Contacts of the helix formed by residues 568 - 579 (chain A) in PDB entry 3Q6N
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 PHE 568 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A LYS* 3.1 26.4 + - + -
565A LYS 3.8 2.2 - - - -
567A LYS* 1.3 93.2 - - + +
569A GLU* 1.3 65.1 + - - +
570A ASN 3.3 2.2 - - - -
571A LEU* 3.4 21.9 + - + +
572A CYS* 3.0 27.3 + - - -
588A VAL* 3.6 18.6 - - + -
636A ILE* 4.5 7.2 - - + -
638A PRO* 3.4 45.8 - - + -
643A ILE* 3.8 28.3 - - + -
644A GLU* 4.3 17.5 - - + -
647A ARG* 3.6 26.9 - - + -
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Residues in contact with GLU 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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565A LYS 3.1 14.2 + - - +
566A THR* 3.3 21.1 + - + +
568A PHE* 1.3 77.2 - - - +
570A ASN* 1.3 69.6 + - - +
572A CYS* 3.4 8.7 + - - +
573A LYS* 3.3 26.9 + - + +
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Residues in contact with ASN 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 THR 4.7 1.0 + - - -
567A LYS 4.6 2.5 + - - +
568A PHE 3.3 0.4 - - - -
569A GLU* 1.3 83.8 - - - +
571A LEU* 1.3 66.8 + - - +
573A LYS* 3.1 15.8 + - - +
574A ILE* 3.1 30.7 + - + +
651A GLU* 3.3 34.3 + - + +
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Residues in contact with LEU 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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568A PHE* 3.4 27.2 + - + +
570A ASN* 1.3 76.9 - - - +
572A CYS* 1.3 62.7 + - - +
574A ILE* 3.3 8.8 + - + +
575A MET* 3.0 41.1 + - + +
636A ILE* 4.0 13.2 - - + -
643A ILE* 3.8 26.2 - - + +
646A LEU* 3.8 22.0 - - + +
647A ARG* 4.0 18.6 - - + +
650A ALA* 3.7 28.5 - - + -
651A GLU* 4.5 3.6 + - - -
663A VAL* 5.7 0.2 - - + -
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Residues in contact with CYS 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 PHE 3.0 23.8 + - - +
569A GLU* 3.5 10.8 - - - +
571A LEU* 1.3 77.9 - - - +
573A LYS* 1.3 58.3 + - - +
575A MET 3.4 0.3 + - - -
576A LYS* 2.9 30.9 + - - +
586A VAL* 3.5 51.0 - - - +
587A VAL* 3.9 11.2 - - - -
588A VAL* 4.0 7.2 - - - -
636A ILE* 3.8 15.9 - - - -
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Residues in contact with LYS 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 GLU* 3.3 16.6 + - + +
570A ASN* 3.1 18.2 + - - +
572A CYS* 1.3 79.7 - - - +
574A ILE* 1.3 57.9 + - + +
576A LYS* 3.3 7.5 + - + +
577A ASP* 3.0 40.2 + - - +
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Residues in contact with ILE 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 ASN* 3.1 27.1 + - + +
571A LEU* 3.5 10.3 - - + +
573A LYS* 1.3 77.7 - - + +
575A MET* 1.3 58.5 + - + +
577A ASP* 3.1 10.8 + - + +
578A ILE* 2.8 50.0 + - + +
650A ALA* 4.0 35.4 - - + +
651A GLU* 4.8 6.7 - - + -
654A LYS* 4.2 34.8 - - + +
659A VAL* 5.2 1.1 - - + -
663A VAL* 6.1 0.2 - - + -
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Residues in contact with MET 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 LEU* 3.0 41.4 + - + +
572A CYS 3.9 3.4 - - - +
574A ILE* 1.3 72.4 - - + +
576A LYS* 1.3 55.8 + - - +
578A ILE* 3.7 7.6 - - - +
579A LEU* 2.7 40.1 + - + +
586A VAL* 4.0 14.1 - - + -
634A LEU* 3.7 27.4 - - + -
636A ILE* 3.9 21.5 - - + -
643A ILE* 5.2 2.5 - - + -
646A LEU* 4.1 18.2 - - + -
663A VAL* 3.9 35.4 - - + +
666A LEU* 5.2 6.1 - - + -
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Residues in contact with LYS 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 CYS 2.9 17.3 + - - +
573A LYS* 3.5 8.7 - - + +
575A MET* 1.3 77.1 - - - +
577A ASP* 1.3 65.8 + - - +
579A LEU* 3.3 4.0 + - - -
580A GLU* 3.0 38.8 + - - +
581A LYS* 6.3 1.0 - - - +
583A VAL* 3.5 19.1 - - + -
584A GLU* 3.5 20.8 + - - +
585A LYS* 4.6 2.0 - - - -
586A VAL* 3.8 21.7 - - + +
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Residues in contact with ASP 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 LYS* 3.0 24.8 + - - +
574A ILE* 3.1 12.0 + - + +
576A LYS* 1.3 79.6 - - - +
578A ILE* 1.3 65.5 + - + +
580A GLU* 3.1 21.6 + - - +
654A LYS* 6.1 0.9 - - - -
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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 ILE* 2.8 41.2 + - + +
575A MET* 3.7 5.6 - - - +
577A ASP* 1.3 74.4 - - + +
579A LEU* 1.3 59.1 + - - +
580A GLU* 3.2 13.7 + - - +
582A LYS* 5.6 2.1 + - - +
654A LYS 4.7 7.2 - - - +
656A ASP 5.9 0.2 - - - +
659A VAL* 4.3 8.1 - - + -
660A LYS* 3.7 53.3 - - + +
663A VAL* 4.0 29.8 - - + -
664A ILE* 4.3 11.6 - - + +
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Residues in contact with LEU 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 MET* 2.7 24.6 + - + +
576A LYS 4.0 1.3 - - - +
578A ILE* 1.3 72.9 - - - +
580A GLU* 1.3 68.0 + - - +
581A LYS 3.0 0.5 + - - -
582A LYS* 2.9 36.5 + - + +
583A VAL* 3.8 30.2 + - + -
586A VAL* 4.2 4.0 - - + -
634A LEU* 4.0 25.6 - - + -
663A VAL* 4.1 18.4 - - + +
664A ILE* 4.7 9.4 - - + -
667A TYR* 3.6 43.3 - - + -
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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