Contacts of the helix formed by residues 575 - 592 (chain C) in PDB entry 5J87
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 575 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU* 3.4 19.6 - - - +
567C GLU* 4.8 4.7 + - - +
573C LYS* 3.8 22.8 + - - +
574C PHE* 1.3 73.9 - - - +
576C SER* 1.3 64.6 + - - +
577C LYS* 3.5 11.6 + - - +
578C SER* 3.1 30.4 + - - -
579C ASP* 3.5 4.2 + - - +
638C ALA* 5.1 2.8 - - - +
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Residues in contact with SER 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C GLU* 4.6 21.8 - - - -
518C LEU* 3.6 17.8 - - - +
575C SER* 1.3 75.1 - - - +
577C LYS* 1.3 77.9 + - - +
578C SER 3.4 0.2 - - - -
579C ASP* 3.2 9.7 - - - +
580C ILE* 3.1 25.7 + - - +
644C PHE* 4.2 2.8 - - - -
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Residues in contact with LYS 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C GLU* 4.3 4.8 + - - -
567C GLU* 4.5 1.6 - - - -
575C SER* 3.2 10.5 + - - +
576C SER* 1.3 93.0 + - - +
578C SER* 1.3 59.5 + - - +
579C ASP 3.2 1.6 - - - -
580C ILE* 3.4 10.5 + - + +
581C TRP 3.1 18.7 + - - -
638C ALA* 3.1 41.1 - - + +
639C ASP* 5.1 3.8 - - - +
641C ARG* 3.6 38.1 + - + -
642C PRO 3.4 9.6 + - - -
643C THR* 3.4 34.2 - - - +
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Residues in contact with SER 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU* 5.4 0.2 - - - +
563C TRP 4.6 0.2 - - - +
565C PRO* 3.4 32.6 - - - +
567C GLU* 4.2 4.1 + - - -
568C VAL* 3.7 15.4 - - - +
573C LYS 4.4 1.1 - - - -
574C PHE* 3.5 11.8 - - - +
575C SER* 3.1 31.9 + - - -
577C LYS* 1.3 73.2 - - - +
579C ASP* 1.3 66.2 + - - +
581C TRP* 3.5 3.0 + - - +
582C ALA* 3.4 19.6 + - - +
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Residues in contact with ASP 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C MET* 3.2 20.7 - - - +
517C PHE 4.1 2.3 - - - +
518C LEU* 3.5 15.4 - - + +
519C HIS* 2.9 26.3 + - - +
520C ARG* 3.3 24.3 + - - -
521C ASP 4.8 0.9 + - - -
522C LEU* 4.3 6.8 + - - +
575C SER 3.5 2.3 + - - +
576C SER* 3.2 17.8 + - - +
577C LYS 3.2 0.4 - - - -
578C SER* 1.3 80.6 + - - +
580C ILE* 1.3 61.4 + - - +
582C ALA* 3.2 6.6 + - - +
583C PHE* 3.1 17.8 + - - +
644C PHE* 3.6 18.0 - - + -
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Residues in contact with ILE 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C GLU* 4.0 1.6 - - - +
576C SER 3.1 15.4 + - - +
577C LYS* 3.4 17.9 - - + +
578C SER 3.3 0.2 - - - -
579C ASP* 1.3 76.4 - - - +
581C TRP* 1.3 64.4 + - - +
583C PHE* 3.3 8.7 + - - +
584C GLY 3.4 2.1 + - - -
633C CYS* 3.2 40.1 - - + +
641C ARG* 4.2 9.2 - - + -
642C PRO* 3.3 29.2 - - + +
643C THR* 3.6 2.7 - - - -
644C PHE* 3.5 43.3 - - + +
647C LEU* 3.7 11.0 - - + -
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Residues in contact with TRP 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C ARG 5.0 1.2 + - - -
