Contacts of the helix formed by residues 610 - 633 (chain C) in PDB entry 4Q9U
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 LEU 610 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE* 6.3 1.3 - - + -
416A ALA* 5.1 9.6 - - + +
606C SER* 3.7 3.2 + - - +
607C GLU* 2.9 31.6 - - - +
608C ILE 2.8 0.6 + - - -
609C LEU* 1.3 78.3 - - - +
611C GLU* 1.3 87.5 + - + +
612C GLU 3.0 5.6 - - - -
613C LEU* 2.6 31.8 + - + +
614C GLN 2.8 7.6 + - - -
606D SER* 3.8 28.3 - - - +
609D LEU* 3.4 39.5 - - + -
610D LEU* 4.8 19.3 - - + -
613D LEU* 5.0 2.0 - - + +
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Residues in contact with GLU 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C GLU 3.0 6.9 - - - +
608C ILE* 2.6 49.6 + - - +
610C LEU* 1.3 73.7 - - + +
612C GLU* 1.3 67.6 + - - +
613C LEU 2.8 1.3 - - - -
614C GLN* 2.8 30.2 + - + +
615C GLN* 2.9 17.3 + - - +
582G GLU* 4.8 2.8 - - - +
585G ILE* 4.6 9.0 - - - +
581H LEU* 4.7 15.5 - - + +
584H PHE* 2.8 53.1 - - + -
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Residues in contact with GLU 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C ILE* 3.9 8.7 + - - +
609C LEU* 3.6 24.7 + - - +
610C LEU 3.0 0.2 - - - -
611C GLU* 1.3 79.2 + - - +
613C LEU* 1.3 62.3 + - + +
615C GLN* 3.5 13.1 + - - +
616C GLY* 2.9 21.0 + - - -
582G GLU* 4.4 19.6 - - - +
586G LYS* 4.4 24.3 - - - +
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Residues in contact with LEU 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 5.7 4.0 - - + +
419A LEU* 3.7 44.0 - - + +
420A GLU* 4.8 7.0 - - + +
423A LEU* 4.8 15.9 - - + -
609C LEU 3.3 22.2 - - - +
610C LEU* 2.6 16.2 + - + +
612C GLU* 1.3 77.0 - - + +
614C GLN* 1.3 64.9 + - - +
615C GLN 3.0 1.8 - - - -
616C GLY* 2.6 16.2 + - - +
617C LEU* 2.7 18.5 + - + +
613D LEU* 4.5 12.8 - - + -
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Residues in contact with GLN 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C LEU 2.8 10.5 + - - +
611C GLU* 2.8 30.2 + - + +
613C LEU* 1.3 72.0 - - - +
615C GLN* 1.3 61.2 + - - +
617C LEU* 3.6 18.6 - - + +
618C SER* 3.9 4.9 + - - -
609D LEU* 4.4 20.6 - - + -
613D LEU* 4.1 17.5 - - + +
577H ASP* 5.3 0.5 - - - +
580H GLU* 2.5 49.7 + - - +
581H LEU* 4.2 16.3 + - + +
584H PHE* 5.1 4.8 - - + +
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Residues in contact with GLN 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611C GLU 2.9 11.6 + - - +
612C GLU* 3.5 15.7 + - - +
614C GLN* 1.3 78.6 - - - +
616C GLY* 1.3 67.3 + - - +
618C SER* 2.9 15.0 + - - -
619C GLN* 3.0 12.5 + - - +
578G LYS* 2.2 33.0 + - - +
582G GLU* 3.0 30.7 + - - +
577H ASP* 3.5 23.1 - - - +
581H LEU* 3.8 11.2 - - + +
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Residues in contact with GLY 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 5.8 5.1 - - - +
612C GLU 2.9 19.3 + - - -
613C LEU* 2.6 13.7 + - - -
615C GLN* 1.3 74.9 - - - +
617C LEU* 1.3 60.1 + - - -
619C GLN* 3.2 15.7 + - - +
620C ALA* 3.1 22.5 + - - +
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Residues in contact with LEU 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 5.6 11.4 - - + -
613C LEU* 2.7 16.7 + - + +
