Contacts of the helix formed by residues 686 - 705 (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 ASP 686 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682C VAL* 3.7 14.7 - - - +
683C ASP* 2.9 27.3 + - - +
685C SER* 1.3 70.9 - - - +
687C HIS* 1.3 64.9 + - - +
688C GLU* 2.8 11.7 + - + +
689C THR* 3.4 18.9 + - - -
690C LEU* 3.6 9.8 + - - +
34D LYS* 4.7 26.1 + - + +
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Residues in contact with HIS 687 (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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685C SER 2.8 10.4 + - - +
686C ASP* 1.3 70.5 - - - +
688C GLU* 1.3 61.4 + - - +
690C LEU* 3.9 5.7 - - + +
691C THR* 2.6 57.0 + - - +
736C GLU* 3.8 44.0 + - - +
737C MET* 5.0 2.0 - - + -
804C LYS 6.0 0.7 - - - -
806C PHE* 4.7 15.3 - + - -
34D LYS* 6.1 0.4 - - - +
35D GLY* 4.8 15.2 - - - -
36D TRP* 3.5 27.8 + + + +
98D PRO* 4.5 8.3 - - + -
99D ASN* 2.5 30.1 + - - -
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Residues in contact with GLU 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C TRP* 5.3 4.0 - - - -
567C VAL* 5.2 10.3 - - - +
686C ASP* 2.8 9.2 + - + +
687C HIS* 1.3 79.8 - - - +
689C THR* 1.3 74.2 + - - +
691C THR* 3.8 2.4 - - - -
692C ALA* 3.0 26.7 + - - +
16D GLN* 5.1 4.7 - - - +
34D LYS* 4.9 15.8 - - + +
35D GLY* 5.8 1.0 - - - -
73D ARG* 2.2 51.9 + - - +
96D ARG* 5.2 5.2 + - - -
98D PRO* 3.5 18.0 - - + +
100D ASN* 3.8 8.8 - - - +
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Residues in contact with THR 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C TRP* 5.2 7.6 - - + -
571C THR* 3.2 42.5 + - + +
682C VAL* 3.6 24.2 - - + +
686C ASP* 3.4 14.2 + - - -
688C GLU* 1.3 85.0 + - - +
690C LEU* 1.3 63.4 + - - +
692C ALA* 3.6 5.1 - - + +
693C ILE* 3.0 27.3 + - + +
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Residues in contact with LEU 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619C CYS* 5.3 2.7 - - - -
640C VAL* 4.5 16.8 - - + -
680C MET* 3.7 31.6 - - + -
682C VAL* 4.5 5.8 - - + +
683C ASP 4.8 7.0 - - - +
684C GLU* 4.4 11.7 - - - +
686C ASP 3.6 10.5 + - - +
687C HIS* 3.5 8.7 + - + +
688C GLU 3.2 0.6 - - - -
689C THR* 1.3 79.1 - - - +
691C THR* 1.3 58.3 + - - +
693C ILE* 4.0 0.9 - - - +
694C LEU* 2.9 45.2 + - + +
733C MET* 4.0 20.2 - - + -
736C GLU* 4.5 5.8 - - - +
737C MET* 3.7 29.2 - - + -
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Residues in contact with THR 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687C HIS* 2.6 44.3 + - - -
688C GLU 3.8 2.2 - - - -
690C LEU* 1.3 76.4 - - - +
692C ALA* 1.3 63.4 + - - +
695C GLY* 3.0 26.2 + - - -
806C PHE* 3.7 34.6 - - + -
98D PRO 4.3 6.3 - - - -
99D ASN* 3.6 31.6 - - + +
100D ASN* 4.3 6.3 + - - +
172D TRP* 5.8 0.5 - - - -
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Residues in contact with ALA 692 (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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560C TRP* 4.1 23.3 - - + -
688C GLU* 3.0 25.6 + - - +
689C THR* 3.6 11.0 - - + +
691C THR* 1.3 76.6 - - - +
693C ILE* 1.3 63.6 + - + +
695C GLY* 5.1 0.3 - - - -
696C PRO* 4.5 2.4 - - - +
100D ASN* 3.1 27.2 + - - +
172D TRP* 5.6 0.3 - - - -
173D ASN* 2.8 27.7 + - - +
