Contacts of the helix formed by residues 697 - 714 (chain B) in PDB entry 2BKU
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 GLU 697 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B ILE* 3.4 18.9 - - + +
695B ARG* 2.6 50.8 + - - +
696B ARG* 1.3 89.1 + - + +
698B LEU* 1.3 65.2 + - - +
700B PRO* 3.4 17.9 - - - +
701B ALA* 3.6 10.7 + - - +
746B TYR* 4.9 1.8 - - - -
749B LYS* 5.7 8.5 - - - +
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Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B VAL* 3.6 42.0 - - + +
656B SER* 3.7 14.1 - - - +
657B ILE* 4.0 16.2 - - + +
660B VAL* 4.0 13.2 - - + -
688B MET* 3.5 38.8 - - + +
689B ILE* 5.7 1.1 - - - +
694B ALA* 3.9 11.4 - - + -
695B ARG* 3.5 18.7 + - + +
696B ARG 3.2 0.6 - - - -
697B GLU* 1.3 81.1 - - - +
699B LYS* 1.3 57.9 + - - +
701B ALA* 3.1 5.6 + - + +
702B VAL* 2.9 36.0 + - + +
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Residues in contact with LYS 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B ILE* 3.8 38.0 - - + +
694B ALA* 6.0 0.6 - - + +
695B ARG 4.1 2.6 + - - +
696B ARG 3.5 7.9 + - - +
698B LEU* 1.3 77.4 - - - +
700B PRO* 1.4 59.7 - - + +
702B VAL* 3.1 5.7 + - - +
703B LEU* 2.7 46.3 + - + +
727B LEU 5.6 0.9 - - - -
730B ALA 5.8 0.2 - - - -
731B ALA* 4.2 30.2 - - - +
734B THR* 4.7 15.0 + - - +
746B TYR* 4.0 12.0 - - - +
750B VAL* 4.5 14.5 - - + +
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Residues in contact with PRO 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B ARG 3.4 12.6 - - - +
697B GLU* 3.4 16.2 - - - +
699B LYS* 1.4 93.5 - - + +
701B ALA* 1.3 62.8 + - - +
703B LEU* 3.8 3.8 - - + -
704B SER* 3.0 28.4 + - - -
746B TYR* 4.2 13.2 - - + +
749B LYS* 3.9 38.6 - - + +
750B VAL* 4.4 5.6 - - + -
753B ALA* 3.3 12.0 - - + +
838D GLN* 3.5 7.3 + - - +
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Residues in contact with ALA 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B ILE* 4.3 17.7 - - + +
660B VAL* 3.3 30.5 - - + +
697B GLU 3.8 9.2 - - - +
698B LEU* 3.1 11.3 + - + +
700B PRO* 1.3 81.5 - - - +
702B VAL* 1.3 58.2 + - - +
704B SER 3.4 0.2 + - - -
705B VAL* 3.0 22.3 + - - +
838D GLN* 3.5 18.1 - - - +
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Residues in contact with VAL 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B VAL* 3.9 20.6 - - + -
685B LEU* 3.8 17.9 - - + +
688B MET* 4.0 24.7 - - + -
689B ILE* 4.4 13.0 - - + -
698B LEU* 2.9 23.5 + - + +
699B LYS* 3.6 5.8 - - - +
701B ALA* 1.3 74.1 - - - +
703B LEU* 1.3 67.0 + - + +
705B VAL* 3.0 17.4 + - - +
706B PHE* 3.1 43.5 + - + -
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B ILE* 5.6 5.2 - - + -
699B LYS* 2.7 36.8 + - + +
700B PRO* 4.5 0.4 - - + -
702B VAL* 1.3 74.3 - - + +
704B SER* 1.3 60.8 + - - +
706B PHE* 3.6 23.9 + - + +
727B LEU* 4.6 6.5 - - + -
728B CYS* 3.7 36.6 - - + +
731B ALA* 4.0 7.2 - - + -
750B VAL* 4.0 36.1 - - + +
753B ALA* 3.6 20.4 - - + +
754B VAL* 4.0 9.0 - - + -
757B ALA* 3.4 24.1 - - - +
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Residues in contact with SER 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B PRO 3.0 16.5 + - - -
703B LEU* 1.3 76.1 - - - +
705B VAL* 1.3 59.5 + - - +
707B GLY* 3.0 17.0 + - - -
708B ASP* 3.3 16.6 + - - +
753B ALA* 3.3 7.8 - - - +
756B ASP* 2.6 36.8 + - - +
838D GLN* 3.0 33.7 + - - -
842D GLN* 4.4 2.4 - - - +
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Residues in contact with VAL 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B VAL* 3.6 29.6 - - + +
663B ILE* 3.9 14.1 - - + -
664B ALA* 3.8 21.3 - - + +
685B LEU* 3.9 34.5 - - + -
701B ALA 3.0 12.0 + - - +
702B VAL* 3.0 17.5 + - - +
704B SER* 1.3 72.2 - - - +
706B PHE* 1.3 72.6 + - + +
707B GLY 3.1 1.3 - - - -
708B ASP* 3.2 9.5 + - + +
709B ILE* 3.0 27.5 + - - +
838D GLN* 5.0 0.2 + - - -
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Residues in contact with PHE 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B MET* 3.7 21.1 - - + -
