Contacts of the helix formed by residues 558 - 576 (chain D) in PDB entry 4QG0
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 558 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491D VAL* 5.2 1.0 - - - +
556D LYS* 3.5 10.8 - - - +
557D VAL* 1.3 86.8 + - + +
559D ARG* 1.3 61.4 + - - +
560D LYS* 3.7 9.3 + - - +
561D SER* 2.7 44.6 + - - -
562D LEU* 3.0 26.9 + - - +
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Residues in contact with ARG 559 (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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455D LYS* 6.2 1.2 - - - +
557D VAL 3.9 3.8 + - - -
558D ASP* 1.3 71.0 - - - +
560D LYS* 1.3 67.5 + - + +
562D LEU* 3.2 22.3 + - - +
563D TYR* 2.9 25.4 + - + +
566D ARG* 5.9 3.8 - - - +
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Residues in contact with LYS 560 (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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490D ASP* 4.9 20.4 + - + -
491D VAL* 3.6 25.8 - - + +
558D ASP* 3.4 7.1 + - - +
559D ARG* 1.3 79.8 - - + +
561D SER* 1.3 58.9 + - - +
563D TYR* 3.2 10.0 + - - +
564D ALA* 2.9 30.0 + - - +
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Residues in contact with SER 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D VAL* 4.0 21.6 - - - +
493D LEU* 3.7 10.5 - - - +
554D CYS* 4.3 0.6 - - - -
556D LYS* 3.5 31.7 - - - +
558D ASP* 2.7 40.3 + - - -
559D ARG 3.3 0.2 - - - -
560D LYS* 1.3 74.7 - - - +
562D LEU* 1.3 56.9 + - - +
564D ALA* 4.6 1.1 - - - -
565D ALA* 2.9 31.1 + - - +
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Residues in contact with LEU 562 (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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455D LYS* 4.0 42.2 - - + -
456D TYR 4.1 13.0 - - - +
457D VAL* 4.5 12.1 - - + -
554D CYS* 5.1 1.3 - - + -
556D LYS 4.5 3.5 + - - +
557D VAL 5.1 0.7 - - - +
558D ASP 3.0 17.6 + - - +
559D ARG* 3.2 24.2 + - - +
561D SER* 1.3 73.2 - - - +
563D TYR* 1.3 67.4 + - - +
565D ALA* 3.4 3.7 + - + -
566D ARG* 2.9 70.6 + - + +
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Residues in contact with TYR 563 (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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487D VAL* 3.4 22.4 - - + +
488D LEU 4.5 3.6 - - - -
489D LEU* 3.7 25.8 - - + -
559D ARG* 2.9 15.2 + - + +
560D LYS* 3.5 11.9 - - - +
562D LEU* 1.3 76.7 - - - +
564D ALA* 1.3 65.6 + - - +
566D ARG* 3.1 14.4 + - - +
567D GLN* 3.0 47.0 + - + +
587D ILE 5.0 4.0 - - - -
589D PRO* 6.1 4.5 - - + +
590D LEU* 4.8 7.8 - - - +
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Residues in contact with ALA 564 (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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489D LEU* 3.9 34.0 - - + +
491D VAL* 4.2 19.1 - - + +
493D LEU* 4.2 9.6 - - + -
560D LYS 2.9 16.9 + - - +
561D SER 3.8 4.0 - - - +
563D TYR* 1.3 77.4 - - - +
565D ALA* 1.3 62.7 + - - +
567D GLN* 3.1 4.4 + - - +
568D TYR* 2.9 30.5 + - + -
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Residues in contact with ALA 565 (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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457D VAL* 3.6 11.7 - - + +
493D LEU* 3.7 15.9 - - + +
498D PHE* 3.9 14.5 - - + -
554D CYS* 3.9 24.7 - - + -
561D SER 2.9 19.3 + - - +
562D LEU* 3.6 5.8 - - - +
563D TYR 3.3 0.2 - - - -
564D ALA* 1.3 76.5 - - - +
566D ARG* 1.3 58.0 + - - +
568D TYR* 3.4 1.7 + - - +
569D PHE* 2.9 31.2 + - - +
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Residues in contact with ARG 566 (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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523B LYS* 5.5 9.5 - - - +
524B THR* 4.8 18.7 + - - +
456D TYR 5.0 5.5 + - - -
457D VAL* 3.7 23.1 + - + +
559D ARG* 5.9 4.6 - - - +
562D LEU* 2.9 55.1 + - + +
563D TYR* 3.1 15.2 + - - +
565D ALA* 1.3 77.2 - - - +
567D GLN* 1.3 70.9 + - - +
569D PHE* 3.3 1.4 + - - +
570D VAL* 3.0 30.2 + - - +
587D ILE* 4.0 44.5 - - + +
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Residues in contact with GLN 567 (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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485D PRO* 3.8 23.1 - - + +
487D VAL* 3.7 26.5 - - + +
489D LEU* 4.4 6.5 - - + -
563D TYR* 3.0 44.7 + - + +
564D ALA* 3.1 6.0 + - - +
566D ARG* 1.3 79.0 - - - +
568D TYR* 1.3 64.0 + - - +
570D VAL* 3.9 1.0 - - - +
571D GLN* 3.0 24.8 + - - +
587D ILE 2.9 25.0 + - - -
588D ALA* 3.5 20.1 - - - +
589D PRO* 5.1 1.5 - - - +
590D LEU* 5.2 1.0 + - - +
591D ILE* 3.7 13.6 - - - +
