Contacts of the helix formed by residues 654 - 670 (chain D) 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 PRO 654 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D TYR* 3.8 13.7 - - + +
652D ASP 4.4 0.4 - - - +
653D SER* 1.3 88.6 - - - +
655D VAL* 1.3 54.7 + - - +
657D ILE* 2.8 38.6 + - + +
658D THR* 3.4 7.6 + - + +
695D ARG* 3.5 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D ASP* 3.9 21.3 - - + +
619D PHE* 3.7 30.2 - - + -
620D TYR* 3.4 23.8 + - + +
647D ALA* 3.9 15.7 - - + +
650D GLN* 3.7 24.9 - - + +
653D SER* 3.2 23.8 + - - +
654D PRO* 1.3 77.8 - - - +
656D SER* 1.3 59.4 + - - +
658D THR* 3.3 3.8 + - - -
659D ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D ALA 3.6 9.4 - - - -
648D LEU* 3.6 22.5 - - - +
650D GLN 3.1 18.0 + - - -
651D VAL* 3.7 10.4 + - - -
653D SER 2.7 20.1 + - - -
655D VAL* 1.3 82.9 - - - +
657D ILE* 1.3 58.5 + - - +
659D ALA* 3.5 5.3 - - - +
660D VAL* 3.1 31.9 + - - +
688D MET* 5.2 0.2 - - - -
695D ARG* 5.1 0.3 - - - +
698D LEU* 3.7 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D PRO* 2.8 18.2 + - + +
656D SER* 1.3 79.6 - - - +
658D THR* 1.3 61.6 + - + +
660D VAL* 3.3 6.4 + - - +
661D GLY* 3.0 20.3 + - - -
695D ARG* 3.8 17.0 - - + +
697D GLU* 3.3 45.1 - - + +
698D LEU* 4.1 20.6 - - + +
701D ALA* 4.4 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D PHE* 3.5 15.2 - - - -
620D TYR* 3.6 32.4 - - + -
623D SER* 4.5 8.3 + - - -
654D PRO* 3.4 8.1 + - + +
655D VAL 3.3 7.8 + - - -
657D ILE* 1.3 76.6 - - + +
659D ALA* 1.3 56.9 + - - +
661D GLY* 3.0 4.4 + - - +
662D PHE* 2.6 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D PHE* 3.6 24.7 - - + -
644D LEU* 4.0 4.3 - - + +
647D ALA* 4.1 0.7 - - + -
648D LEU* 3.9 32.8 - - + +
655D VAL 3.0 18.8 + - - +
656D SER 3.5 7.9 - - - +
658D THR* 1.3 75.2 + - - +
660D VAL* 1.3 63.9 + - - +
662D PHE* 3.3 4.4 + - - +
663D ILE* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D LEU* 4.3 1.6 - - + -
656D SER 3.1 16.3 + - - +
657D ILE 3.5 7.4 - - - +
658D THR 3.3 0.4 - - - -
659D ALA* 1.3 72.6 - - - +
661D GLY* 1.3 65.7 + - - +
663D ILE* 3.2 10.4 + - - +
664D ALA* 3.0 18.5 + - + +
685D LEU* 4.3 4.7 - - + -
688D MET* 3.7 28.0 - - + -
698D LEU* 3.8 11.4 - - + -
701D ALA* 3.4 33.7 - - + +
702D VAL* 4.1 4.9 - - + +
705D VAL* 3.6 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 661 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B GLY* 5.2 10.5 - - - -
657D ILE 3.0 11.7 + - - -
658D THR* 3.0 9.9 + - - -
660D VAL* 1.3 77.7 - - - +
662D PHE* 1.3 60.5 + - - +
664D ALA* 3.0 19.3 + - - +
665D ASP* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 662 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D PHE* 4.7 0.2 - - + -
623D SER* 4.2 24.2 - - - +
626D ALA* 3.5 33.2 - - + -
633D PHE* 3.6 20.9 - + - -
637D LEU* 4.8 9.2 - - + -
640D PHE* 3.5 27.6 - + - -
644D LEU* 3.3 36.8 - - + -
658D THR 2.6 15.4 + - - +
659D ALA* 3.5 11.2 - - - +
660D VAL 3.3 0.4 - - - -
661D GLY* 1.3 71.4 - - - +
663D ILE* 1.3 61.5 + - - +
665D ASP* 3.5 9.4 + - + +
666D ILE* 3.0 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 663 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D LEU* 4.3 9.4 - - + -
648D LEU* 3.5 34.1 - - + -
659D ALA 3.1 8.2 + - - +
