Contacts of the helix formed by residues 568 - 583 (chain A) in PDB entry 3NR8
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 LYS 568 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A THR* 5.1 2.7 - - + +
564A SER 3.5 15.9 - - - +
565A GLY* 3.2 16.5 + - - +
566A ASN 3.3 1.8 + - - -
567A GLU* 1.3 78.1 - - - +
569A THR* 1.3 64.3 + - - +
570A ALA* 3.2 5.8 - - - +
571A ARG* 3.2 32.8 + - + +
572A ARG* 3.4 21.5 + - - +
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Residues in contact with THR 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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566A ASN 4.2 0.7 + - - -
567A GLU* 3.8 1.3 - - - -
568A LYS* 1.3 72.7 + - - +
570A ALA* 1.3 64.0 + - - +
572A ARG* 3.2 7.3 - - - +
573A ASN* 3.0 32.6 + - - +
610A TYR* 3.6 26.7 - - + -
636A GLN* 3.2 36.8 + - + +
640A GLU* 3.8 28.9 - - + +
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Residues in contact with ALA 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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567A GLU 6.0 0.4 - - - +
568A LYS* 4.9 2.5 - - - -
569A THR* 1.3 80.0 - - - +
571A ARG* 1.3 65.8 + - + +
573A ASN* 3.5 8.4 - - - +
574A GLN* 3.2 21.7 + - - +
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Residues in contact with ARG 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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563A THR* 3.9 30.6 - - - +
568A LYS* 3.2 22.9 + - + +
570A ALA* 1.3 78.7 - - + +
572A ARG* 1.3 54.0 + - - +
574A GLN* 2.9 11.0 + - - +
575A ASN* 2.5 41.6 + - - +
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Residues in contact with ARG 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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562A LEU* 3.9 18.2 - - + +
563A THR* 2.9 19.7 + - - +
564A SER 3.6 8.1 + - - -
565A GLY 2.3 37.6 + - - +
566A ASN 4.1 2.0 + - - -
568A LYS* 3.4 12.5 + - - +
569A THR* 3.2 25.8 + - - +
571A ARG* 1.3 74.4 - - - +
573A ASN* 1.3 53.4 + - - +
575A ASN* 3.0 11.1 + - - +
576A TYR* 2.7 37.1 + - - +
608A LEU 3.5 10.3 - - - -
609A ASN 2.7 28.7 + - - -
610A TYR* 3.2 30.3 + - + +
611A ARG* 4.3 2.6 - - - +
636A GLN* 3.0 25.7 + - - -
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Residues in contact with ASN 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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569A THR* 3.0 20.1 + - - +
570A ALA* 3.5 11.7 - - - +
572A ARG* 1.3 74.3 - - - +
574A GLN* 1.3 61.5 - - - +
576A TYR* 3.1 6.7 + - - +
577A LEU* 2.9 29.6 + - + +
610A TYR* 2.9 24.8 + - - -
640A GLU* 3.1 25.4 + - - +
645A LYS* 4.4 10.1 + - - +
646A VAL* 3.5 28.3 - - + +
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Residues in contact with GLN 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 ALA 3.2 10.7 + - - +
571A ARG* 2.9 14.9 + - - +
573A ASN* 1.3 74.9 - - - +
575A ASN* 1.3 65.3 + - - +
577A LEU* 3.1 23.4 + - + +
578A ASP* 2.9 63.6 + - - +
581A ARG* 4.7 5.5 - - - +
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Residues in contact with ASN 575 (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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532A THR* 3.9 29.8 + - + +
541A LYS* 6.0 0.4 - - - +
562A LEU* 3.8 20.0 - - + +
563A THR* 2.5 46.1 + - - +
571A ARG* 2.5 20.6 + - - +
572A ARG* 3.4 8.7 - - - +
574A GLN* 1.3 74.0 - - - +
576A TYR* 1.3 59.9 + - - +
578A ASP* 3.5 9.0 + - - +
579A ILE* 3.1 34.0 + - - +
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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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562A LEU* 5.0 5.6 - - + +
572A ARG 2.7 16.6 + - - +