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Residues in contact with ILE 693 (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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556C GLY* 3.3 30.4 - - - +
557C LEU* 4.2 14.6 - - - +
558C SER* 5.3 3.1 - - - -
560C TRP* 5.4 9.9 - - + -
571C THR* 4.2 24.9 - - + +
573C SER* 4.0 6.7 - - - +
575C ARG* 5.3 8.5 + - - +
678C CYS* 4.7 6.3 - - - -
680C MET* 3.4 36.1 - - + -
689C THR* 3.0 19.5 + - + +
692C ALA* 1.3 82.9 - - + +
694C LEU* 1.3 65.4 + - - +
695C GLY 3.2 3.7 + - - -
696C PRO* 3.2 17.2 - - - +
697C VAL* 5.0 1.4 + - - +
173D ASN* 5.5 0.4 - - - +
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Residues in contact with LEU 694 (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* 5.4 6.5 - - - -
642C PHE* 4.3 29.2 - - + -
678C CYS* 4.7 11.2 - - - -
680C MET* 4.6 19.5 - - + -
690C LEU* 2.9 28.5 + - + +
691C THR* 4.2 3.4 - - - +
693C ILE* 1.3 76.2 - - - +
695C GLY* 1.3 63.4 - - - +
696C PRO 3.4 0.2 - - - -
697C VAL* 2.9 31.0 + - + +
698C VAL* 3.3 13.5 + - + +
737C MET* 4.6 8.3 - - + -
806C PHE* 4.4 15.7 - - + -
807C MET* 4.4 24.9 - - + -
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Residues in contact with GLY 695 (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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691C THR* 3.0 16.3 + - - +
694C LEU* 1.3 75.3 - - - +
696C PRO* 1.3 72.3 - - - +
698C VAL* 2.8 22.4 + - - +
699C ALA* 2.9 11.1 + - - +
806C PHE* 5.0 5.8 - - - -
172D TRP* 3.8 20.7 - - - -
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Residues in contact with PRO 696 (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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558C SER* 4.3 11.2 - - - +
575C ARG* 3.8 17.0 - - - +
692C ALA 4.5 2.0 - - - +
693C ILE 3.2 16.4 - - - +
695C GLY* 1.3 88.6 - - - +
697C VAL* 1.3 61.9 + - - +
699C ALA* 3.1 10.8 + - + +
700C GLU* 3.0 28.3 + - - +
169D THR* 3.8 23.1 - - - +
172D TRP* 3.5 32.3 - - + -
173D ASN* 3.9 12.3 - - - +
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Residues in contact with VAL 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C ARG* 4.3 25.6 - - - +
578C TYR* 3.8 30.7 - - + -
642C PHE* 4.2 22.7 - - + -
677C LEU* 4.3 17.3 - - + -
678C CYS* 5.1 5.6 - - + -
693C ILE 5.4 0.9 - - - +
694C LEU* 2.9 24.5 + - + +
696C PRO* 1.3 76.8 - - + +
698C VAL* 1.3 59.1 + - + +
700C GLU* 3.2 9.8 + - + +
701C ARG* 2.9 30.6 + - + +
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Residues in contact with VAL 698 (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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694C LEU* 3.3 11.4 + - + +
695C GLY* 2.8 11.7 + - - +
697C VAL* 1.3 79.5 - - + +
699C ALA* 1.3 63.6 + - - +
701C ARG* 3.3 10.0 + - + +
702C LYS* 3.0 39.7 + - - +
806C PHE* 3.8 46.4 - - + +
807C MET* 4.4 19.3 - - + -
172D TRP* 6.5 0.4 - - + -
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Residues in contact with ALA 699 (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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544C ASN* 4.8 13.4 + - - +
545C VAL* 5.9 0.9 - - - -
695C GLY 2.9 10.5 + - - +
696C PRO* 3.4 13.2 - - + +
698C VAL* 1.3 80.4 - - - +
700C GLU* 1.3 56.4 + - - +
702C LYS* 3.4 6.0 + - - +
703C ALA* 2.9 31.4 + - - +
169D THR* 4.9 6.3 - - + -