614C GLN* 3.6 18.2 - - - +
616C GLY* 1.3 71.9 - - - -
618C SER* 1.3 80.9 + - - +
620C ALA* 3.1 5.9 + - - +
621C LYS* 2.9 37.8 + - + +
613D LEU* 5.0 26.7 - - + +
616D GLY* 4.6 7.4 - - - +
617D LEU* 4.5 26.7 - - + +
620D ALA* 6.0 2.7 - - + -
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Residues in contact with SER 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614C GLN* 4.2 5.8 + - - -
615C GLN 2.9 6.9 + - - -
617C LEU* 1.3 90.7 - - - +
619C GLN* 1.3 54.9 + - - +
621C LYS* 3.0 21.9 + - - +
622C ARG* 3.0 34.5 + - - +
576H LYS* 2.7 27.0 + - - -
577H ASP* 3.4 24.4 + - - -
580H GLU* 5.1 2.3 + - - -
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Residues in contact with GLN 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A THR* 5.7 2.6 - - - +
615C GLN 3.0 11.2 + - - +
616C GLY* 3.2 18.7 + - - +
617C LEU 3.1 0.2 - - - -
618C SER* 1.3 74.1 - - - +
620C ALA* 1.3 76.7 + - - +
621C LYS 3.1 1.8 - - - -
622C ARG* 3.0 17.1 + - + +
623C ASP* 2.9 42.5 + - - +
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Residues in contact with ALA 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 5.2 4.9 - - + -
426A TRP* 4.6 10.4 - - + -
427A THR* 3.8 28.7 - - + -
616C GLY 3.1 10.5 + - - +
617C LEU* 3.1 7.8 + - - +
619C GLN* 1.3 91.2 - - - +
621C LYS* 1.3 56.8 + - - +
623C ASP* 3.2 12.0 - - - +
624C VAL* 3.0 31.9 + - + +
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Residues in contact with LYS 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TRP* 5.3 6.9 - - + -
617C LEU* 2.9 19.7 + - + +
618C SER* 3.0 34.9 + - - +
620C ALA* 1.3 78.9 - - - +
622C ARG* 1.3 60.3 + - - +
624C VAL* 5.3 0.2 - - - -
625C GLN* 3.0 31.7 + - - +
620D ALA* 5.6 9.6 - - + -
276E ILE* 6.1 3.4 - - - +
573H LYS* 4.5 15.5 - - - +
576H LYS* 3.0 34.7 - - - +
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Residues in contact with ARG 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C SER* 3.0 19.9 + - - +
619C GLN* 3.0 21.4 + - + +
621C LYS* 1.3 79.0 - - + +
623C ASP* 1.3 65.1 - - + +
625C GLN* 3.6 4.7 + - - +
626C GLU* 3.0 25.6 + - - +
575G MET* 6.3 1.0 - - - +
570H GLN* 3.3 28.1 - - - +
573H LYS* 3.3 45.5 + - - +
574H THR* 4.0 12.9 + - - +
576H LYS* 5.4 0.6 - - - +
577H ASP* 4.4 12.7 + - - -
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Residues in contact with ASP 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A THR* 5.4 2.3 - - - -
619C GLN* 2.9 28.2 + - - +
620C ALA* 3.2 27.9 - - - +
622C ARG* 1.3 77.2 - - + +
624C VAL* 1.3 67.0 + - - +
626C GLU* 2.6 41.1 + - - +
627C GLN* 2.8 29.8 + - - +
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Residues in contact with VAL 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TRP* 4.9 10.8 - - + -
427A THR* 4.5 12.3 - - - +
430A ILE* 3.4 42.0 - - + -
431A ALA* 6.2 0.2 - - + -
620C ALA* 3.0 18.6 + - + +
621C LYS* 5.3 0.4 - - - -
623C ASP* 1.3 89.3 - - - +
625C GLN* 1.3 65.9 + - - +
626C GLU 3.0 0.9 - - - -
627C GLN* 3.4 19.1 + - + +
628C MET* 3.8 13.0 + - + +
624D VAL* 3.6 28.5 - - + +
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Residues in contact with GLN 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621C LYS 3.0 23.4 + - - +
