516A LEU* 4.4 16.4 - - + -
517A ASN* 2.9 46.0 + - - +
518A HIS* 3.5 41.5 - + + +
521A VAL* 4.3 10.8 - - + -
572A LYS 2.9 12.8 + - - +
573A GLY 3.3 10.3 - - - +
575A GLU* 1.3 73.8 - - - +
577A LEU* 1.3 71.1 + - + +
579A ASN* 3.3 3.9 + - - -
580A LEU* 3.2 46.3 + - + +
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Residues in contact with LEU 577 (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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516A LEU* 3.6 23.8 - - + -
521A VAL* 4.3 6.3 - - + -
573A GLY 3.2 14.7 + - - +
574A MET* 3.3 31.2 + - + +
576A TYR* 1.3 86.8 - - + +
578A HIS* 1.3 63.8 + - + +
579A ASN 3.3 0.3 + - - -
580A LEU* 3.4 14.9 + - + +
583A PRO* 3.5 0.7 - - - +
584A ILE* 3.1 46.5 + - + +
586A HIS* 4.6 7.9 - - + -
604A VAL* 4.6 1.1 - - + -
607A PHE* 3.5 40.4 - - + -
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Residues in contact with HIS 578 (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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574A MET* 2.9 21.2 + - + +
575A GLU* 4.0 4.3 - - - +
577A LEU* 1.3 78.6 - - + +
579A ASN* 1.3 66.0 + - - +
580A LEU 3.5 0.2 - - - -
583A PRO* 3.4 23.6 - - - +
584A ILE 3.4 18.8 - - - -
585A ILE* 4.6 0.6 - - - -
644A ILE* 3.2 61.9 + - + +
647A ASP* 3.0 22.8 + - - +
648A VAL* 4.7 1.7 - - + +
711A GLU* 5.0 3.8 + - - +
712A PHE* 3.5 36.3 + + + +
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Residues in contact with ASN 579 (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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575A GLU* 2.8 47.4 + - + +
576A TYR* 3.8 3.4 - - - +
577A LEU 3.2 0.2 - - - -
578A HIS* 1.3 82.3 - - - +
580A LEU* 1.3 67.9 + - - +
581A THR* 3.7 0.7 + - - -
711A GLU* 5.8 2.2 + - - -
712A PHE* 5.9 0.4 - - - +
713A SER* 5.2 6.5 - - - +
687D GLY* 5.3 0.7 - - - -
688D TYR* 4.4 27.2 + - + +
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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
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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