Contacts of the helix formed by residues 602 - 624 (chain C) in PDB entry 3A8P
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 602 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584C HIS* 3.5 19.9 + - - +
600C ALA* 3.4 4.4 + - - +
601C THR* 1.3 81.6 + - - +
603C GLN* 1.3 60.6 + - - +
604C THR* 3.3 10.1 + - - -
605C ASP* 3.0 20.1 + - - +
606C LEU* 2.9 27.9 + - - +
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Residues in contact with GLN 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C PRO* 6.1 0.3 - - - +
584C HIS* 3.4 19.6 + - + +
602C SER* 1.3 74.9 - - - +
604C THR* 1.3 59.2 + - - +
606C LEU* 3.3 22.7 + - - +
607C GLU* 2.8 63.3 + - - +
712D ALA* 3.7 36.6 - - + +
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Residues in contact with THR 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C SER* 3.2 8.1 + - - -
603C GLN* 1.3 80.0 - - - +
605C ASP* 1.3 61.8 + - - +
607C GLU* 3.2 12.1 + - + +
608C ASN* 2.9 44.4 + - - +
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Residues in contact with ASP 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C LYS* 3.1 27.2 + - - -
509C GLY* 6.0 0.7 - - - -
510C TRP 4.4 3.1 - - - +
600C ALA* 3.3 8.1 - - - +
601C THR* 2.9 46.7 + - - +
602C SER* 3.0 18.1 + - - +
604C THR* 1.3 76.9 - - - +
606C LEU* 1.3 63.0 + - - +
608C ASN* 3.1 9.4 + - - +
609C TRP* 2.9 36.4 + - - -
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Residues in contact with LEU 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C SER* 4.0 22.0 - - - -
584C HIS* 3.6 22.0 - - - +
585C VAL 3.5 26.7 - - - +
586C PHE* 4.0 12.5 - - + -
600C ALA* 3.5 14.2 - - + +
602C SER 2.9 13.8 + - - +
603C GLN* 3.5 30.3 - - - +
605C ASP* 1.3 76.5 - - - +
607C GLU* 1.3 69.1 + - + +
609C TRP* 3.0 7.2 + - - +
610C VAL* 2.9 40.7 + - + +
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Residues in contact with GLU 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603C GLN* 2.8 50.3 + - - +
604C THR* 3.5 13.3 - - + +
606C LEU* 1.3 82.1 - - + +
608C ASN* 1.3 63.0 + - - +
610C VAL* 3.5 5.0 + - - +
611C THR* 2.9 32.6 + - - +
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Residues in contact with ASN 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C LYS* 3.5 25.3 - - + +
604C THR* 2.9 36.8 + - - +
605C ASP* 3.1 8.2 + - - +
607C GLU* 1.3 78.8 - - - +
609C TRP* 1.3 58.6 + - - +
611C THR* 3.9 5.0 - - - -
612C ALA* 3.0 31.0 + - - +
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Residues in contact with TRP 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C LYS* 3.4 42.9 - - + +
508C ALA 3.9 3.4 - - - -
509C GLY* 3.8 22.4 - - - -
510C TRP 4.8 1.2 + - - -
511C LEU* 3.4 44.7 - - + +
538C VAL* 3.6 24.0 - - + -
539C THR 4.6 0.2 - - - -
540C LEU* 4.3 5.4 - - + -
545C LEU* 4.0 21.8 - - + -
586C PHE* 3.7 22.9 - + + -
600C ALA* 4.5 0.2 - - + -
605C ASP* 2.9 41.6 + - - -
606C LEU 3.5 7.4 - - - +
608C ASN* 1.3 76.0 - - - +
610C VAL* 1.3 63.4 + - - +
612C ALA* 3.9 1.5 - - + +
613C ILE* 3.0 49.4 + - + +
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Residues in contact with VAL 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C VAL* 3.9 28.7 - - + +
575C SER* 5.3 4.9 - - - +
586C PHE* 4.7 6.7 - - + -
