Contacts of the helix formed by residues 675 - 696 (chain B) in PDB entry 2XWU
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 ASN 675 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ILE* 5.3 1.8 - - - -
674B PRO* 1.3 82.5 - - - +
676B PRO* 1.3 65.5 - - - +
677B VAL* 3.1 3.4 - - - +
678B VAL* 2.7 53.5 + - + -
679B VAL* 3.1 8.8 + - - +
716B LEU* 5.4 3.6 - - + -
719B ASP* 5.4 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 676 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B VAL* 5.1 8.3 - - + +
606B ILE* 3.7 17.7 - - + -
607B LEU* 3.6 36.1 - - + -
610B LEU* 3.6 15.0 - - + -
653B ILE* 3.2 33.2 - - + -
674B PRO* 3.4 6.4 - - + +
675B ASN* 1.3 86.1 - - - +
677B VAL* 1.3 63.5 + - + +
679B VAL* 3.3 4.6 + - + +
680B VAL* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 677 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LEU* 4.9 1.3 - - + -
648B PHE* 3.8 31.9 - - + -
651B LEU* 4.0 34.5 - - + +
653B ILE* 4.3 15.3 - - + -
675B ASN 3.1 0.4 - - - -
676B PRO* 1.3 77.1 - - + +
678B VAL* 1.3 57.9 + - - +
680B VAL* 3.4 7.6 + - - +
681B LEU* 2.8 40.5 + - + +
712B SER* 4.8 2.7 - - - +
715B THR* 5.3 3.6 - - + -
716B LEU* 3.7 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B ASN* 2.7 37.6 + - + +
677B VAL* 1.3 69.8 - - - +
679B VAL* 1.3 61.3 + - + +
681B LEU* 3.2 10.0 + - + +
682B GLN* 2.9 28.3 + - + +
716B LEU* 4.0 22.0 - - + -
719B ASP 3.8 19.7 - - - +
720B PHE* 4.9 1.3 - - - -
722B PRO* 4.2 27.1 - - + -
723B MET* 4.2 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 679 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B LEU* 4.8 11.4 - - + -
611B HIS* 6.0 0.9 - - + +
674B PRO 3.4 14.6 - - - +
675B ASN 3.2 16.6 - - - +
676B PRO* 3.7 8.7 - - + +
678B VAL* 1.3 72.5 - - + +
680B VAL* 1.3 68.7 + - + +
682B GLN* 3.0 7.7 + - + +
683B GLN* 2.9 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 680 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B LEU* 5.4 3.1 - - + -
610B LEU* 3.9 26.2 - - + -
611B HIS* 5.3 11.2 - - + +
614B ILE* 3.5 30.3 - - + -
648B PHE* 4.2 13.2 - - + -
676B PRO* 2.8 27.2 + - + +
677B VAL* 3.6 6.5 - - - +
679B VAL* 1.3 76.4 - - + +
681B LEU* 1.3 57.4 + - - +
683B GLN* 3.5 9.6 + - - +
684B VAL* 2.9 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B PHE* 4.6 13.9 - - + -
677B VAL* 2.8 24.1 + - + +
678B VAL* 3.3 7.9 - - - +
679B VAL 3.0 0.2 - - - -
680B VAL* 1.3 74.7 - - - +
682B GLN* 1.3 55.5 + - - +
684B VAL* 3.2 6.6 + - + +
685B PHE* 2.6 37.9 + - - +
708B ILE* 4.9 5.4 - - + -
709B PHE* 4.3 18.0 - - + -
712B SER* 3.7 19.7 - - - +
716B LEU* 3.3 33.7 - - + -
720B PHE* 3.5 20.6 - - + -
723B MET* 3.5 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B VAL* 2.9 14.6 + - + +
679B VAL* 3.5 10.8 - - + +
681B LEU* 1.3 77.3 - - - +
683B GLN* 1.3 63.8 + - + +
685B PHE* 3.6 14.2 + - - +
686B GLN* 3.8 7.3 + - - +
723B MET* 3.8 15.9 - - - +
726B GLN* 4.9 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B HIS* 3.5 31.6 + - - -
679B VAL* 2.9 43.3 + - + +
680B VAL* 3.8 7.1 - - - +
682B GLN* 1.3 82.3 - - + +
684B VAL* 1.3 62.6 + - + +
686B GLN* 3.8 14.8 + - - +
687B LEU* 4.3 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B ILE* 4.6 15.9 - - + -
618B ILE* 5.6 7.6 - - + -
621B LEU* 5.6 7.0 - - + -
641B LEU* 6.3 1.8 - - + -
644B LEU* 4.5 21.3 - - + -
680B VAL* 2.9 31.6 + - + +
681B LEU* 3.9 6.3 - - + +
683B GLN* 1.3 75.2 - - + +
685B PHE* 1.3 56.8 + - - +
686B GLN 3.1 2.5 - - - -
687B LEU* 2.8 12.3 + - + +
688B ILE* 2.7 41.0 + - + +
708B ILE* 6.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B LEU 2.6 23.3 + - - +
682B GLN 3.6 8.5 - - - +
683B GLN 3.3 0.4 - - - -
684B VAL* 1.3 72.9 - - - +
686B GLN* 1.3 65.5 + - - +
