Contacts of the helix formed by residues 674 - 690 (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 PHE 674 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637D LEU* 5.8 0.7 - - + -
663D ILE* 4.0 14.8 - - + -
666D ILE* 3.5 28.5 - - + -
667D SER* 3.7 28.9 - - - +
670D LEU* 3.9 11.0 - - + +
671D GLU 3.6 15.8 + - - +
672D GLU 3.2 0.4 - - - -
673D ASP* 1.3 73.5 - - - +
675D ARG* 1.3 54.9 + - - +
676D ARG 3.0 3.1 - - - -
677D TYR* 2.6 47.9 + + + -
678D SER* 2.8 23.3 + - - -
681D MET* 3.9 25.8 - - + -
709D ILE* 3.8 27.8 - - + -
712D ASN* 5.7 0.2 - - + -
713D ILE* 3.6 18.8 - - + -
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Residues in contact with ARG 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672D GLU* 3.2 46.5 + - - +
673D ASP 3.1 0.2 - - - -
674D PHE* 1.3 75.0 - - - +
676D ARG* 1.3 61.8 + - - +
677D TYR 3.3 0.7 + - - -
678D SER* 3.4 16.8 + - - -
679D ASP* 4.7 3.6 + - - +
713D ILE* 3.0 56.3 + - + +
714D GLY* 4.3 1.8 - - - +
715D ALA* 4.2 12.5 - - - +
716D ASP* 3.6 32.5 - - - +
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Residues in contact with ARG 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D GLU* 3.7 20.0 + - - -
673D ASP* 3.5 18.7 + - - +
674D PHE 2.9 0.2 + - - -
675D ARG* 1.3 79.0 - - - +
677D TYR* 1.3 82.7 + - + +
679D ASP 5.3 0.5 + - - -
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Residues in contact with TYR 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634D GLU* 2.6 39.9 + - - +
637D LEU* 3.8 38.5 - - + +
638D GLU* 5.4 7.6 - - + -
670D LEU* 3.8 17.0 - - + -
673D ASP 3.7 18.6 - - - -
674D PHE* 2.6 26.7 + + + +
676D ARG* 1.3 100.0 + - + +
678D SER* 1.3 64.2 + - - +
679D ASP 3.4 3.0 + - - -
680D ALA* 3.6 10.0 + - + +
681D MET* 3.5 23.9 + - + +
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Residues in contact with SER 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674D PHE* 2.8 28.4 + - - -
675D ARG* 3.4 21.6 + - - -
677D TYR* 1.3 75.6 - - - +
679D ASP* 1.3 73.0 + - - +
681D MET* 3.0 6.4 + - - +
682D MET* 2.9 32.2 + - - +
709D ILE* 5.0 3.4 - - - +
713D ILE* 4.6 12.4 - - - +
716D ASP* 4.6 7.7 + - - -
720D TYR* 4.1 9.5 - - - -
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Residues in contact with ASP 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675D ARG 4.7 3.1 + - - -
676D ARG 5.3 0.6 + - - -
677D TYR 3.5 0.8 - - - -
678D SER* 1.3 89.0 + - - +
680D ALA* 1.3 64.9 + - - +
682D MET 3.3 0.5 + - - -
683D ASN* 3.0 32.9 + - - +
716D ASP* 5.0 7.4 - - - +
720D TYR* 2.6 34.2 + - - +
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Residues in contact with ALA 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645D LEU* 5.8 3.6 - - + -
677D TYR* 3.6 11.8 + - - +
679D ASP* 1.3 78.7 - - - +
681D MET* 1.3 73.4 + - + +
683D ASN* 3.9 5.2 + - - +
684D VAL* 3.2 27.9 + - - +
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Residues in contact with MET 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641D SER* 5.6 4.3 - - - +
644D LEU* 3.7 22.2 - - + -
645D LEU* 3.9 26.7 - - + -
648D LEU* 4.2 4.0 - - + -
663D ILE* 3.7 35.4 - - + -
674D PHE* 3.9 26.0 - - + -
677D TYR* 3.5 16.4 + - + +
678D SER 3.0 8.3 + - - +
680D ALA* 1.3 88.6 - - + +
682D MET* 1.3 66.1 - - - +
684D VAL* 3.2 5.6 + - - +
685D LEU* 2.9 29.8 + - + +
709D ILE* 4.9 2.0 - - + -
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Residues in contact with MET 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678D SER* 2.9 24.8 + - - +
679D ASP 3.3 2.0 + - - +
681D MET* 1.3 73.1 - - - +
683D ASN* 1.3 63.6 + - - +
