Contacts of the strand formed by residues 747 - 755 (chain A) in PDB entry 1QAS
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 THR 747 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 4.4 6.5 - - + +
638A GLY* 3.4 2.9 - - - -
639A GLN* 2.7 60.1 + - - +
641A LEU* 3.7 3.7 - - - +
732A HIS* 3.8 13.0 - - + -
733A VAL 3.0 15.5 - - - +
734A HIS* 3.6 34.8 - - + +
735A LEU* 4.3 3.7 - - - +
745A SER* 4.1 7.7 + - - +
746A ALA* 1.3 80.2 - - - +
748A LEU* 1.3 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ILE* 4.9 4.7 - - + -
637A SER 3.3 5.4 - - - +
638A GLY* 3.9 13.5 - - - -
639A GLN* 3.4 2.0 - - - -
641A LEU* 4.5 6.7 - - + -
656A VAL* 3.5 41.7 - - + -
684A TRP* 4.3 5.8 - - + -
702A PHE* 4.3 17.7 - - + -
704A VAL* 3.7 26.9 - - + -
732A HIS* 3.3 3.8 - - - -
733A VAL* 2.8 37.9 + - + +
735A LEU* 4.1 13.5 - - + -
747A THR* 1.3 83.6 - - - +
749A PHE* 1.3 61.6 + - - +
750A VAL* 3.6 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ARG* 3.4 11.2 - - - +
213A GLU* 3.1 32.3 - - + -
214A ILE* 4.1 10.8 - - + -
217A ALA* 5.0 3.1 - - + -
279A LEU* 4.0 11.4 - - + -
635A ILE 4.0 0.3 - - - -
636A ILE* 3.0 55.4 + - + -
637A SER* 2.6 31.7 + - - +
639A GLN* 3.2 4.5 + - - +
730A TYR* 3.3 41.3 - + + -
731A ARG 3.7 10.3 - - - -
732A HIS* 3.2 32.8 - + - +
748A LEU* 1.3 70.0 - - - +
750A VAL* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A VAL* 4.5 4.7 - - + -
634A ARG 3.1 9.9 - - - +
635A ILE* 3.5 30.7 - - + -
636A ILE* 3.8 8.1 - - - +
702A PHE* 4.4 2.7 - - + -
730A TYR* 3.4 4.5 - - - +
731A ARG* 2.9 45.6 + - + +
733A VAL* 3.8 25.4 - - + -
748A LEU* 4.1 13.0 - - + +
749A PHE* 1.3 82.3 - - - +
751A LYS* 1.3 62.0 + - - +
752A ILE* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 4.2 4.2 + - - -
240A GLN* 2.7 34.6 - - - +
632A ARG 3.7 1.4 - - - +
633A VAL* 3.4 4.0 - - - +
634A ARG* 2.8 52.0 + - + +
636A ILE* 3.9 9.1 - - + +
729A GLY* 3.1 19.3 - - - +
730A TYR* 3.1 34.9 + - + +
750A VAL* 1.3 76.5 - - - +
752A ILE* 1.3 66.4 + - - +
753A SER* 5.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ARG* 5.8 0.2 - - - +
286A ALA* 4.0 13.9 - - + -
631A LEU* 3.7 21.8 - - + -
632A ARG 3.5 2.2 - - - -
633A VAL* 4.4 14.4 - - + -
702A PHE* 4.7 3.8 - - + -
726A LEU* 3.8 30.5 - - + -
727A LYS 3.2 30.3 - - - +
728A GLN* 3.5 13.8 - - + +
729A GLY* 2.9 33.5 + - - +
731A ARG* 4.4 5.2 - - + -
750A VAL* 3.8 23.8 - - + -
751A LYS* 1.3 80.5 - - - +
753A SER* 1.3 66.5 + - - +
754A ILE* 4.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A ARG 3.3 2.4 - - - +
631A LEU* 3.2 4.9 - - - +
632A ARG* 2.7 55.9 + - - +
728A GLN* 3.9 3.8 + - - +
751A LYS* 5.7 4.0 - - - -
752A ILE* 1.3 77.4 - - - +
754A ILE* 1.3 62.9 + - - +
755A GLN* 3.7 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A GLU* 3.4 26.9 - - + +
630A ARG 3.5 3.4 - - - -
631A LEU* 3.9 15.9 - - + -
723A TRP* 3.7 37.9 - - + +
726A LEU* 4.1 29.6 - - + +
728A GLN* 2.9 38.4 + - + +
752A ILE* 4.5 0.9 - - + -
753A SER* 1.3 75.9 + - - +
755A GLN* 1.3 67.8 + - - +
756A ASP* 4.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ARG* 5.6 5.0 - - - -
629A GLU* 3.4 5.1 - - - -
630A ARG* 2.8 37.4 + - + +
632A ARG* 3.2 29.9 - - - +
728A GLN* 5.0 1.9 + - - -
753A SER* 3.7 16.0 + - - +
754A ILE* 1.3 88.4 - - - +
756A ASP* 1.3 67.9 + - - +
----------------------------------------------------------
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