563C TRP 3.5 20.0 + - - -
564C SER 3.7 9.1 + - - -
565C PRO* 3.5 21.8 - - + -
566C PRO* 3.3 25.8 - - + -
577C LYS 3.1 6.8 + - - +
578C SER 3.8 5.4 - - - +
579C ASP 3.2 0.6 - - - -
580C ILE* 1.3 77.7 - - - +
582C ALA* 1.3 62.0 + - - +
584C GLY 3.3 7.3 + - - -
585C VAL* 3.5 21.7 + - + +
598C TYR* 4.7 8.3 + - - -
610C ILE* 5.3 8.7 - - + -
615C ARG* 3.8 28.0 - - - -
633C CYS 3.5 16.4 - - - -
634C TRP* 3.4 51.9 + + + +
635C HIS 4.0 0.9 - - - -
641C ARG* 2.6 46.9 - - - +
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Residues in contact with ALA 582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LEU* 3.3 37.0 - - + +
563C TRP* 3.7 28.3 + - + +
578C SER 3.4 8.7 + - - +
579C ASP* 3.2 10.3 + - - +
581C TRP* 1.3 80.9 - - - +
583C PHE* 1.3 56.3 + - - +
585C VAL* 3.2 6.0 + - - +
586C LEU* 3.0 23.6 + - - +
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Residues in contact with PHE 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C CYS* 3.8 19.1 - - + -
505C VAL* 4.0 24.9 - - + -
506C CYS* 4.0 22.0 - - + -
522C LEU* 3.7 13.4 - - + +
579C ASP 3.1 6.4 + - - +
580C ILE 3.3 5.6 + - - +
582C ALA* 1.3 76.2 - - - +
584C GLY* 1.3 65.6 + - - +
586C LEU* 3.2 11.4 + - + +
587C MET* 3.0 56.5 + - + +
629C ILE* 5.6 0.2 - - + -
633C CYS* 4.0 5.8 - - - -
644C PHE* 3.4 25.6 - + + -
647C LEU* 3.8 36.3 - - + -
651C ILE* 4.2 7.6 - - + -
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Residues in contact with GLY 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C ILE 3.4 4.8 + - - -
581C TRP 3.3 6.7 + - - -
582C ALA 3.2 0.8 - - - -
583C PHE* 1.3 81.7 - - - +
585C VAL* 1.3 61.3 + - - +
587C MET* 3.2 10.7 - - - +
588C TRP* 3.1 20.1 + - - +
630C MET* 3.9 14.0 - - - +
633C CYS* 3.8 23.3 - - - -
634C TRP* 4.1 6.2 - - - -
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Residues in contact with VAL 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C ARG 3.9 15.9 - - - +
563C TRP* 3.5 28.9 - - + +
581C TRP* 3.5 27.1 - - + +
582C ALA 3.2 2.1 + - - +
584C GLY* 1.3 72.6 - - - +
586C LEU* 1.3 60.6 + - - +
588C TRP* 3.1 7.0 + - - +
589C GLU* 2.7 27.7 + - - +
597C PRO* 3.8 22.0 - - + -
598C TYR* 5.0 0.2 - - - +
616C LEU* 3.9 13.0 - - + -
634C TRP* 3.3 25.4 - - + +
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Residues in contact with LEU 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C LEU* 3.5 31.2 - - + -
502C CYS* 5.4 0.2 - - - -
505C VAL* 3.8 36.1 - - + -
522C LEU* 5.0 7.2 - - + +
523C ALA* 4.9 3.4 - - - -
524C ALA* 3.6 23.1 - - + +
527C CYS* 4.3 5.6 - - - -
563C TRP* 4.2 0.4 - - - +
582C ALA 3.0 13.0 + - - +
583C PHE* 3.2 19.0 + - + +
585C VAL* 1.3 76.6 - - - +
587C MET* 1.3 58.8 + - + +
589C GLU* 2.8 14.7 + - - +
590C ILE* 2.8 47.1 + - + +
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Residues in contact with MET 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499C LEU* 5.4 3.1 - - + -
