Contacts of the helix formed by residues 568 - 575 (chain A) in PDB entry 3GQL
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 568 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GQL 5.5 6.0 - - - -
567A GLY* 1.3 74.9 - - - -
569A LEU* 1.3 65.2 + - - +
570A ARG* 2.8 13.1 + - - +
571A GLU* 2.8 59.3 + - - +
572A TYR* 3.0 19.4 + - - +
626A ALA 3.6 1.1 - - - +
627A ARG* 3.2 29.8 + - - +
629A VAL 3.2 9.2 - - - +
630A LEU* 3.6 11.7 - - + +
631A VAL* 4.2 1.8 - - - -
661A ARG* 4.0 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ASN* 1.3 72.1 - - - +
570A ARG* 1.3 57.6 + - - +
572A TYR* 3.2 12.5 - - + +
573A LEU* 2.9 45.8 + - + +
603A CYS* 3.6 26.7 - - - -
607A VAL* 4.7 2.5 - - + -
626A ALA* 3.1 22.8 + - + +
629A VAL* 2.6 29.5 + - + +
631A VAL* 4.0 7.5 - - + +
637A MET* 3.7 11.4 - - - -
689A LEU* 4.0 14.6 - - + -
693A ILE* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ASN* 2.8 15.8 + - - +
569A LEU* 1.3 70.2 - - - +
571A GLU* 1.3 71.4 + - + +
573A LEU* 3.2 5.7 + - - +
574A GLN* 3.1 42.1 + - - +
626A ALA* 3.6 16.2 - - + +
627A ARG* 4.5 7.0 - - - +
661A ARG* 3.8 27.9 - - - +
666A TRP* 5.8 2.6 - - - -
692A GLU* 4.2 16.3 + - - -
697A GLY* 3.7 21.3 + - - +
698A GLY 4.1 6.4 + - - -
699A SER* 3.3 8.9 + - - +
774A ASP* 2.4 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GQL 5.9 0.9 - - - -
566A LYS 5.2 0.9 - - - +
567A GLY* 4.0 9.6 - - - -
568A ASN* 2.8 53.4 + - - +
570A ARG* 1.3 75.9 - - + +
572A TYR* 1.3 57.9 + - - +
574A GLN* 3.8 9.1 - - - +
575A ALA* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LYS* 4.0 17.6 + - + +
568A ASN 3.0 12.1 + - - +
569A LEU* 3.2 21.5 - - + +
571A GLU* 1.3 77.8 - - - +
573A LEU* 1.3 66.8 + - + +
575A ALA* 4.7 0.4 - - - -
576A ARG* 3.0 79.3 + - - +
595A LEU* 3.9 22.1 - - + +
603A CYS* 5.9 2.5 - - - -
631A VAL* 3.7 33.4 - - + -
635A ASN* 2.7 36.1 + - + +
637A MET* 4.8 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A LEU* 2.9 40.4 + - + +
570A ARG* 3.6 4.7 - - - +
572A TYR* 1.3 74.0 - - + +
574A GLN* 1.3 57.7 - - - +
576A ARG* 2.7 32.6 + - - +
577A ARG* 3.4 2.4 + - - +
595A LEU* 3.6 26.8 - - + +
600A LEU* 4.1 14.8 - - + -
603A CYS* 5.5 2.5 - - - -
626A ALA* 5.7 0.7 - - + -
692A GLU* 3.4 28.3 - - + +
693A ILE* 3.5 23.1 - - + -
696A LEU* 3.3 22.6 - - + +
697A GLY* 3.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ARG* 3.1 35.4 + - - +
571A GLU* 3.8 7.4 - - - +
573A LEU* 1.3 75.3 - - - +
575A ALA* 1.3 62.2 + - - +
576A ARG 3.1 1.0 + - - -
577A ARG* 3.4 36.8 + - - +
696A LEU 3.5 15.3 - - - +
697A GLY* 2.8 24.4 + - - +
774A ASP* 3.5 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLU 3.0 18.6 + - - +
572A TYR* 4.7 0.4 - - - -
573A LEU 3.2 0.4 - - - -
574A GLN* 1.3 76.0 - - - +
576A ARG* 1.3 78.9 + - - +
577A ARG 3.5 2.9 + - - +
593A GLU 4.9 1.7 - - - +
----------------------------------------------------------
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