Contacts of the helix formed by residues 647 - 663 (chain C) in PDB entry 6PUO
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 ASP 647 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C ASP* 4.4 8.5 - - - +
645C SER* 4.2 3.0 + - - -
646C GLN* 1.3 78.6 + - + +
648C CYS* 1.3 64.5 + - - +
649C ILE 3.4 2.2 + - - -
650C ALA* 3.8 6.3 + - + +
651C ALA* 3.4 17.7 + - - +
707C ARG* 3.5 29.9 + - - +
709C SER* 4.0 13.9 - - - -
711C ALA* 4.3 7.8 - - - +
712C TRP* 4.2 18.5 + - - -
1122C LEU* 4.2 10.5 - - + -
1125C GLU* 3.3 12.3 - - - +
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Residues in contact with CYS 648 (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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642C TRP* 3.3 33.8 + - + +
645C SER* 4.3 6.7 - - - +
646C GLN 3.6 2.4 + - - +
647C ASP* 1.3 72.6 - - - +
649C ILE* 1.3 59.4 + - - -
650C ALA 3.5 0.2 - - - -
651C ALA* 3.3 3.5 + - - -
652C ALA* 2.9 26.9 + - - +
689C VAL* 3.8 27.8 - - - -
1125C GLU* 2.8 29.8 + - - -
1129C LYS* 3.6 31.6 - - + -
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Residues in contact with ILE 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647C ASP 3.4 0.8 - - - -
648C CYS* 1.3 74.3 - - - +
650C ALA* 1.3 66.7 + - - +
652C ALA* 3.3 5.7 + - - +
653C LEU* 3.0 30.0 + - + +
686C ALA* 4.4 16.3 - - + +
689C VAL* 3.8 32.1 - - + -
690C PHE* 4.3 22.7 - - + -
693C CYS* 5.4 1.3 - - + -
704C LEU* 3.8 31.0 - - + -
705C LEU* 6.2 0.9 - - + -
717C CYS* 3.7 20.4 - - - -
729C PHE* 4.7 10.5 - - + -
1125C GLU* 3.6 9.8 + - + +
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Residues in contact with ALA 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647C ASP* 3.8 12.8 + - + +
648C CYS 3.5 0.2 - - - -
649C ILE* 1.3 79.2 - - - +
651C ALA* 1.3 57.4 + - - +
653C LEU* 3.4 3.1 + - - +
654C ALA* 2.9 31.4 + - - +
707C ARG* 6.2 0.4 - - - +
709C SER* 4.7 10.3 - - - +
712C TRP* 4.2 21.7 - - + -
716C THR 6.3 0.2 - - - -
717C CYS* 3.9 20.7 - - + -
720C LEU* 4.0 10.0 - - + +
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Residues in contact with ALA 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626C LEU* 4.5 7.4 - - + -
642C TRP* 4.2 13.7 - - + +
645C SER* 4.2 11.0 - - - +
647C ASP* 3.4 13.4 + - - +
648C CYS* 3.3 10.0 + - - +
649C ILE 3.2 0.6 - - - -
650C ALA* 1.3 79.2 - - - +
652C ALA* 1.3 57.1 + - - +
654C ALA* 3.9 1.2 - - - +
655C CYS* 3.0 35.6 + - - -
712C TRP* 3.6 27.4 - - + +
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Residues in contact with ALA 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C TRP* 4.1 15.2 - - + +
648C CYS 2.9 17.0 + - - +
649C ILE 3.3 0.6 + - - +
651C ALA* 1.3 75.5 - - - +
653C LEU* 1.3 59.1 + - - +
655C CYS* 3.4 2.3 + - - +
656C SER* 3.0 28.1 + - - -
682C TYR* 3.7 39.5 - - + +
685C ARG* 4.8 0.4 - - + -
686C ALA* 3.8 19.5 - - + +
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Residues in contact with LEU 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C ILE* 3.0 18.1 + - + +
650C ALA 3.9 3.8 - - - +
652C ALA* 1.3 78.1 - - - +
654C ALA* 1.3 57.3 + - - +
656C SER* 2.8 19.3 + - - -
657C LYS* 3.0 14.0 + - - +
683C GLU* 5.2 4.9 - - - -
686C ALA* 3.9 20.2 - - + -
717C CYS* 3.5 40.4 - - - +
720C LEU* 4.1 17.0 - - + +
721C ALA* 4.1 17.5 - - + +
724C ALA* 4.9 1.6 - - - +
726C ASP* 3.7 20.6 - - - +
729C PHE* 4.2 24.7 - - + -
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Residues in contact with ALA 654 (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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569C LEU* 4.2 12.1 - - + +
650C ALA 2.9 18.5 + - - +
651C ALA 3.9 1.3 - - - +
653C LEU* 1.3 76.0 - - - +
655C CYS* 1.3 59.0 + - - +
657C LYS* 3.3 7.4 + - - +
658C ILE* 2.9 34.6 + - + +
712C TRP* 3.7 34.8 - - + -
720C LEU* 4.2 14.3 - - + +
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Residues in contact with CYS 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626C LEU* 4.0 24.5 - - - -
627C ILE* 5.8 3.4 - - - -
630C ILE* 3.7 33.2 - - + -
651C ALA 3.0 20.6 + - - +
652C ALA 3.8 4.0 - - - +
