Contacts of the helix formed by residues 686 - 696 (chain B) in PDB entry 3U11
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 VAL 686 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B GLY 5.1 3.4 - - - +
630B LYS* 2.7 42.1 + - + +
631B LYS* 4.6 0.2 - - - +
663B LEU* 4.4 23.1 - - + +
666B ARG* 6.5 0.4 - - + -
685B SER* 1.3 71.2 - - - +
687B ASP* 1.3 70.6 + - - +
689B PHE* 3.3 7.8 - - + +
690B ASN* 2.8 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B SER* 3.3 5.1 + - - +
686B VAL* 1.3 83.5 - - - +
688B ASN* 1.3 65.0 + - - +
690B ASN* 3.6 13.3 + - - +
691B GLU* 2.7 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LYS* 3.7 27.5 + - + +
612B ARG* 3.8 23.4 - - - +
684B LEU* 3.8 18.6 - - + -
685B SER* 3.1 26.2 + - - +
687B ASP* 1.3 78.0 - - - +
689B PHE* 1.3 65.2 + - - +
691B GLU* 3.3 16.8 + - - +
692B VAL* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B MET* 4.0 8.3 - - - -
660B GLU 4.7 1.6 - - - -
663B LEU* 3.5 53.2 - - + -
664B LEU* 4.4 12.6 - - + -
684B LEU* 3.6 25.4 - - + +
685B SER 2.7 17.2 + - - +
686B VAL* 3.3 9.2 - - + +
688B ASN* 1.3 71.3 - - - +
690B ASN* 1.3 69.5 + - - +
692B VAL* 3.2 5.0 + - - +
693B LEU* 2.9 61.9 + - + +
700B ARG* 5.6 1.3 - - - -
703B PHE* 3.3 40.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LEU 5.2 2.4 - - - +
686B VAL* 2.8 39.0 + - - +
687B ASP* 3.7 13.0 + - - +
689B PHE* 1.3 86.3 - - - +
691B GLU* 1.3 64.1 + - - +
693B LEU* 3.4 8.3 + - - +
694B GLU* 3.3 22.3 + - - +
700B ARG* 5.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LYS* 3.7 26.2 + - - -
687B ASP 2.7 21.3 + - - +
688B ASN* 3.6 16.0 - - - +
689B PHE 3.3 0.2 - - - -
690B ASN* 1.3 73.8 - - - +
692B VAL* 1.3 60.6 + - - +
694B GLU* 3.3 24.8 + - - +
695B GLU* 3.3 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B PHE* 4.5 2.7 - - + -
606B SER* 4.7 7.4 - - - +
607B MET* 3.7 31.6 - - + -
610B LYS* 3.3 40.8 - - + +
684B LEU* 5.3 2.2 - - + -
688B ASN 3.0 9.8 + - - +
689B PHE* 4.0 3.4 - - - +
691B GLU* 1.3 73.6 - - - +
693B LEU* 1.3 54.0 + - + +
694B GLU 2.9 5.4 - - - -
695B GLU* 4.3 6.1 - - - +
696B TYR* 2.7 57.1 + - + +
699B MET* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B LEU* 4.8 0.4 - - + -
689B PHE* 2.9 62.3 + - + +
690B ASN* 3.4 8.7 + - - +
692B VAL* 1.3 76.7 - - + +
694B GLU* 1.3 56.7 + - - +
696B TYR 3.9 8.1 - - - -
697B PRO* 3.3 23.4 - - + +
699B MET* 3.6 27.1 - - + -
700B ARG* 3.6 55.4 - - + +
703B PHE* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B ASN 3.3 9.5 + - - +
691B GLU* 3.3 24.5 - - - +
692B VAL 2.9 0.2 - - - -
693B LEU* 1.3 81.3 - - - +
695B GLU* 1.3 70.5 + - - +
697B PRO* 3.8 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B SER* 4.1 15.1 + - - -
610B LYS* 4.6 5.2 + - - -
691B GLU* 3.3 38.8 + - - +
692B VAL* 3.3 4.4 + - - +
694B GLU* 1.3 92.1 - - - +
696B TYR* 1.3 79.1 + - + +
697B PRO* 3.5 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP* 4.8 6.4 + - - -
602B ASN* 3.9 8.5 + - - +
603B PHE* 3.4 60.8 + + + +
606B SER* 3.9 19.4 - - - -
692B VAL* 2.7 31.7 + - + +
693B LEU* 3.9 1.0 - - - -
695B GLU* 1.3 96.7 - - + +
697B PRO* 1.4 60.3 - - - +
698B MET* 3.2 29.6 - - + -
699B MET* 3.0 27.7 + - + +
----------------------------------------------------------
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