Contacts of the helix formed by residues 763 - 774 (chain N) in PDB entry 3HOU
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 GLN 763 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804M TYR* 2.9 23.3 - - + +
816M HIS* 4.6 3.4 - - + +
762N ASN* 1.3 71.7 - - - +
764N SER* 1.3 66.5 + - - +
765N PRO* 3.2 29.4 - - + +
766N ARG* 2.7 31.5 + - + +
767N ASN 3.8 1.0 + - - -
1019N SER 4.3 3.0 - - - +
1020N ARG* 2.9 20.5 - - - +
1021N MET* 3.3 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 764 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813M PHE* 6.2 2.2 - - - -
816M HIS* 3.3 43.4 + - - -
817M ALA* 3.4 21.1 + - - +
820M GLY* 3.9 7.5 - - - -
821M ARG 4.7 0.7 + - - -
525N ALA* 4.9 2.9 - - - +
762N ASN 3.2 6.2 + - - -
763N GLN* 1.3 69.4 - - - +
765N PRO* 1.3 71.8 - - - +
767N ASN* 3.3 25.8 + - - +
768N THR* 3.7 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 765 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816M HIS* 4.6 3.1 - - + -
820M GLY* 4.8 10.1 - - - -
824M LEU* 4.4 25.4 - - + -
763N GLN* 3.2 34.3 - - + +
764N SER* 1.3 95.4 - - - +
766N ARG* 1.3 68.5 + - - +
768N THR* 2.8 27.5 + - - +
769N TYR* 3.3 16.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 766 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762N ASN* 4.2 14.6 - - + +
763N GLN* 2.7 28.8 + - + +
765N PRO* 1.3 73.1 - - - +
767N ASN* 1.3 63.4 + - - +
769N TYR* 3.0 51.1 + - - +
770N GLN* 3.3 12.5 + - - +
984N HIS* 4.1 16.9 + - - +
985N GLY 3.3 20.4 + - - -
986N GLN* 4.9 0.8 + - - -
987N LYS* 4.4 2.4 - - - +
1020N ARG* 2.6 81.9 + - - +
1022N THR* 4.2 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 767 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813M PHE* 3.9 13.5 - - + -
525N ALA* 4.0 15.5 - - + -
753N ALA* 6.1 0.2 - - + -
756N ILE* 3.4 27.2 - - + +
759N PRO* 2.9 36.5 + - - +
762N ASN* 3.4 33.3 + - - +
764N SER* 3.3 15.9 + - - +
765N PRO 3.1 0.8 - - - -
766N ARG* 1.3 77.6 - - - +
768N THR* 1.3 52.3 + - - +
770N GLN* 4.8 1.3 - - - -
771N SER* 2.6 33.7 + - - -
984N HIS* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 768 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821M ARG* 5.6 1.6 + - - -
824M LEU* 3.8 30.2 - - + +
525N ALA* 3.0 30.0 + - - +
527N THR* 3.3 25.4 - - + +
529N GLU* 5.1 4.8 - - + +
764N SER* 3.8 4.5 + - - -
765N PRO* 2.8 19.3 + - - +
767N ASN* 1.3 76.6 - - - +
769N TYR* 1.3 69.4 + - + +
771N SER* 3.1 14.6 - - - -
772N ALA* 3.4 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 769 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824M LEU* 3.9 24.0 - - + +
529N GLU* 3.0 39.8 + - + +
765N PRO* 3.5 21.7 - - + +
766N ARG* 3.0 34.6 + - - +
768N THR* 1.3 77.6 - - - +
770N GLN* 1.3 55.1 + - - +
771N SER 2.6 4.8 + - - -
772N ALA* 2.5 29.6 + - - +
773N MET* 2.7 17.8 + - + +
985N GLY* 3.9 10.1 - - - -
987N LYS* 2.9 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 770 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752N ALA 5.6 0.7 - - - +
755N ILE* 6.1 4.4 - - + +
756N ILE* 3.9 23.5 - - + +
766N ARG 3.3 7.7 + - - +
767N ASN* 4.8 0.4 - - - -
769N TYR* 1.3 76.7 - - - +
771N SER* 1.3 55.6 + - - +
773N MET* 3.8 11.7 - - - +
774N GLY* 3.1 24.1 + - - +
982N SER 2.6 21.8 - - - +
983N ARG* 2.9 43.6 - - + +
984N HIS* 3.4 2.1 + - - -
985N GLY* 3.5 15.0 + - - +
1093N GLN* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 771 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525N ALA 4.4 0.2 - - - -
526N GLU* 3.7 30.3 + - - +
527N THR 5.2 0.2 - - - -
752N ALA* 3.7 14.3 - - - +
753N ALA* 3.9 14.5 + - - +
756N ILE* 3.8 10.9 - - - +
767N ASN 2.6 18.7 + - - -
768N THR* 3.1 13.9 - - - -
769N TYR 2.6 4.4 + - - -
770N GLN* 1.3 78.1 - - - +
772N ALA* 1.3 58.8 + - - -
774N GLY* 4.4 1.7 + - - -
775N LYS* 3.5 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 772 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 C 4.5 18.4 + - - +
526N GLU* 5.8 0.4 - - - -
527N THR 5.0 9.4 - - - +
528N PRO* 5.6 5.6 - - + -
529N GLU* 5.3 9.0 - - + +
768N THR 3.4 7.2 + - - +
769N TYR* 2.5 14.8 + - - +
771N SER* 1.3 75.2 - - - +
773N MET* 1.3 62.5 + - + +
775N LYS* 3.3 27.4 - - + +
776N GLN* 4.1 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 773 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106 U 5.8 2.2 - - - +
769N TYR* 2.7 15.3 + - + +
770N GLN* 4.1 12.6 - - - +
772N ALA* 1.3 73.9 - - + +
774N GLY* 1.3 54.2 + - - +
775N LYS 2.5 5.4 + - - -
776N GLN* 2.4 50.0 + - - +
777N ALA* 3.4 3.1 + - - +
979N LYS* 5.5 0.9 - - - -
981N ALA* 4.1 16.8 - - + -
985N GLY* 3.2 39.7 - - - +
986N GLN 3.8 3.1 - - - +
987N LYS* 3.5 43.7 - - + +
1093N GLN* 5.3 1.3 - - - +
1095N LEU* 4.1 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 774 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487N THR* 4.4 12.0 - - - +
489N SER* 4.5 7.9 + - - -
490N SER* 4.9 0.8 - - - -
755N ILE* 5.9 7.2 - - - -
770N GLN* 3.1 21.6 + - - +
771N SER 4.4 1.8 + - - -
772N ALA 3.6 0.4 - - - -
773N MET* 1.3 75.6 - - - +
775N LYS* 1.3 58.8 + - - +
776N GLN 3.2 0.9 - - - -
777N ALA* 3.4 16.7 + - - +
1093N GLN* 3.8 23.6 + - - -
----------------------------------------------------------
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