688B ILE* 3.3 7.2 - - + +
689B GLN* 2.9 59.2 + - - +
709B PHE* 4.1 19.1 - + + -
723B MET* 4.2 4.3 - - + -
726B GLN* 2.7 66.9 - - + +
727B LEU 4.6 0.4 - - - -
729B GLU* 6.3 0.9 - - + -
730B MET* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B GLN 3.8 6.2 + - - +
683B GLN* 3.8 12.5 + - - +
684B VAL 3.1 0.6 - - - -
685B PHE* 1.3 82.9 - - - +
687B LEU* 1.3 60.7 + - - +
689B GLN* 3.8 10.2 + - - +
690B LYS* 3.6 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ILE* 5.8 2.2 - - + +
621B LEU* 3.7 24.5 - - + -
622B GLU* 4.9 17.5 - - + +
625B ALA* 5.0 1.5 - - + +
683B GLN 4.3 1.9 + - - +
684B VAL* 2.8 17.5 + - + +
686B GLN* 1.3 74.0 - - - +
688B ILE* 1.3 69.6 + - - +
690B LYS* 3.0 23.0 + - - +
691B VAL* 3.1 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LEU* 5.0 2.0 - - - +
641B LEU* 6.1 5.4 - - + -
684B VAL* 2.7 19.7 + - + +
685B PHE* 3.3 15.7 - - + +
687B LEU* 1.3 76.1 - - - +
689B GLN* 1.3 64.8 + - - +
691B VAL* 2.8 21.1 + - - +
692B LEU* 3.0 21.4 + - + +
705B VAL* 5.2 5.6 - - + -
709B PHE* 5.3 4.9 - - + -
730B MET* 4.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B PHE* 2.9 62.6 + - + +
686B GLN* 3.9 9.2 - - - +
688B ILE* 1.3 75.5 - - - +
690B LYS* 1.3 65.0 + - - +
692B LEU* 3.1 21.6 + - - +
693B SER* 3.2 16.4 + - - -
729B GLU* 6.1 2.8 - - - +
730B MET* 4.5 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ALA* 4.2 21.0 - - + +
686B GLN 3.6 7.8 + - - +
687B LEU* 3.0 19.4 + - - +
689B GLN* 1.3 81.0 - - - +
691B VAL* 1.3 60.9 + - - +
693B SER* 3.3 19.1 + - - -
694B LYS* 4.0 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LEU* 4.3 25.4 - - + -
625B ALA* 4.2 21.1 - - + +
637B ILE* 5.2 10.3 - - + -
641B LEU* 5.3 10.5 - - + -
687B LEU 3.1 14.3 + - - +
688B ILE* 2.8 9.7 + - - +
690B LYS* 1.3 76.8 - - - +
692B LEU* 1.3 66.0 + - + +
693B SER 3.1 0.7 + - - -
694B LYS* 3.3 1.4 + - - -
695B TRP* 3.0 53.3 + - + +
701B VAL* 4.2 15.9 - - + -
705B VAL* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B ILE 3.0 29.9 + - - +
689B GLN* 3.1 10.3 + - - +
691B VAL* 1.3 77.6 - - + +
693B SER* 1.3 57.2 + - - +
695B TRP* 4.7 2.0 - - - -
696B LEU* 2.7 56.2 + - + +
701B VAL* 6.3 0.2 - - - -
702B VAL* 6.5 0.9 - - - -
705B VAL* 3.9 35.0 - - + -
730B MET* 3.3 40.2 - - + +
733B ARG* 5.9 1.6 - - + -
734B MET* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B GLN 3.2 13.8 + - - -
690B LYS* 3.4 12.2 + - - -
691B VAL 3.1 1.0 - - - -
692B LEU* 1.3 78.9 - - - +
694B LYS* 1.3 59.9 + - - +
696B LEU* 4.4 5.1 + - - +
697B ASN* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ALA 5.2 8.1 - - - +
627B GLU 5.4 0.4 - - - +
629B PRO* 4.0 33.0 - - + +
690B LYS 4.0 3.5 + - - +
691B VAL 3.3 3.2 + - - +
693B SER* 1.3 79.2 - - - +
695B TRP* 1.3 76.2 + - + +
696B LEU 3.7 0.9 - - - -
697B ASN* 5.2 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B LEU 5.1 7.8 + - - -
625B ALA* 5.4 4.6 + - - +
627B GLU 5.5 0.2 + - - -
629B PRO* 3.6 34.3 - - + +
630B ASN 3.7 9.9 - - - -
633B ASN* 3.8 18.6 - - - -
634B LYS* 3.3 44.6 - - + -
637B ILE* 5.0 6.4 - - + +
691B VAL* 3.0 44.1 + - + +
692B LEU* 3.6 3.1 - - - -
694B LYS* 1.3 95.2 - - + +
696B LEU* 1.3 57.1 + - - +
697B ASN* 2.8 13.1 + - - +
698B ASP* 2.8 41.3 + - + +
701B VAL* 3.7 29.5 - - + +
702B VAL* 4.6 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LEU* 2.7 47.9 + - + +
693B SER* 4.4 4.7 + - - +
694B LYS 3.7 1.2 - - - -
695B TRP* 1.3 74.1 - - - +
697B ASN* 1.3 66.7 + - - +
698B ASP 4.9 0.7 - - - -
702B VAL* 4.6 4.9 - - + +
733B ARG* 3.8 16.6 - - + +
734B MET* 4.0 26.7 - - + +
737B THR* 3.0 43.1 - - + +
738B ILE* 3.7 13.5 - - - +
----------------------------------------------------------
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