Contacts of the strand formed by residues 888 - 898 (chain A) in PDB entry 1QWN
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 VAL 888 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A PRO* 4.0 15.5 - - + +
424A TYR* 3.7 32.3 - - + -
427A ARG* 4.2 10.5 - - + -
531A TRP* 5.2 1.1 - - + -
536A VAL* 4.4 1.8 - - - -
778A ASN 3.2 2.4 - - - +
779A LEU* 3.5 4.8 - - - -
780A VAL* 2.8 43.6 + - + +
867A ASP* 4.9 2.2 - - - +
886A LYS 4.1 6.3 - - - +
887A PRO* 1.3 75.8 - - - +
889A LEU* 1.3 64.4 + - - +
890A HIS* 3.6 40.7 + - + +
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Residues in contact with LEU 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 3.9 23.6 + - - +
529A SER 4.7 2.2 - - - +
530A ARG* 4.0 22.1 - - - +
531A TRP* 5.7 1.2 - - + -
532A PRO 3.9 15.9 + - - +
533A GLY* 3.8 20.9 - - - -
534A SER* 4.4 10.1 - - - +
536A VAL* 3.9 10.2 - - + +
766A GLN* 4.0 9.4 - - - +
777A ARG* 4.0 31.4 - - + +
778A ASN 3.4 20.0 - - - +
779A LEU* 3.9 12.1 - - + +
888A VAL* 1.3 73.3 - - - +
890A HIS* 1.3 61.9 + - - +
891A ILE* 3.8 12.5 + - + +
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Residues in contact with HIS 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A PRO* 3.6 25.3 - - + +
427A ARG* 4.7 0.8 - - - +
776A ILE 3.9 0.2 - - - +
777A ARG* 3.2 5.4 - - - +
778A ASN* 2.9 35.5 + - + +
780A VAL* 4.0 13.5 - - + -
850A GLN* 3.3 28.9 + - + +
852A LEU* 3.8 8.4 - - + +
866A GLN* 2.9 47.3 + - - +
888A VAL* 3.6 23.3 + - + +
889A LEU* 1.3 73.7 + - - +
891A ILE* 1.3 61.7 + - - +
892A TYR* 3.6 24.1 - - + +
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Residues in contact with ILE 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 3.5 31.6 - - - +
530A ARG* 3.7 40.2 - - + +
775A GLU* 4.4 4.3 - - - +
776A ILE 3.4 4.7 - - - +
777A ARG* 4.1 16.8 - - + -
849A GLY* 2.9 38.4 + - - -
850A GLN* 3.0 17.7 + - - +
889A LEU* 4.1 18.6 - - + +
890A HIS* 1.3 79.5 - - - +
892A TYR* 1.3 65.9 + - - +
925A LEU* 3.8 19.1 - - + +
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Residues in contact with TYR 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A GLU* 3.3 13.2 - - - +
776A ILE* 2.9 51.4 + - + +
778A ASN* 3.9 17.0 - - - -
792A MET* 3.9 13.7 - - + -
846A LEU* 3.8 23.3 - - + -
847A LEU 3.1 17.3 - - - +
848A THR* 3.9 17.0 - - + -
850A GLN* 3.5 15.3 - - - -
852A LEU* 3.2 13.2 - - - +
864A ILE* 4.0 11.7 - - + -
866A GLN* 2.8 30.5 + - - -
890A HIS* 3.6 21.9 - - + +
891A ILE* 1.3 76.8 - - - +
893A ARG* 1.3 64.5 + - - +
925A LEU* 3.9 6.0 - - - +
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Residues in contact with ARG 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A ARG* 6.0 0.4 - - - +
772A GLY* 4.4 3.2 - - - -
773A ALA* 2.8 45.4 + - - +
774A PRO 3.3 8.5 + - - -
775A GLU* 3.7 17.1 - - - +
776A ILE* 5.2 0.4 - - - -
845A THR 3.7 1.0 - - - +
846A LEU* 3.5 7.3 - - - +
847A LEU* 2.9 34.5 + - + +
892A TYR* 1.3 81.5 - - - +
894A LEU* 1.3 60.3 + - - +
895A VAL* 4.1 2.5 - - + -
920A LYS 5.3 0.2 - - - -
921A ALA* 3.7 46.1 - - + +
924A SER* 2.9 31.8 + - - +
925A LEU* 3.7 11.6 - - + +
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Residues in contact with LEU 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694A LEU* 3.7 30.5 - - + -
697A ILE* 4.3 8.4 - - + +
708A VAL* 4.3 5.2 - - + -
710A PHE* 3.8 17.3 - - + -
773A ALA* 3.2 15.6 - - - +
774A PRO* 3.1 31.6 + - + +
776A ILE* 4.4 10.3 - - + +
794A LEU* 3.7 29.4 - - + -
844A LEU* 3.7 26.9 - - + -
845A THR 3.6 8.3 - - - +
846A LEU* 4.1 8.5 - - + -
893A ARG* 1.3 72.7 - - - +
895A VAL* 1.3 60.5 + - - +
896A LEU 4.0 1.6 + - - -
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Residues in contact with VAL 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773A ALA* 3.7 20.4 - - + -
843A ARG 3.7 1.4 - - - +
844A LEU* 3.5 5.4 - - - -
845A THR* 2.8 44.6 + - - +
847A LEU* 3.8 24.9 - - + -
894A LEU* 1.3 77.4 - - - +
896A LEU* 1.3 60.9 + - - +
897A GLU* 3.4 36.4 + - + +
917A ALA* 4.5 13.7 - - + +
918A ALA* 4.3 7.4 - - + +
921A ALA* 4.0 13.9 - - + -
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Residues in contact with LEU 896 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697A ILE* 3.8 37.4 - - + +
699A LEU* 3.5 33.1 - - + +
706A VAL* 3.8 38.8 - - + -
708A VAL* 4.5 6.5 - - + -
773A ALA* 5.6 0.2 - - - +
798A ILE* 4.8 2.5 - - + -
842A THR* 3.6 22.2 - - + -
843A ARG 3.5 15.7 - - - +
844A LEU* 3.9 20.8 - - + +
894A LEU 4.0 2.6 + - - -
895A VAL* 1.3 74.2 - - - +
897A GLU* 1.3 65.3 + - - +
898A LYS* 6.5 0.4 - - + -
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Residues in contact with GLU 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A LEU* 4.4 5.8 - - - -
842A THR* 3.5 6.0 - - - +
843A ARG* 2.9 52.9 + - + +
845A THR* 4.1 5.2 + - - -
895A VAL* 3.4 24.6 - - + +
896A LEU* 1.3 80.9 - - - +
898A LYS* 1.3 70.6 + - - +
899A VAL* 4.6 4.0 - - + -
915A THR* 2.5 46.8 + - + +
917A ALA* 3.8 14.6 - - + +
918A ALA* 4.5 1.2 - - - +
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Residues in contact with LYS 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A LEU* 4.3 19.5 - - + +
706A VAL* 6.3 3.1 - - + -
841A ASN* 2.9 34.4 + - - +
842A THR* 3.7 14.8 - - + +
896A LEU* 6.5 0.2 - - + -
897A GLU* 1.3 78.3 - - - +
899A VAL* 1.3 63.4 + - - +
900A ASN* 2.9 36.1 + - - +
901A ASN 5.4 0.2 + - - -
902A CYS* 4.4 5.4 - - - -
987A CYS* 5.7 0.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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