Contacts of the helix formed by residues 567 - 579 (chain D) in PDB entry 4YJL
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 GLY 567 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530D VAL* 4.3 0.2 - - - +
564D ARG 3.1 15.3 + - - -
565D GLU 3.2 2.4 + - - -
566D VAL* 1.3 78.8 - - - +
568D SER* 1.3 65.3 + - - +
569D VAL 3.3 3.7 + - - -
570D LYS* 3.7 7.9 + - - +
571D ALA* 3.0 25.3 + - - +
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Residues in contact with SER 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D VAL* 4.0 23.1 - - - -
533D LEU* 5.6 0.2 - - - -
548D LEU* 4.6 8.5 - - - -
563D LEU* 2.6 43.6 + - - +
566D VAL* 3.3 4.0 - - - -
567D GLY* 1.3 77.3 - - - +
569D VAL* 1.3 57.2 + - - +
571D ALA* 3.8 3.1 - - - +
572D LEU* 2.9 38.7 + - - +
595D LEU* 3.9 16.3 - - - +
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Residues in contact with VAL 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D LEU 5.2 2.5 - - - +
564D ARG* 5.4 3.8 - - + +
567D GLY* 3.3 1.6 - - - -
568D SER* 1.3 79.3 - - - +
570D LYS* 1.3 59.8 + - - +
573D MET* 2.9 26.6 + - - +
592D LEU* 3.5 14.1 - - + +
595D LEU* 4.1 22.2 - - + -
602D ASN* 3.6 47.3 - - + +
605D ASP* 4.1 16.2 - - + +
606D ILE* 3.6 33.2 - - + +
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Residues in contact with LYS 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D GLY* 3.7 9.1 + - - +
569D VAL* 1.3 80.2 - - - +
571D ALA* 1.3 58.4 + - - +
573D MET* 3.8 0.5 - - - +
574D GLU* 2.8 63.9 + - + +
605D ASP* 5.0 11.8 + - + +
609D VAL* 4.3 22.2 - - + -
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Residues in contact with ALA 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D VAL* 3.6 26.7 - - + +
533D LEU* 3.9 13.6 - - + +
534D LYS* 5.9 6.9 + - - +
567D GLY 3.0 20.0 + - - +
568D SER 3.8 2.7 - - - +
570D LYS* 1.3 77.4 - - - +
572D LEU* 1.3 58.9 + - - +
574D GLU* 3.6 6.2 + - - +
575D CYS* 3.0 28.8 + - - +
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Residues in contact with LEU 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D LEU* 3.7 31.0 - - + -
545D ALA* 4.1 15.9 - - + -
548D LEU* 4.0 16.2 - - + -
568D SER* 2.9 22.5 + - - +
569D VAL 3.7 0.9 - - - +
571D ALA* 1.3 75.5 - - - +
573D MET* 1.3 59.0 + - - +
575D CYS* 3.4 2.5 + - - +
576D ALA* 2.9 23.9 + - - +
588D VAL* 3.3 33.1 - - + +
591D ALA* 3.8 15.7 - - + -
592D LEU* 3.7 17.3 - - + -
595D LEU* 3.5 27.4 - - + -
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Residues in contact with MET 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D VAL 2.9 17.4 + - - +
570D LYS* 3.3 3.6 + - - +
572D LEU* 1.3 73.3 - - - +
574D GLU* 1.3 65.1 + - - +
576D ALA* 3.3 16.6 + - + -
577D LEU* 3.3 23.6 + - + +
592D LEU* 3.8 19.5 - - + +
606D ILE* 4.0 24.5 - - + +
609D VAL* 4.0 19.5 - - + -
612D ALA* 3.7 35.9 - - + -
615D PHE* 3.9 28.9 - - + -
616D LEU* 4.3 15.0 - - + -
638D ILE* 5.7 0.7 - - - -
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Residues in contact with GLU 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720C MET* 4.5 20.1 - - - +
534D LYS* 5.4 12.2 + - - +
570D LYS* 2.8 61.6 + - + +
571D ALA* 3.9 5.6 - - - +
573D MET* 1.3 74.6 - - - +
575D CYS* 1.3 64.7 + - - +
577D LEU* 3.3 23.2 + - - +
578D GLU* 3.6 12.2 + - - +
609D VAL* 3.6 9.3 - - + +
497H ARG* 2.7 32.4 + - - -
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Residues in contact with CYS 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D LEU* 3.8 31.9 - - + +
541D GLN* 3.4 27.5 - - - +
571D ALA 3.0 20.5 + - - +
572D LEU* 3.4 9.6 - - - +
574D GLU* 1.3 76.5 - - - +
576D ALA* 1.3 62.5 + - - +
578D GLU* 2.9 18.8 + - - +
579D VAL* 3.2 15.3 + - - +
588D VAL* 3.9 22.7 - - + -
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Residues in contact with ALA 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D LEU 2.9 19.0 + - - +
573D MET* 3.3 22.4 + - + +
575D CYS* 1.3 73.8 - - - +
577D LEU* 1.3 61.5 + - - +
578D GLU 3.2 0.9 + - - -
579D VAL* 3.4 24.5 + - - +
585D LEU* 4.1 13.5 - - + -
588D VAL* 3.7 17.5 - - + -
589D LEU* 4.2 5.8 - - + -
592D LEU* 4.5 1.1 - - + -
615D PHE* 3.4 19.5 - - + -
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Residues in contact with LEU 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D MET* 3.4 17.3 - - + +
574D GLU* 3.3 12.5 + - - +
575D CYS 3.2 0.4 - - - -
576D ALA* 1.3 76.6 - - - +
578D GLU* 1.3 67.0 + - + +
579D VAL 4.9 1.5 - - - +
609D VAL* 4.0 19.1 - - + -
610D ASP 3.7 22.2 - - - +
611D GLY* 4.1 9.6 - - - +
612D ALA 4.8 0.4 - - - +
615D PHE* 3.5 46.1 - - + -
497H ARG* 4.2 17.0 - - + +
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Residues in contact with GLU 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C TRP* 3.5 27.8 + - + -
538D GLU* 4.0 1.7 - - - +
541D GLN* 6.0 1.8 - - - +
574D GLU 3.9 12.1 - - - +
575D CYS* 2.9 10.3 + - - +
577D LEU* 1.3 84.8 - - + +
579D VAL* 1.3 62.5 + - - +
580D LYS* 2.9 38.1 + - - +
496H PRO* 2.8 46.6 - - - +
497H ARG 4.5 0.2 + - - -
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Residues in contact with VAL 579 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D GLU* 3.5 12.3 - - - +
541D GLN* 3.7 20.6 - - - +
575D CYS* 3.2 23.6 - - - +
576D ALA* 3.4 17.9 + - - +
577D LEU 4.9 1.4 - - - +
578D GLU* 1.3 79.5 - - - +
580D LYS* 1.3 63.1 + - - +
581D LYS 4.4 1.3 - - - +
584D THR* 3.8 17.5 - - + -
585D LEU* 3.4 38.6 - - + +
588D VAL* 4.5 4.0 - - + -
615D PHE* 5.4 0.6 - - + -
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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