Contacts of the strand formed by residues 639 - 651 (chain C) in PDB entry 6DBT
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 ALA 639 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621C GLY* 3.6 1.4 - - - -
622C MET* 2.8 41.8 + - + +
625C VAL* 5.8 2.5 - - + -
637C GLU 5.0 1.3 - - - +
638C LYS* 1.3 79.3 - - - +
640C VAL* 1.3 74.3 + - - +
679C LEU* 6.3 1.1 - - + -
680C MET 3.5 10.5 - - - +
681C PHE* 4.5 10.3 - - + -
682C VAL 3.2 4.6 + - - +
684C GLU 5.5 0.5 + - - -
990C PHE* 4.8 20.2 - - + -
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Residues in contact with VAL 640 (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* 3.8 25.8 - - - -
620C ASP 3.3 15.9 - - - +
621C GLY* 4.5 3.1 - - - -
622C MET* 4.7 1.1 - - - +
639C ALA* 1.3 82.1 - - - +
641C ARG* 1.3 66.1 + - - +
642C PHE* 4.2 0.4 - - + -
678C CYS 4.2 0.2 - - - +
679C LEU* 3.8 9.0 - - - +
680C MET* 3.3 51.0 + - + +
682C VAL* 3.8 15.3 - - + +
683C ASP 4.2 3.8 - - - +
684C GLU* 4.2 21.8 - - + +
690C LEU* 4.5 10.3 - - + -
694C LEU* 6.3 0.2 - - + -
733C MET* 5.9 2.2 - - + -
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Residues in contact with ARG 641 (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 3.6 2.8 - - - +
619C CYS* 3.5 2.5 - - - -
620C ASP* 3.0 33.2 + - - +
622C MET* 3.0 23.2 - - + +
640C VAL* 1.3 75.2 - - - +
642C PHE* 1.3 67.5 + - - +
643C SER* 4.6 2.5 - - - -
674C CYS* 4.6 4.4 - - - -
676C PRO* 4.2 20.0 - - + -
678C CYS 3.9 4.5 - - - +
679C LEU* 4.9 13.5 - - + -
983C ASN* 2.4 47.0 + - - +
986C GLY* 3.3 9.9 + - - -
987C ASN* 2.6 48.3 + - - +
990C PHE* 4.7 7.4 - - - +
1013C HIS* 4.3 15.5 + - - -
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Residues in contact with PHE 642 (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 12.6 - + - -
617C GLU* 3.6 31.4 - - + -
618C SER 3.5 5.2 - - - -
619C CYS* 3.5 26.2 - - + +
640C VAL* 4.2 1.5 - - + +
641C ARG* 1.3 70.7 - - - +
643C SER* 1.3 69.9 + - - +
644C PHE* 5.4 0.9 - - + -
676C PRO* 3.7 1.4 - - - +
677C LEU* 2.9 39.1 + - + -
678C CYS* 3.3 29.8 + - + +
680C MET* 6.0 1.3 - - + +
694C LEU* 4.3 29.6 - - + -
697C VAL* 4.2 22.9 - - + -
701C ARG* 5.1 4.5 - - + -
729C TYR* 4.3 12.8 - - - -
807C MET* 4.8 4.9 - - - -
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Residues in contact with SER 643 (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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617C GLU* 3.6 0.9 - - - -
618C SER* 2.9 38.0 + - - +
641C ARG* 4.6 3.8 - - - -
642C PHE* 1.3 78.7 - - - +
644C PHE* 1.3 61.5 + - - +
674C CYS* 2.8 34.9 - - - -
675C ARG 2.7 24.6 + - - -
676C PRO* 3.6 10.5 - - - -
677C LEU 4.3 0.7 - - - +
983C ASN* 3.9 10.1 - - - -
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Residues in contact with PHE 644 (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* 4.8 11.2 - + - +
581C ALA* 4.3 10.1 - - + -
582C LEU* 4.2 31.4 - - + -
585C ALA* 4.7 4.5 - - + -
615C VAL* 4.2 12.8 - - + -
616C LYS* 3.1 15.0 - - - +
617C GLU* 4.0 14.6 - - - +
642C PHE* 5.5 1.8 - + + -
643C SER* 1.3 76.2 + - - +
645C THR* 1.3 75.0 + - - +
646C ILE* 4.1 25.1 - - + -
675C ARG* 2.9 55.8 + - + +
677C LEU* 3.5 37.7 - - + -
1014C TRP* 5.0 2.7 - + - -
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Residues in contact with THR 645 (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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615C VAL* 3.7 1.6 - - - -