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Residues in contact with TYR 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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480D VAL* 3.4 25.1 - - + +
481D ALA* 3.6 16.3 + - - -
483D ALA* 3.5 26.5 - - + +
484D LYS* 4.7 10.4 + - - -
485D PRO* 4.0 13.9 - - + +
489D LEU* 4.0 22.1 - - + +
491D VAL 4.3 1.9 + - - -
492D LYS* 4.0 17.5 - - - +
493D LEU* 3.8 33.5 + - + -
498D PHE* 3.9 19.7 - + + -
564D ALA* 2.9 37.6 + - + -
565D ALA 3.7 5.2 - - - +
567D GLN* 1.3 73.5 - - - +
569D PHE* 1.3 58.0 + - - +
571D GLN* 3.3 1.9 + - - +
572D TRP* 2.9 30.8 + - - +
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Residues in contact with PHE 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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457D VAL* 3.7 17.9 - - + -
458D GLY* 3.5 37.2 - - - -
459D GLU 3.6 13.0 - - - -
460D THR* 4.1 8.1 - - + -
480D VAL* 4.4 8.9 - - + +
550D ILE 4.9 0.2 - - - -
552D VAL* 3.6 38.8 - - + -
565D ALA 2.9 18.3 + - - +
566D ARG 3.7 2.7 - - - +
568D TYR* 1.3 76.1 - - - +
570D VAL* 1.3 75.3 + - + +
572D TRP* 3.3 9.6 + + - +
573D CYS* 2.9 48.5 + - - -
581D PRO* 3.6 21.8 - - + -
587D ILE* 4.8 3.6 - - + -
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Residues in contact with VAL 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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566D ARG 3.0 16.2 + - - +
567D GLN 4.2 1.6 - - - +
569D PHE* 1.3 84.4 - - + +
571D GLN* 1.3 63.4 + - - +
573D CYS* 3.1 7.0 + - - +
574D ALA* 2.9 21.3 + - - +
581D PRO* 4.4 10.8 - - + -
584D GLY* 4.9 2.7 - - - -
587D ILE* 4.0 20.2 - - + -
588D ALA* 3.7 19.3 - - + -
591D ILE* 3.6 19.5 - - + -
592D THR* 3.9 14.4 - - + -
598D TRP* 3.9 21.4 - - + -
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Residues in contact with GLN 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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483D ALA* 4.2 2.7 - - + -
484D LYS 4.0 13.3 + - - +
485D PRO* 3.7 35.4 - - + +
486D LYS 4.5 1.6 + - - -
567D GLN 3.0 18.0 + - - +
568D TYR 3.7 3.8 - - - +
570D VAL* 1.3 78.6 - - - +
572D TRP* 1.3 56.5 + - - +
574D ALA* 3.1 5.3 + - - +
575D ASP* 2.9 62.6 + - - +
591D ILE* 3.6 12.1 - - + +
594D GLN* 2.9 41.5 + - - +
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Residues in contact with TRP 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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460D THR* 4.4 6.3 - - + -
476D LEU* 4.3 16.4 - - + -
479D GLU* 3.1 51.2 + - + +
480D VAL* 3.6 28.9 - - + -
483D ALA* 4.2 4.4 - - + +
500D VAL* 4.4 8.3 - - + -
550D ILE* 3.9 22.0 - - + -
552D VAL* 4.1 17.7 - - + -
568D TYR 2.9 16.6 + - - +
569D PHE* 3.5 14.6 - + - +
571D GLN* 1.3 75.9 - - - +
573D CYS* 1.3 68.3 + - - +
575D ASP* 3.4 11.0 + - + +
576D ARG* 3.1 41.5 + - + +
578D PHE* 3.7 28.9 - + - -
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Residues in contact with CYS 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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460D THR* 3.6 25.4 - - - -
569D PHE* 2.9 51.4 + - - -
570D VAL* 3.4 7.6 - - - +
572D TRP* 1.3 79.4 - - - +
574D ALA* 1.3 62.0 + - - +
576D ARG 3.4 0.2 + - - -
577D ASN* 3.1 3.5 + - - -
578D PHE* 3.0 40.2 + - + +
579D THR 4.3 3.1 - - - +
581D PRO* 4.2 6.3 - - + -
598D TRP* 4.0 16.4 - - + -
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Residues in contact with ALA 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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570D VAL 2.9 12.0 + - - +
571D GLN* 3.3 12.3 - - - +
573D CYS* 1.3 75.9 - - - +
575D ASP* 1.3 62.2 + - - +
577D ASN 3.1 3.8 + - - -
591D ILE* 5.0 0.2 - - + -
594D GLN* 4.2 23.3 - - - +
595D LYS* 2.4 42.7 + - + +
598D TRP* 3.6 22.0 - - + -
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Residues in contact with ASP 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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483D ALA* 4.2 11.6 - - - +
484D LYS 4.9 1.2 + - - -
571D GLN* 2.9 54.8 + - - +
572D TRP* 3.4 12.0 + - + +
574D ALA* 1.3 73.0 - - - +
576D ARG* 1.3 64.4 + - + +
577D ASN* 3.2 1.6 + - - +
595D LYS* 4.9 0.9 + - - -
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Residues in contact with ARG 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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463D THR* 5.2 0.3 + - - -
466D ILE* 4.5 12.9 - - - +
468D ILE* 3.7 25.9 - - - +
476D LEU* 4.2 12.7 - - - +
479D GLU* 2.5 44.9 + - - -
572D TRP* 3.1 36.2 + - + +
573D CYS 3.4 0.2 + - - -
575D ASP* 1.3 79.5 - - + +
577D ASN* 1.3 69.9 + - - +
578D PHE* 3.1 41.9 + - + -
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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