622C ARG* 3.9 5.2 - - - +
624C VAL* 1.3 75.7 - - - +
626C GLU* 1.3 61.4 + - - +
628C MET* 3.6 15.6 + - + +
629C ALA* 4.0 4.5 + - - +
624D VAL* 5.9 1.3 - - - -
627D GLN* 3.7 28.4 + - - +
220E TYR* 5.3 7.1 + - - -
282E ARG* 5.2 1.9 + - - -
330E ARG* 6.0 3.4 - - - +
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Residues in contact with GLU 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622C ARG 3.0 15.2 + - - +
623C ASP* 2.6 34.8 + - - +
625C GLN* 1.3 73.8 - - - +
627C GLN* 1.3 72.7 + - - +
628C MET 3.0 2.9 - - - -
629C ALA* 2.6 32.9 + - + +
630C VAL* 2.9 34.7 + - - +
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Residues in contact with GLN 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ILE* 5.4 9.4 - - + +
431A ALA* 4.6 20.0 - - - +
434A VAL* 5.5 9.2 - - + -
623C ASP* 2.8 48.6 + - - +
624C VAL* 3.4 20.4 + - + +
626C GLU* 1.3 92.9 + - - +
628C MET* 1.3 61.3 + - + +
630C VAL* 3.0 16.9 + - + +
631C LEU* 2.9 29.4 + - - +
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Residues in contact with MET 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ILE* 4.9 8.3 - - + -
624C VAL* 3.8 15.0 - - + +
625C GLN* 3.9 13.0 - - + +
626C GLU 3.0 0.4 - - - -
627C GLN* 1.3 79.5 - - + +
629C ALA* 1.3 57.3 + - - +
631C LEU* 3.1 20.6 - - + +
632C MET* 3.0 34.3 + - + +
624D VAL* 4.2 23.6 - - + +
627D GLN* 3.8 27.1 - - - +
628D MET* 3.5 51.1 - - + -
631D LEU* 3.8 14.6 - - + -
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Residues in contact with ALA 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C GLN* 4.0 3.4 + - - +
626C GLU* 2.6 27.6 + - + +
628C MET* 1.3 71.5 - - - +
630C VAL* 1.3 61.1 + - - +
631C LEU 3.1 1.6 - - - -
632C MET* 3.1 27.3 + - + +
633C GLN* 3.9 9.2 + - - +
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Residues in contact with VAL 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C GLU* 2.9 24.7 + - - +
627C GLN* 3.0 32.5 + - + +
629C ALA* 1.3 77.0 - - - +
631C LEU* 1.3 61.9 + - + +
633C GLN* 4.7 2.4 + - - +
634C SER* 3.7 13.3 + - - -
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Residues in contact with LEU 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627C GLN 2.9 9.4 + - - +
628C MET* 3.1 46.7 - - + +
630C VAL* 1.3 82.0 - - + +
632C MET* 1.3 57.0 + - - +
633C GLN 3.2 0.7 - - - -
634C SER* 2.6 39.5 + - - -
628D MET* 5.4 1.6 - - + -
631D LEU* 3.5 31.9 - - + -
632D MET* 3.7 33.9 - - + -
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Residues in contact with MET 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C MET* 3.0 23.8 + - + +
629C ALA* 3.1 19.5 + - - +
631C LEU* 1.3 82.9 - - + +
633C GLN* 1.3 66.0 + - + +
634C SER 3.3 1.1 - - - -
627D GLN* 5.2 0.2 - - - +
631D LEU* 3.7 25.1 - - + -
134E GLU* 4.3 8.3 - - - +
282E ARG* 3.2 39.0 - - - +
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Residues in contact with GLN 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629C ALA 3.9 8.2 + - - +
630C VAL 4.7 2.7 + - - +
631C LEU 3.2 0.8 - - - -
632C MET* 1.3 82.5 + - + +
634C SER* 1.3 64.7 + - - +
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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