573A ASN* 3.3 9.2 - - - +
575A ASN* 1.3 71.2 - - - +
577A LEU* 1.3 79.1 + - + +
579A ILE* 3.4 6.7 + - - +
580A LEU* 2.9 55.0 + - + +
596A SER* 5.4 0.7 - - - -
604A TRP* 3.7 28.3 - + - -
610A TYR* 5.1 1.3 - - - +
646A VAL* 4.1 18.8 - - + -
647A PHE* 3.3 73.1 + + + -
648A LEU* 4.0 4.7 + - + +
650A PHE* 3.7 12.1 - - - -
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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
----------------------------------------------------------
573A ASN* 2.9 20.7 + - + +
574A GLN* 3.5 25.6 - - + +
576A TYR* 1.3 93.9 - - + +
578A ASP* 1.3 64.9 + - - +
580A LEU* 3.5 8.7 + - + +
581A ARG* 3.1 61.1 + - - +
645A LYS 5.4 7.4 - - - +
646A VAL* 5.6 1.6 - - + -
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Residues in contact with ASP 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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530A VAL* 5.1 4.3 - - + -
532A THR* 5.9 8.0 - - + -
574A GLN* 2.9 46.6 + - - +
575A ASN* 4.0 9.6 - - - +
577A LEU* 1.3 75.7 - - - +
579A ILE* 1.3 58.6 + - + +
581A ARG* 3.7 7.4 - - - +
582A LEU* 2.8 57.1 + - + +
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Residues in contact with ILE 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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530A VAL* 4.8 12.3 - - + -
532A THR* 4.8 10.5 - - + -
542A GLY 4.5 1.8 - - - -
543A ALA* 3.3 44.4 - - + +
558A VAL* 4.4 1.1 - - + -
560A CYS* 4.3 4.9 - - + -
562A LEU* 3.8 26.2 - - + -
575A ASN 3.1 20.8 + - - +
576A TYR 3.9 2.2 - - - +
578A ASP* 1.3 73.3 - - + +
580A LEU* 1.3 67.4 + - - +
581A ARG 2.9 1.7 + - - -
583A LEU* 3.1 45.8 + - + +
604A TRP* 3.9 22.7 - - + -
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Residues in contact with LEU 580 (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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576A TYR* 2.9 47.4 + - + +
577A LEU* 3.7 9.9 - - + +
579A ILE* 1.3 77.7 - - - +
581A ARG* 1.3 55.1 - - + +
594A ASP* 2.7 41.3 - - - +
595A ILE* 3.3 40.8 + - + +
596A SER* 3.9 26.2 - - - +
598A ARG* 5.0 0.3 + - - -
604A TRP* 3.4 28.4 - - + -
650A PHE* 5.3 1.6 - - + -
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Residues in contact with ARG 581 (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 GLN* 4.7 5.9 - - - +
577A LEU* 3.1 59.9 + - - +
578A ASP* 3.9 8.0 + - - +
579A ILE 3.0 1.0 - - - -
580A LEU* 1.3 79.3 - - + +
582A LEU* 1.3 75.2 + - + +
583A LEU 3.3 2.4 + - - -
590A LEU* 3.4 21.0 - - - +
594A ASP* 3.5 21.7 + - - +
598A ARG* 4.3 4.2 + - - -
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Residues in contact with LEU 582 (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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529A SER 5.3 0.2 - - - +
530A VAL* 3.8 25.2 - - + +
531A LYS 6.0 0.4 - - - +
578A ASP* 2.8 39.3 + - + +
581A ARG* 1.3 82.1 - - + +
583A LEU* 1.3 61.1 + - - +
584A SER* 3.4 6.1 + - - -
590A LEU* 4.6 5.7 - - - +
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Residues in contact with LEU 583 (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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528A SER* 4.4 10.1 - - - +
529A SER* 4.1 18.8 - - - +
530A VAL* 3.1 30.3 - - + +
543A ALA* 4.3 8.5 - - + +
545A GLY* 4.9 4.9 - - - +
558A VAL* 4.0 18.6 - - + -
579A ILE* 3.1 29.6 + - + +
581A ARG 3.3 1.8 - - - +
582A LEU* 1.3 75.7 - - - +
584A SER* 1.3 54.2 + - - +
585A LEU* 3.1 12.4 + - + -
590A LEU* 4.6 1.1 - - - -
595A ILE* 3.6 34.2 - - + +
598A ARG* 2.6 34.1 + - - -
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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