616C LYS* 2.9 56.7 + - - +
644C PHE* 1.3 85.4 + - - +
646C ILE* 1.3 75.7 + - - +
647C MET* 3.2 6.6 + - - -
665C GLU* 5.4 1.1 - - + -
668C PRO* 5.0 5.4 - - + +
673C SER* 2.9 50.8 + - - +
674C CYS* 3.2 8.8 - - - +
675C ARG* 4.7 4.9 - - + -
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Residues in contact with ILE 646 (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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582C LEU* 4.5 11.2 - - + -
585C ALA* 4.5 9.2 - - + -
586C LEU* 5.0 6.7 - - + -
589C LEU* 4.4 24.7 - - + -
613C VAL* 3.8 28.9 - - + -
614C VAL 4.0 2.0 - - - +
615C VAL* 3.7 22.7 - - + -
644C PHE* 4.1 18.6 - - + -
645C THR* 1.3 79.3 - - - +
647C MET* 1.3 64.5 + - - +
648C SER 4.5 5.4 - - - +
649C ILE* 5.6 0.4 - - + -
663C PHE* 4.5 12.5 - - + -
665C GLU* 3.9 11.3 - - - +
673C SER* 5.0 1.4 + - - -
675C ARG* 4.4 20.1 - - - +
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Residues in contact with MET 647 (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* 3.0 19.1 + - + +
616C LYS* 3.7 24.2 - - + +
645C THR* 3.2 5.4 + - - +
646C ILE* 1.3 74.5 - - - +
648C SER* 1.3 66.5 + - - +
663C PHE* 4.6 1.0 - - - -
664C GLN* 4.0 5.3 - - + +
665C GLU* 3.0 36.2 + - - +
668C PRO* 3.6 32.8 - - + -
977C ALA* 3.5 31.2 - - + +
978C TRP* 3.6 33.0 - - + -
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Residues in contact with SER 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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612C THR 3.8 0.9 - - - +
613C VAL* 3.4 2.9 - - - +
614C VAL* 2.9 45.3 + - - +
646C ILE* 3.7 5.1 - - - -
647C MET* 1.3 84.8 - - - +
649C ILE* 1.3 61.4 + - - +
650C SER* 5.4 1.8 + - - -
661C THR* 5.4 2.5 - - - -
663C PHE* 3.2 13.9 - - - -
664C GLN* 4.1 16.6 - - - -
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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
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586C LEU* 5.9 1.1 - - + -
589C LEU* 6.0 1.1 - - + -
593C ILE* 4.3 17.0 - - + -
611C PHE* 3.8 24.7 - - + -
612C THR 3.3 32.8 - - - +
613C VAL* 3.5 21.5 - - + -
646C ILE* 5.6 1.1 - - + -
648C SER* 1.3 75.2 - - - +
650C SER* 1.3 73.7 + - - +
661C THR* 4.0 1.1 - - - -
662C ILE* 2.9 31.2 + - + +
663C PHE* 2.9 50.7 + - + +
720C PHE* 4.7 2.0 - - + -
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Residues in contact with SER 650 (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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611C PHE* 4.0 1.2 - - - -
612C THR* 3.3 28.2 + - - -
648C SER* 4.3 2.2 - - - -
649C ILE* 1.3 90.8 - - - +
651C ILE* 1.3 74.9 + - - +
659C GLY* 5.5 2.1 - - - -
660C ILE 3.2 25.8 - - - -
661C THR* 4.2 4.0 - - - -
662C ILE* 3.8 5.8 - - - +
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Residues in contact with ILE 651 (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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597C LEU* 4.7 5.8 - - + -
602C LEU* 4.0 24.9 - - + -
606C MET 6.1 0.2 - - - +
607C CYS* 5.0 5.2 - - + -
610C GLY 3.6 9.4 - - - +
611C PHE* 3.6 37.9 - - + -
612C THR* 5.7 0.7 - - - -
650C SER* 1.3 86.9 + - - +
652C ARG* 1.3 69.1 - - - +
653C LEU* 4.4 15.7 - - + +
657C ASP* 3.1 17.1 - - + +
659C GLY* 5.5 0.2 - - - -
660C ILE* 3.0 38.5 + - + +
662C ILE* 3.6 19.1 - - + -
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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