Contacts of the helix formed by residues 707 - 727 (chain A) in PDB entry 3KN5
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 SER 707 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ILE* 3.7 5.3 + - - +
704A LEU 3.1 3.8 + - - -
705A GLY 2.9 6.3 + - - -
706A SER* 1.3 83.5 - - - +
708A GLY* 1.3 56.9 + - - +
709A ALA* 3.1 9.8 + - - +
710A ALA* 3.5 26.4 + - - +
711A VAL* 3.6 20.4 + - - +
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Residues in contact with GLY 708 (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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511A LYS* 3.7 21.3 + - - +
704A LEU* 2.6 24.5 + - - -
705A GLY 4.5 0.6 + - - -
707A SER* 1.3 71.6 - - - +
709A ALA* 1.3 59.2 + - - +
710A ALA 3.6 0.2 - - - -
711A VAL* 3.7 13.8 - - - +
712A HIS* 3.0 27.0 + - - +
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Residues in contact with ALA 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LYS* 4.8 0.6 - - - +
707A SER* 4.2 8.3 - - - +
708A GLY* 1.3 75.2 - - - +
710A ALA* 1.3 67.2 - - - +
712A HIS* 3.1 17.7 + - - +
713A THR* 3.3 13.1 + - - +
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Residues in contact with ALA 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A CYS* 5.1 0.2 - - - -
707A SER* 3.5 20.5 + - - +
709A ALA* 1.3 79.4 - - - +
711A VAL* 1.3 57.3 + - + +
713A THR* 3.1 8.3 + - - -
714A CYS* 3.0 30.5 + - - +
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Residues in contact with VAL 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A PHE* 4.9 8.5 - - + -
614A THR* 4.6 9.6 - - + -
618A GLY 3.8 21.5 - - - +
619A GLN* 5.3 0.4 - - - -
620A VAL* 4.6 11.2 - - + -
703A ILE* 5.4 2.7 - - + -
704A LEU* 4.1 19.7 - - + -
707A SER 3.6 14.1 + - - +
708A GLY* 3.6 14.4 + - - +
709A ALA 3.1 0.6 - - - -
710A ALA* 1.3 80.0 - - + +
712A HIS* 1.3 57.9 + - - +
714A CYS* 3.7 5.0 - - - +
715A VAL* 2.9 41.9 + - + +
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Residues in contact with HIS 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ANP 4.5 5.1 + - - -
505A GLU* 5.4 3.4 + - - -
548A GLU* 3.0 35.2 - - + +
708A GLY 3.0 19.0 + - - +
709A ALA* 3.1 7.1 + - - +
711A VAL* 1.3 81.1 - - - +
713A THR* 1.3 69.6 + - + +
715A VAL* 3.4 5.2 + - - +
716A LYS* 3.1 49.7 + - + +
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Residues in contact with THR 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A CYS* 4.9 0.7 - - - -
709A ALA 3.3 8.5 + - - +
710A ALA* 3.1 17.5 + - - -
712A HIS* 1.3 79.5 - - + +
714A CYS* 1.3 58.6 + - - +
716A LYS* 3.1 30.8 + - - +
717A ALA* 2.8 29.6 + - - +
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Residues in contact with CYS 714 (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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620A VAL* 3.7 26.9 - - + -
623A GLN 3.8 16.8 - - - -
631A CYS* 2.0 49.5 - - - -
637A ILE* 5.3 0.4 - - - +
710A ALA 3.0 19.7 + - - +
711A VAL* 3.7 1.3 - - - +
713A THR* 1.3 76.2 - - - +
715A VAL* 1.3 59.9 + - - +
717A ALA* 3.3 3.9 + - - +
718A THR* 3.0 27.3 + - - -
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Residues in contact with VAL 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A PHE* 5.2 1.1 - - + -
546A LYS* 5.3 2.7 - - + -
547A PRO* 3.7 28.9 - - + -
610A VAL* 5.0 4.0 - - + -
614A THR* 4.4 14.4 - - + +
620A VAL* 4.0 20.0 - - + -
711A VAL* 2.9 31.3 + - + +
712A HIS* 3.8 5.4 - - - +
714A CYS* 1.3 74.1 - - - +
716A LYS* 1.3 65.9 - - + +
718A THR* 3.1 6.5 + - - -
719A PHE* 3.1 47.4 + - + -
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Residues in contact with LYS 716 (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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400A ANP 3.3 32.1 + - - +
546A LYS* 5.0 12.8 - - + +
548A GLU* 4.5 2.5 - - - +
712A HIS* 3.1 45.4 + - + +
713A THR* 3.1 30.6 + - - +
715A VAL* 1.3 78.3 - - + +
717A ALA* 1.3 61.2 + - - +
719A PHE* 3.4 5.8 + - - +
720A HIS* 3.2 22.2 + - - +
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Residues in contact with ALA 717 (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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631A CYS* 4.6 5.8 - - - -
634A ALA* 4.8 6.4 - - + +
637A ILE* 4.0 18.7 - - + +
713A THR 2.8 15.8 + - - +
714A CYS* 3.5 12.8 - - - +
715A VAL 3.2 0.2 - - - -
716A LYS* 1.3 73.3 - - - +
718A THR* 1.3 58.4 + - - +
720A HIS* 3.3 8.8 + - - +
721A ALA* 3.0 28.2 + - - +
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Residues in contact with THR 718 (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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606A TRP* 3.8 21.7 - - + -