502C CYS* 4.1 30.5 - - + -
583C PHE* 3.0 51.6 + - + +
584C GLY* 3.2 10.8 - - - +
586C LEU* 1.3 76.8 - - + +
588C TRP* 1.3 58.7 + - - +
590C ILE* 3.4 1.0 + - - +
591C TYR* 2.9 36.2 + - + -
626C VAL* 3.9 29.8 - - + +
629C ILE* 4.3 16.6 - - + -
630C MET* 4.0 32.8 - - + +
651C ILE* 5.1 5.4 - - + -
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Residues in contact with TRP 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584C GLY 3.1 9.7 + - - +
585C VAL 3.3 8.1 - - - +
587C MET* 1.3 79.1 - - - +
589C GLU* 1.3 62.3 + - - +
591C TYR 3.2 0.3 + - - -
592C SER* 2.8 46.1 + - - -
595C LYS* 3.5 35.4 - - + -
596C MET 3.7 16.2 - - - -
597C PRO* 3.6 26.5 - - + -
598C TYR 4.9 0.2 - - - -
616C LEU* 3.7 37.8 - - + +
617C TYR* 2.9 69.4 + + - -
619C PRO* 3.5 14.8 - - + -
630C MET* 4.2 9.8 - - + -
634C TRP* 5.6 0.9 - - + -
620D HIS* 5.0 0.2 - + - -
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Residues in contact with GLU 589 (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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483C LEU* 3.8 16.1 - - + +
486C LEU* 3.9 2.7 - - - +
523C ALA* 5.0 0.2 - - - +
524C ALA* 3.0 43.8 + - + +
525C ARG 4.9 0.2 + - - -
563C TRP* 2.9 38.4 + - - +
585C VAL 2.7 19.9 + - - +
586C LEU* 2.8 12.9 + - - +
588C TRP* 1.3 80.7 - - - +
590C ILE* 1.3 55.9 + - - +
592C SER* 3.6 1.1 + - - -
593C LEU 3.1 6.4 + - - -
594C GLY* 2.9 29.6 + - - -
595C LYS 4.5 6.3 - - - +
597C PRO* 4.0 21.4 - - + +
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Residues in contact with ILE 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C LEU* 4.3 7.4 - - + -
486C LEU* 3.9 22.4 - - + +
498C LEU* 3.6 39.6 - - + +
501C MET* 4.0 21.8 - - + +
502C CYS* 3.6 25.1 - - - +
505C VAL* 5.2 0.7 - - + -
535C VAL* 6.4 0.2 - - + -
586C LEU* 2.8 48.9 + - + +
587C MET 3.6 6.1 - - - +
589C GLU* 1.3 73.2 - - - +
591C TYR* 1.3 62.2 + - + +
593C LEU* 3.1 25.1 + - - +
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Residues in contact with TYR 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C THR* 4.2 8.7 + - - -
498C LEU* 4.3 20.6 - - + -
499C LEU* 3.4 33.3 + - + +
502C CYS* 3.9 25.1 - - - -
587C MET* 2.9 25.1 + - + +
590C ILE* 1.3 77.3 - - + +
592C SER* 1.3 59.9 + - - +
593C LEU 3.2 1.1 + - - -
619C PRO* 3.4 30.2 - - + +
620C HIS* 4.8 0.5 + - - +
621C LEU* 3.4 46.2 - - + +
622C ALA* 3.4 30.3 - - + -
623C SER 5.0 0.2 - - - -
626C VAL* 3.3 29.1 - - + +
630C MET* 4.4 5.2 - - + -
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Residues in contact with SER 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C TRP* 2.8 41.3 + - - -
589C GLU 4.1 2.0 - - - -
591C TYR* 1.3 74.3 - - - +
593C LEU* 1.3 70.9 + - - +
594C GLY 3.2 0.4 - - - -
595C LYS* 3.2 56.5 + - - +
619C PRO* 3.2 16.6 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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