685D LEU* 3.0 3.5 + - - +
686D ALA* 2.8 29.9 + - + +
706D PHE* 3.8 25.1 - - + -
709D ILE* 3.9 31.9 - - + -
717D PHE* 3.9 11.9 - - + -
720D TYR* 3.6 50.7 - - + -
724D ILE* 3.6 31.0 - - + -
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Residues in contact with ASN 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679D ASP* 3.0 20.7 + - - +
680D ALA* 4.0 6.3 - - - +
682D MET* 1.3 74.0 - - - +
684D VAL* 1.3 62.6 + - + +
686D ALA* 4.2 4.2 - - - +
687D GLN* 3.3 25.3 + - - +
720D TYR* 3.5 25.4 + - - -
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Residues in contact with VAL 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645D LEU* 3.7 22.7 - - + -
648D LEU* 4.1 22.4 - - + -
649D ASN* 4.2 17.9 - - - +
680D ALA 3.2 16.8 + - - +
681D MET* 3.2 7.5 + - - +
682D MET 3.2 0.8 - - - -
683D ASN* 1.3 76.0 - - + +
685D LEU* 1.3 60.4 + - + +
687D GLN* 3.6 11.5 - - + +
688D MET* 2.8 43.7 + - - +
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Residues in contact with LEU 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648D LEU* 4.5 0.2 - - + -
660D VAL* 4.3 7.2 - - + -
663D ILE* 4.4 20.2 - - + -
681D MET 2.9 22.8 + - - +
682D MET* 3.6 4.3 - - - +
684D VAL* 1.3 73.4 - - + +
686D ALA* 1.3 68.0 + - - +
687D GLN 3.0 1.1 - - - -
688D MET* 2.9 41.0 + - + +
689D ILE* 3.1 15.4 + - - +
702D VAL* 4.0 19.7 - - + +
705D VAL* 3.6 28.3 - - + -
706D PHE* 4.0 17.0 - - + -
709D ILE* 3.8 22.2 - - + -
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Residues in contact with ALA 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682D MET* 2.8 20.2 + - + +
683D ASN* 4.2 4.5 - - - +
685D LEU* 1.3 72.3 - - - +
687D GLN* 1.3 62.6 + - - +
689D ILE* 3.2 22.6 - - - +
690D SER* 3.3 10.0 + - - -
706D PHE* 4.4 8.1 - - + -
720D TYR* 6.5 1.3 - - + -
723D ASP* 6.1 3.4 - - + -
724D ILE* 5.1 9.9 - - + -
727D LEU* 4.6 12.2 - - + +
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Residues in contact with GLN 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649D ASN* 4.9 14.0 - - - +
683D ASN* 3.3 20.0 + - - +
684D VAL* 3.6 12.2 - - - +
686D ALA* 1.3 77.9 - - - +
688D MET* 1.3 67.4 + - + +
690D SER* 2.8 24.1 + - - -
691D ASN* 3.6 9.9 + - - +
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Residues in contact with MET 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648D LEU* 3.3 50.7 - - + +
649D ASN* 4.9 4.9 - - - +
651D VAL* 3.9 15.3 - - + +
656D SER 4.8 0.7 - - - +
660D VAL* 3.7 30.1 - - + -
684D VAL* 2.8 33.1 + - + +
685D LEU* 2.9 20.1 + - + +
687D GLN* 1.3 73.0 - - + +
689D ILE* 1.3 59.5 + - - +
691D ASN* 3.4 20.5 + - - +
694D ALA* 3.6 12.5 - - - +
698D LEU* 3.9 16.1 - - + +
702D VAL* 3.8 10.5 - - + -
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Residues in contact with ILE 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685D LEU 3.1 9.4 + - - +
686D ALA* 3.2 20.9 - - - +
687D GLN 3.0 0.4 + - - -
688D MET* 1.3 76.5 - - - +
690D SER* 1.3 58.9 + - - +
691D ASN 3.1 9.1 + - - +
694D ALA* 4.6 5.8 - - - +
698D LEU* 5.8 1.6 - - - -
699D LYS* 4.2 47.3 - - + +
702D VAL* 4.3 18.1 - - + +
703D LEU* 5.6 4.7 - - + -
706D PHE* 5.3 1.6 - - + -
727D LEU* 3.7 35.4 - - + -
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Residues in contact with SER 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686D ALA 3.3 14.0 + - - -
687D GLN* 2.8 12.3 + - - -
689D ILE* 1.3 78.6 - - - +
691D ASN* 1.3 61.0 + - - +
692D PRO* 3.6 6.9 - - - +
727D LEU* 4.8 5.9 - - - +
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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