172D TRP* 4.5 22.4 - - + +
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Residues in contact with GLU 700 (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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542C LEU* 5.3 0.9 - - - +
545C VAL* 3.4 28.4 - - - +
575C ARG* 5.9 3.8 - - - +
577C ARG* 5.8 3.9 + - - +
578C TYR* 4.0 33.7 - - + +
579C ASP* 4.4 8.9 - - - +
696C PRO* 3.0 21.4 + - + +
697C VAL* 3.5 7.4 - - + +
699C ALA* 1.3 73.5 - - - +
701C ARG* 1.3 65.6 + - - +
703C ALA* 3.3 3.4 + - - +
704C MET* 2.9 42.0 + - + +
169D THR* 2.6 39.9 + - - +
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Residues in contact with ARG 701 (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* 3.6 23.3 - - + -
617C GLU* 2.4 43.3 + - - +
642C PHE* 5.1 3.8 - - + -
697C VAL* 2.9 19.9 + - + +
698C VAL* 3.4 13.9 - - + +
700C GLU* 1.3 79.3 - - - +
702C LYS* 1.3 62.0 + - - +
704C MET* 3.2 6.5 + - - +
705C MET* 3.1 30.0 + - - +
724C PHE* 3.3 44.2 + - - +
726C GLY* 5.1 3.8 - - - +
729C TYR* 4.9 0.4 + - - -
807C MET* 4.6 19.4 - - - +
808C GLU* 3.9 25.9 + - - -
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Residues in contact with LYS 702 (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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698C VAL* 3.0 30.9 + - - +
699C ALA* 4.0 5.4 - - - +
701C ARG* 1.3 77.6 - - - +
703C ALA* 1.3 60.0 + - - +
705C MET* 4.2 20.2 + - + +
706C GLU* 4.3 10.4 - - - +
772C HIS* 5.9 4.6 + - - -
806C PHE 5.8 0.8 + - - -
808C GLU* 6.1 3.6 - - - +
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Residues in contact with ALA 703 (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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542C LEU* 3.4 19.3 - - + +
543C LYS* 4.0 38.7 + - + +
544C ASN* 5.2 1.8 - - - +
545C VAL* 4.6 5.4 - - + -
699C ALA 2.9 18.6 + - - +
700C GLU* 4.0 3.4 - - - +
702C LYS* 1.3 77.0 - - - +
704C MET* 1.3 60.9 + - - +
705C MET 3.6 0.2 - - - -
706C GLU* 4.5 4.8 + - - +
707C SER* 4.5 8.1 + - - -
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Residues in contact with MET 704 (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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538C TRP* 3.9 27.7 + - + -
542C LEU* 3.9 16.8 - - + -
578C TYR* 4.2 14.4 - - + -
579C ASP* 3.7 29.8 - - + +
582C LEU* 4.2 24.5 - - - -
700C GLU* 2.9 28.1 + - - +
701C ARG* 3.2 4.2 + - - +
703C ALA* 1.3 77.2 - - - +
705C MET* 1.3 66.5 + - - +
706C GLU 3.0 4.8 + - - -
707C SER 3.3 16.8 + - - +
722C PHE* 4.7 14.1 + - + +
724C PHE* 4.6 13.7 - - + -
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Residues in contact with MET 705 (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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701C ARG* 3.1 26.2 - - - +
702C LYS* 4.2 17.0 + - + +
703C ALA 3.6 0.8 - - - -
704C MET* 1.3 76.6 - - - +
706C GLU* 1.3 76.4 + - - +
707C SER 4.6 0.5 - - - +
721C ARG* 4.6 10.4 + - - -
722C PHE* 4.0 23.1 + - - +
723C PHE* 6.0 0.9 - - - -
724C PHE* 3.7 33.7 - - + -
808C GLU* 4.3 21.5 - - - +
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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
------------------------------------------------------------
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