Contacts of the strand formed by residues 874 - 880 (chain A) in PDB entry 1QU2
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 GLY 874 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A ILE* 5.0 0.7 - - - -
832A ALA 3.4 12.6 - - - -
834A ASN* 2.9 25.4 - - - +
839A ALA* 4.3 2.2 - - - -
871A TYR* 2.7 40.2 + - - +
872A GLU 3.6 0.4 - - - -
873A HIS* 1.3 79.1 - - - +
875A ASP* 1.3 61.2 + - - -
876A ILE* 4.2 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A ILE* 3.1 7.8 - - - +
832A ALA 2.9 34.3 + - - +
833A SER 4.0 10.5 - - - +
834A ASN* 2.6 32.7 + - - +
864A LEU* 3.7 35.2 + - + +
865A ASP 5.5 0.4 - - - +
868A ALA* 3.9 12.3 - - + +
869A THR 3.3 7.6 - - - +
870A ALA* 3.4 13.7 - - - +
874A GLY* 1.3 73.2 - - - -
876A ILE* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A ASP* 3.9 11.0 - - + +
808A VAL* 3.8 37.9 - - + +
811A ALA* 3.6 19.4 - - + +
829A VAL* 4.1 8.1 - - + -
830A THR 3.4 8.5 - - - +
831A ILE* 3.8 18.4 - - + -
868A ALA* 3.8 0.5 - - - +
869A THR* 3.0 32.8 + - - +
871A TYR* 3.7 27.5 - - + -
873A HIS 6.0 1.1 - - - +
874A GLY 4.2 2.2 - - - +
875A ASP* 1.3 81.7 - - - +
877A VAL* 1.3 68.2 + - - +
878A ILE* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A LYS 3.7 2.6 - - - +
830A THR* 2.8 43.6 + - + +
864A LEU* 3.3 26.0 - - + -
867A GLN* 4.1 22.9 - - + +
868A ALA* 3.3 33.4 - - + +
876A ILE* 1.3 73.1 - - - +
878A ILE* 1.3 70.7 + - - +
879A GLU* 4.3 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A VAL* 4.8 1.1 - - + +
811A ALA* 3.6 32.5 - - + +
812A LEU* 3.5 23.8 - - + -
815A ALA* 3.7 27.1 - - + +
820A VAL* 5.0 4.3 - - + +
821A ILE* 5.2 2.9 - - + -
827A ALA* 4.2 5.2 - - + -
828A LYS 3.7 4.9 - - - +
829A VAL* 3.5 30.1 - - + -
876A ILE* 3.8 13.9 + - + -
877A VAL* 1.3 83.5 - - - +
879A GLU* 1.3 73.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A VAL* 4.4 9.6 - - - -
821A ILE* 6.1 0.9 - - - -
827A ALA* 3.6 3.5 - - - -
828A LYS* 2.8 69.8 + - + +
830A THR* 4.8 5.6 + - - +
877A VAL* 4.3 16.7 - - + +
878A ILE* 1.3 80.0 - - - +
880A HIS* 1.3 67.2 + - - +
882A ASP* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A VAL* 3.9 32.3 - - + +
821A ILE* 5.7 0.7 - - - -
826A GLU* 3.2 32.0 + - + +
828A LYS* 4.0 1.0 - - - +
879A GLU* 1.3 85.7 - - - +
881A ALA* 1.3 93.0 + - - +
882A ASP* 3.9 6.4 + - - +
883A GLY 5.5 0.9 - - - -
892A TYR* 3.5 33.1 + + - -
----------------------------------------------------------
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