Contacts of the strand formed by residues 611 - 622 (chain C) in PDB entry 6DBV
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 PHE 611 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593C ILE* 5.8 7.2 - - + -
597C LEU* 4.0 33.4 - - + -
607C CYS* 3.1 27.1 - - + -
608C THR 4.8 3.1 - - - -
609C SER 2.5 10.4 + - - +
610C GLY* 1.3 74.0 - - - -
612C THR* 1.3 67.7 + - - +
649C ILE* 3.5 21.3 - - + -
650C SER 3.0 20.0 - - - -
651C ILE* 3.4 21.1 - - + -
652C ARG* 5.6 0.2 - - - +
662C ILE* 4.7 5.8 - - + -
718C ARG* 4.6 14.8 - - + -
719C SER 3.6 15.5 - - - +
720C PHE* 3.9 28.0 - + + -
721C ARG* 3.3 24.1 + - - +
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Residues in contact with THR 612 (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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610C GLY 5.6 0.2 - - - -
611C PHE* 1.3 82.0 + - - +
613C VAL* 1.3 66.8 + - - +
614C VAL* 4.3 6.9 + - + +
648C SER 4.1 0.5 - - - +
649C ILE* 3.3 5.2 - - - +
650C SER* 3.0 37.7 + - - -
651C ILE 6.0 1.1 - - - -
652C ARG* 5.1 9.7 - - - +
721C ARG* 3.2 18.8 + - - +
723C PHE* 3.6 46.8 - - + -
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Residues in contact with VAL 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582C LEU* 6.3 0.2 - - + -
586C LEU* 3.8 15.5 - - + -
612C THR* 1.3 73.4 - - - +
614C VAL* 1.3 72.8 + - - +
615C VAL* 4.4 5.6 - - + -
646C ILE* 4.1 20.0 - - + -
648C SER 3.2 10.1 - - - +
649C ILE* 3.6 27.1 - - + -
720C PHE* 3.6 24.2 - - + -
721C ARG 3.1 5.5 + - - -
722C PHE* 3.3 29.4 - - + +
723C PHE 3.1 22.7 + - - -
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Residues in contact with VAL 614 (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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612C THR* 4.8 10.1 - - + +
613C VAL* 1.3 78.7 - - - +
615C VAL* 1.3 61.9 + - - +
647C MET* 2.9 32.4 + - + +
648C SER* 2.9 26.7 + - - +
723C PHE* 3.7 18.8 - - + +
725C ARG* 4.4 20.6 - - + +
978C TRP* 3.7 30.7 - - + -
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Residues in contact with VAL 615 (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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578C TYR* 4.2 8.7 - - - +
582C LEU* 4.4 17.9 - - + -
613C VAL* 4.4 6.1 - - + -
614C VAL* 1.3 79.4 - - - +
616C LYS* 1.3 72.7 - - - +
617C GLU* 5.1 2.0 - - + -
644C PHE* 4.4 10.1 - - + -
645C THR 4.3 2.2 - - - +
646C ILE* 5.0 6.3 - - + -
722C PHE* 4.4 22.7 - - + -
723C PHE 3.2 11.8 + - - +
724C PHE* 3.7 32.3 - - + -
725C ARG* 3.3 29.5 + - - +
978C TRP* 5.0 0.4 - - - -
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Residues in contact with LYS 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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614C VAL 4.2 1.2 + - - -
615C VAL* 1.3 76.2 - - - +
617C GLU* 1.3 74.6 + - - +
618C SER* 6.0 2.9 - - - -
644C PHE* 3.2 9.2 - - - +
645C THR* 3.0 54.2 + - - +
647C MET* 4.0 16.2 - - + +
668C PRO* 3.2 37.2 + - - +
669C ASN* 5.3 0.6 + - - +
673C SER 5.6 0.2 + - - -
674C CYS* 6.1 1.8 - - - -
725C ARG 4.1 2.9 - - - -
727C THR* 3.8 15.0 - - + +
728C GLY* 6.1 0.2 - - - -
977C ALA 4.1 7.3 + - - +
978C TRP* 4.0 37.8 - - + +
979C ALA 4.0 14.1 + - - +
982C GLY* 6.0 2.4 - - - -