610A VAL* 5.0 9.2 - - + -
620A VAL* 3.4 19.5 - - + +
621A PRO* 4.0 5.7 + - + +
622A PHE* 4.1 20.9 - - + -
623A GLN 4.4 2.4 + - - -
637A ILE* 4.2 15.1 - - + +
641A ILE* 4.2 1.0 - - + +
714A CYS 3.0 14.6 + - - -
715A VAL* 3.1 8.5 + - - -
717A ALA* 1.3 76.7 - - - +
719A PHE* 1.3 64.9 + - - +
721A ALA* 3.3 8.1 + - - +
722A PHE* 3.1 20.8 + - - +
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Residues in contact with PHE 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ASP* 5.5 4.0 - - - +
545A LEU 3.4 29.2 - - - -
546A LYS* 3.6 31.9 - - + -
547A PRO* 4.5 3.1 - - + -
606A TRP* 4.7 9.0 - + - -
607A SER* 3.6 24.0 - - - -
610A VAL* 3.5 40.4 - - + -
611A ILE* 5.0 0.9 - - + -
715A VAL* 3.1 42.8 + - + +
716A LYS 3.9 3.8 - - - +
718A THR* 1.3 75.9 - - - +
720A HIS* 1.3 66.6 + - - +
722A PHE* 3.2 11.5 + + + +
723A ASN* 3.2 26.8 + - - +
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Residues in contact with HIS 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA* 4.1 13.5 - - + -
716A LYS 3.2 11.6 + - - +
717A ALA* 3.5 9.9 - - - +
719A PHE* 1.3 75.5 - - - +
721A ALA* 1.3 67.1 + - - +
723A ASN* 2.8 28.0 + - + +
724A LYS* 3.0 54.9 + - + +
727A ARG* 5.8 3.6 - - - -
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Residues in contact with ALA 721 (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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634A ALA* 3.7 21.5 - - - +
637A ILE* 3.9 20.4 - - + -
638A MET* 4.0 6.7 - - - +
641A ILE* 3.9 10.8 - - + -
717A ALA 3.0 12.8 + - - +
718A THR 3.5 9.4 - - - +
720A HIS* 1.3 76.5 - - - +
722A PHE* 1.3 61.0 + - - +
724A LYS* 3.6 14.6 + - - +
725A TYR* 3.1 24.3 + - - +
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Residues in contact with PHE 722 (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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602A SER 5.0 0.7 - - - -
603A CYS* 4.0 28.9 - - + -
606A TRP* 3.5 73.8 - + + -
607A SER* 5.8 0.7 - - - -
641A ILE* 3.8 9.4 - - + +
670A VAL* 4.7 3.4 - - + -
718A THR 3.1 7.2 + - - +
719A PHE* 3.4 11.0 - + - +
720A HIS 3.0 1.0 - - - -
721A ALA* 1.3 75.0 - - - +
723A ASN* 1.3 76.4 + - - +
725A TYR* 3.5 25.9 + + - -
726A LYS* 3.0 53.6 + - + +
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Residues in contact with ASN 723 (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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543A ARG 5.3 5.9 + - - -
603A CYS* 6.3 0.6 - - - -
719A PHE* 3.4 15.4 + - - +
720A HIS* 2.8 19.9 + - + +
722A PHE* 1.3 85.5 - - - +
724A LYS* 1.3 67.2 + - - +
726A LYS* 2.9 17.0 + - - +
727A ARG* 3.0 33.7 + - - +
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Residues in contact with LYS 724 (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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634A ALA* 4.2 14.4 - - + -
635A VAL* 4.6 13.2 - - - +
638A MET* 3.0 42.8 - - + +
720A HIS* 3.0 50.4 + - + +
721A ALA* 3.8 7.4 - - - +
723A ASN* 1.3 75.1 - - - +
725A TYR* 1.3 59.1 + - - +
727A ARG* 2.9 17.7 + - - +
728A GLU* 2.9 32.2 - - + +
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Residues in contact with TYR 725 (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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638A MET* 3.6 24.1 - - + -
641A ILE* 3.9 10.8 - - + -
642A LYS* 3.8 34.1 - - + -
670A VAL* 3.5 31.4 + - + +
721A ALA 3.1 15.1 + - - +
722A PHE* 3.5 28.3 - + - -
724A LYS* 1.3 78.3 - - - +
726A LYS* 1.3 89.9 + - + +
728A GLU* 3.1 23.9 - - - +
729A GLY* 3.8 4.2 - - - -
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Residues in contact with LYS 726 (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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600A ASP* 3.0 27.8 - - - +
602A SER* 3.5 18.1 + - - -
603A CYS* 3.9 10.3 - - - -
670A VAL* 5.8 1.4 - - - +
722A PHE* 3.0 47.9 + - + +
723A ASN* 2.9 9.6 + - - +
725A TYR* 1.3 101.2 + - + +
727A ARG* 1.3 67.9 + - - +
728A GLU* 3.7 0.2 - - - -
729A GLY* 3.4 12.6 - - - +
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Residues in contact with ARG 727 (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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720A HIS* 5.8 3.2 - - - -
723A ASN* 3.0 33.6 + - - +
724A LYS* 2.9 17.3 + - - +
726A LYS* 1.3 82.5 - - - +
728A GLU* 1.3 66.6 + - + +
729A GLY* 3.6 4.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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