Contacts of the helix formed by residues 569 - 586 (chain A) in PDB entry 3C7N
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 569 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A ALA 3.0 22.9 + - - +
566A GLU* 3.3 20.4 - - - +
567A THR 3.0 0.6 - - - -
568A GLU* 1.3 76.9 - - - +
570A ARG* 1.3 64.9 + - - +
572A ASN* 3.2 5.0 + - - +
573A THR* 2.9 29.9 + - - +
278B THR* 2.6 36.6 + - + +
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Residues in contact with ARG 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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566A GLU* 3.4 26.4 + - - +
567A THR 3.0 3.8 + - - +
569A ASP* 1.3 75.7 - - - +
571A LYS* 1.3 54.2 + - - +
572A ASN 2.7 15.5 + - - -
573A THR* 3.9 12.1 - - - +
574A LEU* 2.7 28.4 + - - +
621A LYS* 3.4 41.2 - - + +
624A TYR* 3.6 28.5 - - + +
625A ILE* 4.0 29.7 - - + +
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Residues in contact with LYS 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 THR 3.2 4.7 + - - +
568A GLU* 3.8 26.7 - - + +
570A ARG* 1.3 77.0 - - - +
572A ASN* 1.3 55.3 + - - +
574A LEU* 4.2 2.5 - - - +
575A GLU* 3.3 24.9 + - - +
612A LEU* 4.2 15.5 + - + +
617A PHE* 2.9 32.4 + - - +
618A ASP* 5.7 1.1 - - + -
624A TYR* 3.4 39.2 - - + +
279B GLN* 6.2 5.4 - - + +
298B THR* 4.9 10.3 + - - +
301B ARG* 3.3 33.6 - - - +
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Residues in contact with ASN 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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568A GLU 3.6 11.8 + - - +
569A ASP 3.2 9.4 + - - +
570A ARG 2.7 1.6 + - - -
571A LYS* 1.3 79.2 - - - +
573A THR* 1.3 57.4 + - - +
574A LEU 3.0 1.6 - - - -
575A GLU* 4.2 2.7 - - - -
576A GLU* 2.6 41.9 + - - +
278B THR* 3.6 24.5 + - - +
298B THR* 3.2 11.9 + - - +
299B ARG* 3.2 25.5 + - - +
300B ALA* 2.7 36.5 + - - +
303B GLU* 5.6 0.2 - - - +
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Residues in contact with THR 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ASP* 2.9 22.0 + - - +
570A ARG* 3.0 12.1 + - - -
572A ASN* 1.3 76.5 + - - +
574A LEU* 1.3 65.0 + - - +
576A GLU* 4.0 10.8 - - - +
577A TYR* 2.9 20.8 + - + +
625A ILE* 6.5 0.7 - - - -
628A TYR* 3.4 30.0 - - + +
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Residues in contact with LEU 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 ARG 2.7 16.4 + - - +
571A LYS 4.2 2.0 - - - +
573A THR* 1.3 72.8 - - - +
575A GLU* 1.3 57.6 - - - +
577A TYR* 2.6 27.1 + - + +
578A ILE* 2.9 16.5 + - + +
608A ALA* 4.6 3.8 - - + +
611A TRP* 4.6 2.9 - - + -
612A LEU* 3.2 37.9 - - + -
624A TYR* 4.0 22.6 + - + +
627A LYS* 3.9 17.0 - - + -
628A TYR* 3.7 41.3 - - + +
631A LEU* 3.9 18.4 - - + -
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Residues in contact with GLU 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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571A LYS* 3.3 18.3 + - - +
572A ASN* 3.3 4.2 + - - +
574A LEU* 1.3 79.7 - - - +
576A GLU* 1.3 60.1 + - - +
578A ILE* 3.3 9.4 + - - +
579A TYR* 2.7 40.9 + - + -
612A LEU* 3.8 16.6 - - + -
298B THR* 3.0 21.2 + - - +
300B ALA* 3.2 16.4 - - + -
301B ARG* 2.6 58.3 + - - +
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Residues in contact with GLU 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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572A ASN* 2.6 27.1 + - - +
573A THR* 4.0 10.3 - - - +
575A GLU* 1.3 70.8 - - - +
577A TYR* 1.3 80.2 + - - +
578A ILE 3.2 0.2 + - - -
579A TYR* 3.3 6.4 + - + +
580A THR* 3.0 38.7 + - + +
300B ALA* 3.6 16.4 - - + -
303B GLU* 4.1 19.7 - - - +
345B LYS* 5.7 5.5 + - - +
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Residues in contact with TYR 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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573A THR 2.9 19.3 + - - +
574A LEU* 2.6 13.2 + - + +
576A GLU* 1.3 78.4 + - - +
578A ILE* 1.3 63.2 + - - +
580A THR* 3.2 15.3 - - + +
581A LEU* 3.1 50.6 + - + +
628A TYR* 3.9 30.1 - + + -
631A LEU* 3.9 23.6 - - + -
632A ALA* 3.8 29.9 - - + -
635A GLY* 3.6 24.3 - - - -
636A ASN* 4.1 7.8 + - - -
639A ARG* 5.5 5.9 + - - -
