Contacts of the helix formed by residues 770 - 775 (chain C) in PDB entry 1DQ8
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 770 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655C MET* 3.6 38.4 - - - +
657C MET* 4.8 1.6 - - - +
690C ASP* 3.0 22.2 + - - +
691C LYS* 3.6 28.1 - - + +
702C ARG* 3.9 6.9 - - - +
761C TYR* 4.5 4.5 - - + -
767C ASP* 2.9 29.5 + - + +
769C ALA* 1.3 74.8 - - - +
771C ASN* 1.3 58.9 + - - +
772C VAL 3.0 2.6 + - - -
773C GLY 3.5 1.9 + - - +
774C SER* 2.9 33.6 + - - +
801C GLU* 3.3 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 771 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754C ALA* 5.5 0.2 - - - +
757C VAL* 4.0 16.4 - - + -
758C THR* 2.7 32.8 + - - +
761C TYR* 4.9 0.6 - - + -
767C ASP 4.3 0.4 + - - -
768C ALA* 2.9 25.4 + - - +
770C GLN* 1.3 77.4 - - - +
772C VAL* 1.3 77.3 + - - +
774C SER* 3.9 0.4 - - - -
775C SER* 2.8 36.3 + - - +
768D ALA* 3.1 24.7 + - - +
769D ALA* 3.7 5.7 + - - +
771D ASN* 3.0 21.6 + - - +
772D VAL* 4.0 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 772 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C LYS* 4.1 7.6 - - - +
692C LYS* 3.7 8.5 - - - +
693C PRO* 3.6 41.1 - - + +
769C ALA 3.5 8.1 - - - +
770C GLN 3.0 0.6 - - - -
771C ASN* 1.3 85.3 + - - +
773C GLY* 1.3 61.4 + - - +
775C SER* 4.3 5.5 + - - -
776C ASN* 4.2 8.3 - - - +
693D PRO* 5.3 5.0 - - - +
754D ALA* 3.9 11.7 - - + -
771D ASN* 3.2 40.4 - - - +
772D VAL* 4.3 21.9 - - + +
775D SER* 4.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 773 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C LYS* 5.4 3.4 - - - +
692C LYS 5.3 4.2 + - - -
693C PRO* 6.0 1.8 - - - -
697C ASN* 5.0 9.2 - - - -
770C GLN* 3.5 3.6 + - - +
772C VAL* 1.3 78.4 - - - +
774C SER* 1.3 65.4 + - - +
775C SER 3.2 2.2 - - - -
776C ASN* 3.0 22.7 + - - -
799C SER* 2.9 25.6 + - - -
801C GLU* 4.2 9.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 774 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757C VAL* 4.0 8.5 - - - +
761C TYR* 3.0 27.6 + - - -
770C GLN 2.9 24.1 + - - -
773C GLY* 1.3 76.2 - - - +
775C SER* 1.3 57.3 + - - +
776C ASN 3.2 2.8 + - - +
797C MET* 3.2 23.0 - - - +
799C SER 3.1 12.8 + - - +
800C ILE* 3.9 7.5 - - - +
801C GLU* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 775 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750C ASN* 3.9 6.8 + - - -
753C ALA* 3.8 7.8 - - - +
754C ALA* 3.1 39.7 - - - +
757C VAL* 3.9 17.0 - - - +
771C ASN* 2.8 25.8 + - - +
772C VAL 4.4 3.8 - - - -
773C GLY 3.2 0.2 - - - -
774C SER* 1.3 74.1 - - - +
776C ASN* 1.3 66.0 + - - +
777C CYS* 3.2 11.1 + - - +
797C MET* 4.4 1.8 - - - -
691D LYS 5.4 1.1 - - - -
693D PRO* 6.2 2.9 - - - -
772D VAL* 4.5 4.5 - - - -
----------------------------------------------------------
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