606C LEU* 2.9 39.0 + - + +
607C GLU* 3.8 5.8 - - - +
609C TRP* 1.3 74.9 - - - +
611C THR* 1.3 59.0 + - - +
613C ILE* 4.1 1.0 - - - +
614C HIS* 3.0 56.4 + - + +
698C SER* 4.4 2.7 - - - +
704C LEU* 3.9 22.4 - - + -
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Residues in contact with THR 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C GLU* 2.9 18.9 + - - +
608C ASN* 3.9 5.4 - - - -
610C VAL* 1.3 77.6 - - - +
612C ALA* 1.3 56.7 + - - +
614C HIS 3.9 0.2 - - - -
615C SER* 2.6 41.6 + - - +
698C SER* 3.4 37.6 + - - +
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Residues in contact with ALA 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C ARG* 3.4 24.0 - - + +
507C LYS* 3.8 29.8 - - + -
540C LEU* 3.5 11.1 - - + +
608C ASN 3.0 19.4 + - - +
609C TRP* 3.9 2.9 - - + +
610C VAL 3.4 0.2 - - - -
611C THR* 1.3 78.8 - - - +
613C ILE* 1.3 62.2 + - + +
615C SER* 3.6 1.7 - - - -
616C ALA 3.0 19.1 + - - -
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Residues in contact with ILE 613 (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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540C LEU* 3.9 18.4 - - + -
543C CYS* 5.1 0.2 - - - -
545C LEU* 4.5 15.3 - - + -
568C ALA* 4.4 9.0 - - + -
571C SER* 5.2 1.3 - - - -
573C VAL* 3.5 31.6 - - + -
586C PHE* 4.3 15.9 - - + -
588C LEU* 4.4 20.4 - - + -
609C TRP* 3.0 38.9 + - + +
610C VAL 4.1 0.2 - - - +
612C ALA* 1.3 76.4 - - - +
614C HIS* 1.3 56.6 + - - +
616C ALA* 3.4 4.2 + - - +
617C CYS* 2.9 44.7 + - - -
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Residues in contact with HIS 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C SER 4.4 3.8 - - - -
572C ILE* 3.8 3.4 - - - -
573C VAL* 2.9 53.2 + - + +
610C VAL* 3.0 28.8 + - + +
613C ILE* 1.3 75.1 - - + +
615C SER* 1.3 56.6 + - - +
617C CYS* 3.2 5.2 + - - +
618C ALA* 2.7 36.1 + - - +
694C CYS* 3.5 26.4 + - + +
695C TYR* 3.9 29.4 - + + -
698C SER* 3.1 29.2 + - - +
704C LEU* 3.9 5.3 - - + +
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Residues in contact with SER 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C ARG* 3.3 25.1 - - - -
611C THR* 2.6 28.0 + - - +
612C ALA* 3.6 2.9 - - - -
614C HIS* 1.3 75.7 - - - +
616C ALA* 1.3 56.7 + - - +
618C ALA* 3.1 3.9 + - - +
619C SER* 2.8 30.7 + - - -
698C SER* 4.0 10.8 + - - -
699C LEU* 3.8 29.2 - - - +
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Residues in contact with ALA 616 (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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506C ARG* 3.9 21.2 - - - +
540C LEU* 4.2 7.0 - - + -
542C GLY 3.3 29.7 - - - +
543C CYS* 4.1 8.9 - - - +
612C ALA 3.0 17.7 + - - +
613C ILE* 3.6 4.3 - - - +
615C SER* 1.3 75.4 - - - +
617C CYS* 1.3 57.9 + - - +
619C SER* 3.3 3.0 + - - -
620C LEU* 2.9 30.5 + - - +
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Residues in contact with CYS 617 (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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543C CYS* 3.8 13.9 - - - -
568C ALA* 3.2 27.4 - - - -
570C ASP* 4.2 5.7 + - - +
571C SER* 3.8 15.7 - - - -
613C ILE* 2.9 33.6 + - - -
614C HIS* 3.2 8.0 + - - +
616C ALA* 1.3 77.0 - - - +
618C ALA* 1.3 53.1 + - - +
620C LEU* 3.3 2.2 + - - +