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Residues in contact with ILE 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 LEU* 2.9 20.5 + - + +
575A GLU* 3.5 8.5 - - - +
576A GLU 3.1 0.2 - - - -
577A TYR* 1.3 79.6 - - - +
579A TYR* 1.3 71.6 + - + +
581A LEU* 3.2 6.1 + - - -
582A ARG* 3.3 29.2 + - - +
605A LEU* 3.4 25.6 - - + +
608A ALA* 3.2 39.9 - - + +
609A GLU* 3.6 25.4 - - - +
612A LEU* 4.8 8.1 - - + -
631A LEU* 4.2 19.1 - - + -
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Residues in contact with TYR 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* 2.7 44.7 + - + -
576A GLU* 3.3 5.0 + - - +
578A ILE* 1.3 78.8 - - + +
580A THR* 1.3 57.3 + - - +
581A LEU 3.1 0.3 + - - -
582A ARG* 3.1 35.4 - - - +
583A GLY* 3.0 27.4 + - - -
609A GLU* 4.0 18.0 + - - -
613A TYR* 4.8 6.6 + - - -
300B ALA* 3.5 25.1 - - + -
301B ARG* 3.7 9.8 + - - +
304B GLU* 3.6 44.2 - - + +
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Residues in contact with THR 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 GLU* 3.0 36.5 + - - +
577A TYR* 3.2 29.6 - - + +
579A TYR* 1.3 77.0 - - - +
581A LEU* 1.3 58.8 + - - +
583A GLY* 4.0 2.6 - - - +
584A LYS* 3.6 41.1 + - - +
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Residues in contact with LEU 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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577A TYR* 3.1 56.5 + - + +
578A ILE* 3.7 3.4 - - - +
579A TYR 3.1 0.2 - - - -
580A THR* 1.3 76.5 - - + +
582A ARG* 1.3 66.7 + - - +
583A GLY 3.1 1.1 - - - -
584A LYS* 3.1 3.9 + - - +
585A LEU* 3.0 34.3 + - + +
589A TYR* 4.8 16.7 - - + -
601A LEU* 3.7 30.5 - - + -
605A LEU* 3.8 15.7 - - + -
631A LEU* 4.4 7.6 - - + +
635A GLY* 4.6 9.4 - - - -
639A ARG* 6.3 1.8 - - + -
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Residues in contact with ARG 582 (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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578A ILE* 3.3 14.0 + - - +
579A TYR* 3.1 45.4 - - - +
581A LEU* 1.3 78.2 - - - +
583A GLY* 1.3 61.2 + - - +
584A LYS 3.1 4.5 + - - -
585A LEU* 3.4 11.0 + - + -
586A GLU* 2.9 26.9 - - - +
602A GLN 4.3 5.1 + - - +
605A LEU* 3.5 24.9 - - + +
606A ASN* 3.1 30.7 - - - +
609A GLU* 3.8 22.8 + - - -
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Residues in contact with GLY 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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579A TYR 3.0 17.7 + - - -
580A THR* 4.1 3.1 - - - -
581A LEU 3.1 0.2 - - - -
582A ARG* 1.3 77.0 - - - +
584A LYS* 1.3 64.0 + - - +
586A GLU* 4.5 2.2 - - - -
587A GLU* 3.4 21.9 - - - +
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Residues in contact with LYS 584 (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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580A THR* 3.6 31.6 + - - +
581A LEU* 3.1 3.4 + - - +
582A ARG 3.1 0.4 - - - -
583A GLY* 1.3 80.7 - - - +
585A LEU* 1.3 55.4 + - - +
586A GLU 2.9 6.1 - - - +
587A GLU* 3.7 5.4 - - + +
588A GLU* 3.0 42.6 + - + +
589A TYR* 2.6 67.6 + - + +
639A ARG* 5.4 5.1 - - - +
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Residues in contact with LEU 585 (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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581A LEU* 3.0 28.3 + - + +
582A ARG* 3.4 11.4 + - + +
584A LYS* 1.3 76.4 - - - +
586A GLU* 1.3 71.6 + - - +
589A TYR* 3.5 19.6 - - + -
590A ALA* 2.9 26.9 + - - +
593A ALA* 4.8 1.6 - - + -
598A LYS* 3.6 34.1 + - + +
601A LEU* 4.9 15.0 - - + -
602A GLN* 4.5 25.8 - - + +
605A LEU* 5.2 3.4 - - + -
638A ILE* 4.7 17.9 - - + -
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Residues in contact with GLU 586 (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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582A ARG* 2.9 21.5 + - - +
583A GLY* 5.2 2.2 - - - -
584A LYS 2.9 0.4 - - - -
585A LEU* 1.3 92.0 - - - +
587A GLU* 1.3 67.1 + - + +
588A GLU 3.3 2.9 + - - -
590A ALA* 3.8 17.3 - - + +
591A PRO* 4.9 2.1 - - - +
598A LYS* 5.7 4.2 - - - +
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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