654C ALA* 1.3 74.7 - - - +
656C SER* 1.3 64.4 + - - +
658C ILE* 3.4 8.5 + - - +
659C LEU* 3.0 31.9 + - + +
682C TYR* 4.3 19.7 - - + -
712C TRP* 5.2 7.6 - - - -
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Residues in contact with SER 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C ALA 3.0 15.2 + - - -
653C LEU* 2.8 11.2 + - - -
655C CYS* 1.3 79.9 - - - +
657C LYS* 1.3 59.2 + - - +
660C LYS* 2.9 34.4 + - - +
679C ALA* 3.8 31.7 - - - +
682C TYR* 4.7 1.9 - - - +
683C GLU* 4.5 7.4 - - - -
724C ALA* 4.0 3.5 - - - +
726C ASP* 2.9 29.4 + - - -
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Residues in contact with LYS 657 (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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568C LEU 3.6 19.4 + - - -
569C LEU* 3.6 30.7 - - + +
570C GLY* 4.7 3.2 - - - +
572C PHE* 5.8 1.1 - - + -
653C LEU 3.0 12.8 + - - +
654C ALA* 3.6 6.7 - - - +
655C CYS 3.3 0.2 - - - -
656C SER* 1.3 82.1 + - - +
658C ILE* 1.3 59.4 + - - +
660C LYS* 3.8 2.8 - - + +
661C GLU* 3.0 46.5 + - - +
720C LEU* 4.9 10.1 - - + +
723C GLU* 4.3 21.4 + - + +
724C ALA* 3.8 31.6 - - + +
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Residues in contact with ILE 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C LEU* 4.4 19.5 - - + -
568C LEU* 4.7 18.7 - - + +
569C LEU* 3.8 29.2 - - + -
627C ILE* 4.9 19.1 - - + -
630C ILE* 4.4 19.1 - - + -
631C VAL* 4.4 15.3 - - + -
654C ALA* 2.9 24.6 + - + +
655C CYS* 3.8 8.5 - - - +
657C LYS* 1.3 76.4 - - - +
659C LEU* 1.3 59.2 + - + +
661C GLU* 3.2 6.8 + - - +
662C LEU* 2.9 30.8 + - + +
712C TRP* 5.5 2.5 - - + -
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Residues in contact with LEU 659 (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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630C ILE* 3.8 39.7 - - + +
633C ASN* 5.7 0.7 - - - +
655C CYS 3.0 21.7 + - - +
658C ILE* 1.3 78.0 - - + +
660C LYS* 1.3 58.3 + - - +
662C LEU* 3.8 8.8 - - + +
663C SER* 2.9 32.4 + - - -
675C MET* 4.0 31.3 - - + +
678C LEU* 3.7 36.8 - - + +
679C ALA* 3.7 26.0 - - + +
682C TYR* 5.2 2.7 - - + -
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Residues in contact with LYS 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C SER* 2.9 21.9 + - - +
657C LYS* 3.9 5.2 - - + +
659C LEU* 1.3 78.4 - - - +
661C GLU* 1.3 61.1 + - - +
663C SER* 3.9 7.2 + - - -
664C LYS* 3.9 20.8 + - + +
676C LEU* 4.5 19.9 - - + +
679C ALA* 4.2 20.9 + - - +
680C GLU* 5.4 4.0 - - - +
683C GLU* 5.0 3.8 + - - -
724C ALA* 3.4 23.3 + - + +
725C LYS* 4.7 9.6 + - + -
726C ASP* 3.3 25.2 + - - -
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Residues in contact with GLU 661 (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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567C GLU 5.2 1.8 - - - +
568C LEU* 3.6 42.0 - - + +
657C LYS* 3.0 34.6 + - - +
658C ILE* 3.6 4.5 - - - +
660C LYS* 1.3 78.5 - - - +
662C LEU* 1.3 62.5 + - - +
663C SER 3.4 0.3 + - - -
664C LYS* 3.3 40.3 + - - +
665C GLU* 4.3 14.7 - - - +
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Residues in contact with LEU 662 (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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531C LEU* 4.1 33.2 - - + +
532C PHE* 5.1 10.1 - - + +
535C LYS* 4.8 7.4 - - + -
568C LEU* 3.7 33.4 - - + -
631C VAL* 4.2 29.4 - - + +
658C ILE* 2.9 18.9 + - + +
659C LEU* 3.3 10.3 + - + +
661C GLU* 1.3 77.1 - - - +
663C SER* 1.3 62.3 + - - +
664C LYS 3.2 1.0 + - - -
665C GLU* 3.6 11.0 + - - +
666C GLU* 4.2 5.5 + - - +
675C MET* 4.0 29.0 - - + +
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Residues in contact with SER 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659C LEU 2.9 16.9 + - - -
660C LYS* 4.4 6.5 - - - -
661C GLU 3.3 0.6 - - - -
662C LEU* 1.3 76.9 - - - +
664C LYS* 1.3 61.3 + - - +
665C GLU 3.4 0.4 + - - -
666C GLU* 4.4 7.3 + - - -
672C SER* 3.2 42.6 + - - -
675C MET* 4.1 16.5 - - - -
676C LEU* 4.2 18.2 - - - +
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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