621C PHE* 2.7 36.6 + - - +
695C TYR* 3.4 24.6 - - + +
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Residues in contact with ALA 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614C HIS 2.7 20.7 + - - +
615C SER 3.4 4.7 - - - +
617C CYS* 1.3 72.0 - - - +
619C SER* 1.3 58.9 + - - +
621C PHE* 3.2 4.5 + - - +
622C ALA* 2.8 31.7 + - - +
630C THR* 3.7 20.1 - - + +
634C LEU* 4.3 2.5 - - + -
695C TYR* 3.6 31.3 - - + -
699C LEU* 3.9 13.7 - - + -
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Residues in contact with SER 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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506C ARG* 4.5 11.6 + - - -
615C SER 2.8 19.3 + - - -
616C ALA* 3.5 8.3 - - - -
618C ALA* 1.3 73.8 - - - +
620C LEU* 1.3 57.3 + - - +
622C ALA* 3.1 7.6 + - - +
623C LYS* 2.8 56.3 + - - +
630C THR* 4.3 8.9 - - - +
699C LEU* 5.9 0.2 - - - +
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Residues in contact with LEU 620 (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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543C CYS* 3.6 28.3 - - + -
569C GLU* 3.6 41.7 - - + +
570C ASP 5.3 0.2 - - - +
616C ALA 2.9 17.9 + - - +
617C CYS 3.7 3.4 - - - +
619C SER* 1.3 76.4 + - - +
621C PHE* 1.3 64.3 + - - +
623C LYS* 3.1 12.6 + - + +
624C LYS* 3.0 37.1 + - + +
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Residues in contact with PHE 621 (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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570C ASP* 3.5 24.2 - - - +
617C CYS 2.7 21.6 + - - +
618C ALA* 3.4 7.6 - - - +
620C LEU* 1.3 74.7 - - - +
622C ALA* 1.3 62.2 + - + +
624C LYS* 3.6 13.7 + - - +
625C HIS* 3.1 58.8 + + - -
633C LEU* 3.9 15.5 - - + -
634C LEU* 4.2 15.7 - - + -
637C GLN* 4.0 19.1 - - + -
691C ARG* 4.2 11.2 - - - -
692C MET* 3.8 34.1 - - + -
695C TYR* 4.5 2.9 - + + -
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Residues in contact with ALA 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 ALA 2.8 20.4 + - - +
619C SER 3.5 3.8 - - - +
621C PHE* 1.3 72.4 - - + +
623C LYS* 1.3 60.9 + - + +
625C HIS* 2.9 16.6 + - - +
626C GLY 3.0 8.7 + - - -
627C LYS* 3.2 22.8 + - + +
628C GLU 5.1 0.2 - - - +
630C THR* 3.7 28.5 - - + +
633C LEU* 3.5 21.8 - - + -
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Residues in contact with LYS 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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619C SER* 2.8 40.8 + - - +
620C LEU* 3.7 12.6 - - + +
622C ALA* 1.3 74.1 - - + +
624C LYS* 1.3 60.9 + - + +
625C HIS 3.1 0.2 - - - -
626C GLY* 3.1 14.0 + - - +
627C LYS 4.3 5.4 - - - +
628C GLU* 5.9 3.1 - - - -
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Residues in contact with LYS 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A SER* 4.8 12.6 - - - +
569C GLU* 2.6 41.2 + - - +
570C ASP* 3.5 14.7 + - - -
620C LEU* 3.0 32.5 + - + +
621C PHE* 3.9 13.9 - - - +
623C LYS* 1.3 77.1 - - - +
625C HIS* 1.3 62.1 + - + +
626C GLY 3.3 1.3 + - - -
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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
------------------------------------------------------------
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