685B LEU* 3.8 24.7 - - + -
689B ILE* 4.9 0.7 - - + -
702B VAL* 3.1 42.8 + - + -
703B LEU* 3.6 26.2 - - + +
705B VAL* 1.3 77.8 - - + +
707B GLY* 1.3 63.6 + - - +
709B ILE* 4.7 2.2 - - - -
710B ALA* 3.0 28.6 + - - +
717B PHE* 3.8 9.8 - - + -
724B ILE* 3.5 56.8 - - + -
727B LEU* 3.9 18.6 - - + -
757B ALA* 4.5 5.4 - - + -
761B ILE* 5.6 0.9 - - + -
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Residues in contact with GLY 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU 3.9 2.8 + - - -
704B SER 3.0 11.5 + - - -
706B PHE* 1.3 78.8 - - - +
708B ASP* 1.3 61.4 + - - +
711B SER* 3.1 20.8 + - - -
756B ASP 3.5 22.9 - - - -
757B ALA* 3.8 7.5 - - - +
760B GLY* 3.4 14.1 - - - -
842D GLN* 3.4 8.1 - - - -
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Residues in contact with ASP 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B ALA* 3.7 15.3 - - - +
667B SER* 3.7 15.0 - - - +
668B ASN* 2.9 19.2 + - - +
704B SER* 3.3 18.3 + - - +
705B VAL* 3.2 16.6 + - + +
707B GLY* 1.3 73.3 - - - +
709B ILE* 1.3 62.6 + - + +
711B SER* 2.7 22.1 + - - -
712B ASN* 3.0 15.4 + - - +
838D GLN* 5.8 0.5 - - - +
842D GLN* 3.1 12.5 + - - +
845D LYS* 2.6 39.8 + - - +
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Residues in contact with ILE 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B ILE* 3.9 17.7 - - + -
667B SER* 4.6 7.4 - - - -
674B PHE* 3.9 18.8 - - + -
678B SER* 4.8 2.0 - - - +
681B MET* 5.0 1.3 - - + -
682B MET* 3.5 26.0 - - + -
685B LEU* 3.5 32.8 - - + -
705B VAL* 3.0 17.3 + - + +
706B PHE 3.9 3.1 - - - +
708B ASP* 1.3 73.0 - - + +
710B ALA* 1.3 55.5 + - - +
712B ASN* 2.9 2.8 + - - -
713B ILE* 2.7 61.8 + - + +
717B PHE* 4.1 12.3 - - + -
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Residues in contact with ALA 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B PHE 3.0 18.6 + - - +
707B GLY 3.9 0.2 - - - +
709B ILE* 1.3 75.3 - - - +
711B SER* 1.3 57.2 + - - +
714B GLY* 2.9 27.0 + - - +
717B PHE* 3.7 29.5 - - + -
760B GLY 3.7 2.7 - - - +
761B ILE* 3.8 35.0 - - + +
764B GLY* 3.3 9.4 - - - -
765B LEU* 6.3 1.3 - - + -
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Residues in contact with SER 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B ASN* 4.7 1.6 + - - -
671B GLU* 5.2 2.6 - - - +
707B GLY 3.1 4.3 + - - -
708B ASP* 2.7 20.3 + - - -
710B ALA* 1.3 77.3 - - - +
712B ASN* 1.3 66.7 + - - +
714B GLY 4.6 1.0 + - - -
760B GLY* 3.2 18.2 + - - -
763B ALA* 4.2 6.6 - - - +
764B GLY* 3.7 12.1 - - - +
842D GLN* 3.1 26.6 + - - -
846D ASP* 4.1 11.7 + - - -
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Residues in contact with ASN 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B SER* 2.9 38.7 + - - +
668B ASN* 3.0 18.3 + - - +
671B GLU* 3.0 66.8 + - - +
672B GLU* 3.7 11.6 + - - +
675B ARG* 4.4 1.6 + - - -
708B ASP 3.0 15.5 + - - +
709B ILE 2.9 3.8 + - - +
711B SER* 1.3 84.2 + - - +
713B ILE* 1.3 62.9 + - + +
714B GLY 3.6 0.4 - - - -
835D ARG* 3.7 6.9 - - - +
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Residues in contact with ILE 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B GLU 3.9 3.6 - - - +
674B PHE* 3.3 26.7 - - + -
675B ARG* 3.0 62.5 + - + +
678B SER* 3.7 13.5 - - - +
709B ILE* 2.7 41.4 + - + +
710B ALA* 4.4 2.0 - - - +
712B ASN* 1.3 74.3 - - - +
714B GLY* 1.3 61.7 + - - +
715B ALA 3.4 0.5 + - - -
716B ASP* 3.2 29.8 + - + -
717B PHE* 3.6 14.4 - - + +
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Residues in contact with GLY 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B ARG* 4.4 5.6 - - - -
710B ALA 2.9 14.1 + - - +
711B SER 4.5 1.0 + - - -
712B ASN 3.6 1.6 - - - -
713B ILE* 1.3 76.0 - - - +
715B ALA* 1.3 64.2 + - - -
717B PHE* 3.0 21.5 + - - +
764B GLY* 3.3 25.6 - - - -
765B LEU* 3.9 9.8 - - - +
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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
------------------------------------------------------------
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