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Residues in contact with GLU 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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578C TYR* 4.3 6.7 + - - +
615C VAL* 5.1 0.9 - - + -
616C LYS* 1.3 82.3 - - - +
618C SER* 1.3 63.5 + - - +
642C PHE* 3.9 18.7 - - + -
643C SER 3.4 14.6 - - - +
644C PHE* 3.9 7.0 - - + +
701C ARG* 2.7 36.4 + - - -
724C PHE* 4.3 5.0 - - - -
725C ARG 2.6 28.1 + - - +
726C GLY* 3.0 21.0 + - - -
727C THR* 3.7 3.9 + - - +
728C GLY* 2.9 22.1 + - - -
729C TYR* 4.1 12.3 + - - +
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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
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616C LYS* 6.0 3.1 - - - -
617C GLU* 1.3 80.8 - - - +
619C CYS* 1.3 64.0 + - - +
642C PHE* 3.7 2.3 - - - -
643C SER* 3.0 34.6 + - - +
674C CYS* 4.7 3.1 - - - -
728C GLY* 3.1 22.7 - - - -
729C TYR* 3.7 7.0 - - - -
979C ALA 5.7 0.2 - - - -
980C SER* 4.4 9.2 - - - -
983C ASN* 2.3 38.5 + - - -
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Residues in contact with CYS 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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618C SER* 1.3 81.2 - - - +
620C ASP* 1.3 61.8 + - - +
640C VAL* 3.6 25.8 - - - -
641C ARG 3.8 6.3 - - - -
642C PHE* 3.7 24.9 - - + -
680C MET* 5.7 0.2 - - - -
690C LEU* 5.6 2.5 - - - -
694C LEU* 5.3 3.4 - - - -
728C GLY 3.2 8.0 + - - +
729C TYR* 3.4 27.7 - - + -
730C ASP* 4.8 4.3 + - - +
733C MET* 3.5 30.1 - - - +
737C MET* 5.1 4.9 - - + -
983C ASN* 3.8 0.9 - - - +
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Residues in contact with ASP 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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619C CYS* 1.3 76.3 - - - +
621C GLY* 1.3 83.8 + - - +
640C VAL* 3.3 8.1 - - - +
641C ARG* 3.0 29.3 + - - +
684C GLU* 4.4 10.2 - - - +
728C GLY 5.8 0.9 - - - +
730C ASP* 3.5 15.0 - - - +
733C MET* 5.7 2.5 - - - -
980C SER* 5.8 3.8 - - - +
983C ASN* 4.4 14.6 - - + +
984C GLU* 3.1 14.7 - - - +
987C ASN* 5.5 5.3 - - - +
1102C CA 2.4 24.0 - - - -
1103C CA 2.5 18.5 - - - -
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Residues in contact with GLY 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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620C ASP* 1.3 98.4 + - - +
622C MET* 1.3 62.3 + - - -
623C GLY 4.0 1.0 + - - -
638C LYS* 6.0 0.4 - - - -
639C ALA 2.9 13.2 - - - -
640C VAL* 3.6 14.2 - - - +
641C ARG 4.7 0.2 - - - -
684C GLU* 5.1 9.8 + - - +
733C MET* 6.2 0.2 - - - +
987C ASN* 4.2 6.7 + - - -
1102C CA 3.6 12.0 - - - -
1103C CA 4.2 1.0 - - - -
46H T 5.2 0.5 + - - -
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Residues in contact with MET 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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621C GLY* 1.3 73.2 - - - -
623C GLY* 1.3 66.6 + - - +
625C VAL* 3.5 15.9 - - + -
637C GLU 3.7 1.0 - - - +
638C LYS* 3.4 9.7 - - - +
639C ALA* 2.7 33.3 + - + +
987C ASN* 3.1 59.5 + - - +
990C PHE* 3.9 18.2 - - + -
991C ARG* 2.6 43.3 - - + +
45H G 4.7 4.9 - - - +
46H T 4.3 5.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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