660D VAL* 3.5 10.1 - - - +
661D GLY 3.2 0.4 - - - -
662D PHE* 1.3 74.1 - - - +
664D ALA* 1.3 65.3 + - - +
666D ILE* 3.2 7.5 - - + +
667D SER* 3.0 24.4 + - - -
674D PHE* 4.0 14.4 - - + -
681D MET* 3.7 29.2 - - + -
685D LEU* 4.4 16.2 - - + -
705D VAL* 4.0 7.2 - - + -
709D ILE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 664 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B GLY 4.4 5.4 - - - +
845B LYS* 4.0 11.0 - - - +
660D VAL 3.0 11.2 + - - +
661D GLY* 3.0 15.3 + - - +
663D ILE* 1.3 76.1 - - - +
665D ASP* 1.3 56.3 + - - +
667D SER* 2.7 17.0 + - - -
668D ASN* 2.6 28.7 + - - -
705D VAL* 3.7 10.9 - - + +
708D ASP* 3.5 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 665 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B ARG 4.3 1.2 - - - +
836B SER* 3.5 14.3 + - - -
837B GLY* 3.1 28.2 + - - -
623D SER 5.0 2.6 - - - +
626D ALA 5.4 2.7 - - - +
627D ALA* 3.9 32.2 + - - +
661D GLY 3.0 20.8 + - - +
662D PHE* 3.9 9.9 - - + +
663D ILE 3.3 0.2 - - - -
664D ALA* 1.3 73.5 - - - +
666D ILE* 1.3 61.9 + - + +
668D ASN* 3.0 9.5 + - - +
669D SER* 2.8 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 666 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626D ALA* 5.2 6.1 - - + +
630D GLY 4.6 8.3 - - - +
633D PHE* 4.4 15.5 - - + -
634D GLU* 5.8 0.9 - - - +
637D LEU* 4.8 13.5 - - + -
644D LEU* 6.1 0.4 - - + -
662D PHE* 3.0 48.2 + - + +
663D ILE* 3.2 22.0 - - + +
665D ASP* 1.3 75.6 - - + +
667D SER* 1.3 76.6 - - - +
669D SER* 3.5 12.6 - - - +
670D LEU* 3.1 39.7 + - + +
674D PHE* 3.5 22.9 - - + -
681D MET* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 667 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663D ILE 3.0 18.7 + - - -
664D ALA 2.7 21.3 + - - -
666D ILE* 1.3 77.6 - - - +
668D ASN* 1.3 53.6 + - - +
670D LEU 2.4 20.6 - - - +
671D GLU 3.7 1.7 - - - +
674D PHE* 3.7 34.1 - - - -
708D ASP* 3.6 19.0 - - - +
709D ILE* 4.3 8.5 - - - -
712D ASN* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 668 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B ARG* 3.2 63.8 + - + +
842B GLN* 5.5 1.6 + - - -
845B LYS* 3.9 8.5 - - - +
849B ARG* 4.1 2.9 + - - -
664D ALA 2.6 20.9 + - - -
665D ASP* 3.0 8.3 + - - +
667D SER* 1.3 77.9 + - - +
669D SER* 1.3 59.8 + - - +
670D LEU 2.9 13.2 - - - +
671D GLU* 3.8 9.9 - - - +
708D ASP* 2.8 26.5 + - - +
711D SER* 4.7 2.6 + - - -
712D ASN* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 669 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B ARG* 6.1 0.2 - - - +
849B ARG* 5.1 4.2 + - - +
630D GLY* 3.3 41.6 + - - -
631D LYS* 3.2 26.5 + - - +
665D ASP 2.8 15.0 + - - -
666D ILE* 3.5 17.7 + - - +
668D ASN* 1.3 70.5 - - - +
670D LEU* 1.3 71.7 + - - +
671D GLU* 4.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 670 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630D GLY 5.0 1.1 - - - +
631D LYS* 4.0 28.5 - - + +
634D GLU* 3.7 34.5 - - + +
637D LEU* 4.0 15.9 - - + -
666D ILE* 3.1 21.7 + - + +
667D SER 2.4 27.9 - - - +
668D ASN 2.9 3.6 - - - -
669D SER* 1.3 87.7 + - - +
671D GLU* 1.3 55.7 + - - +
673D ASP* 4.2 8.5 - - + +
674D PHE* 3.9 19.3 - - + +
677D TYR* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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