Contacts of the strand formed by residues 861 - 869 (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 GLU 861 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793A ARG* 3.6 36.0 + - + -
794A LEU 3.2 11.0 - - - +
795A GLU* 4.5 15.5 - - + +
796A THR 5.8 0.4 - - - +
837A ILE* 3.8 4.5 - - - +
856A SER* 2.7 28.3 + - - +
857A LEU* 4.3 11.6 + - - +
858A ALA* 3.0 39.9 + - - +
859A SER 4.2 4.7 - - - +
860A GLY* 1.3 83.9 - - - +
862A LEU* 1.3 70.6 + - - +
863A GLU* 4.5 0.9 - - - +
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Residues in contact with LEU 862 (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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793A ARG* 3.3 2.8 - - - +
794A LEU* 2.7 49.6 + - + +
804A PHE* 5.1 1.8 - - + -
835A MET* 3.9 30.3 - - + +
836A PHE 4.0 11.2 - - - +
837A ILE* 3.7 33.7 - - + -
844A LEU* 3.7 42.4 - - + +
846A LEU* 4.4 15.7 - - + -
855A SER 3.6 5.8 - - - +
856A SER* 4.8 2.2 - - - -
861A GLU* 1.3 75.8 - - - +
863A GLU* 1.3 63.8 + - - +
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Residues in contact with GLU 863 (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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715A TYR* 2.6 26.5 + - - -
791A VAL* 3.6 11.1 - - + +
792A MET 3.2 11.2 - - - +
793A ARG* 2.9 38.0 + - + -
828A TYR* 2.7 25.9 + - + +
835A MET* 3.6 6.5 - - - +
846A LEU* 6.4 0.2 - - - -
854A GLY* 3.1 3.1 - - - -
855A SER 2.9 44.5 + - - +
857A LEU* 3.5 19.6 + - - +
861A GLU* 4.5 1.8 - - + +
862A LEU* 1.3 78.0 - - - +
864A ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 864 (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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791A VAL* 3.8 3.8 - - - -
792A MET* 2.8 56.5 + - + +
831A ILE* 4.0 17.5 - - + -
835A MET* 4.5 4.9 - - - -
846A LEU* 3.8 15.9 - - + -
848A THR* 3.7 30.3 - - + -
852A LEU* 3.7 24.7 - - + -
853A GLY 3.3 12.3 - - - +
854A GLY* 4.1 0.2 - - - -
863A GLU* 1.3 77.0 - - - +
865A MET* 1.3 62.8 + - - +
866A GLN* 2.9 22.3 + - - +
892A TYR* 4.0 7.6 - - + -
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Residues in contact with MET 865 (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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420A THR* 3.4 31.2 - - + +
715A TYR* 3.6 22.4 - - + -
729A PHE* 3.7 13.7 - - + -
789A GLU* 3.5 34.8 - - + +
790A ILE 3.3 26.0 - - - +
791A VAL* 3.7 10.6 - - - +
828A TYR* 3.6 21.9 + - + +
852A LEU* 3.4 32.4 - - - +
853A GLY 2.8 13.4 + - - +
864A ILE* 1.3 72.5 - - - +
866A GLN* 1.3 60.7 + - - +
867A ASP 4.1 7.0 - - - +
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Residues in contact with GLN 866 (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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420A THR* 4.1 2.0 - - - -
423A PRO* 3.6 8.3 - - - +
712A PHE* 4.5 4.3 - - + -
778A ASN* 3.0 26.7 + - - +
780A VAL* 4.0 20.6 - - + +
790A ILE* 2.8 29.3 + - + +
792A MET* 3.8 16.5 - - + +
864A ILE* 2.9 33.9 + - - +
865A MET* 1.3 78.7 + - - +
867A ASP* 1.3 63.6 + - - +
890A HIS* 2.9 35.6 + - - -
892A TYR* 2.8 29.0 + - - -
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Residues in contact with ASP 867 (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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420A THR* 4.1 9.2 - - - +
422A ARG 4.8 0.5 + - - -
423A PRO* 3.1 30.4 - - + +
780A VAL* 4.0 18.5 - - + +
782A ILE* 3.8 18.8 + - + +
789A GLU* 3.4 3.1 - - - +
790A ILE* 3.0 27.9 + - + +
865A MET* 3.9 2.1 - - - +
866A GLN* 1.3 80.1 - - - +
868A ARG* 1.3 80.3 + - - +
885A ASN* 3.1 34.4 + - - +
886A LYS 4.5 8.7 - - - +
888A VAL* 4.9 2.2 - - + +
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Residues in contact with ARG 868 (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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417A GLY* 3.3 33.9 + - - -
420A THR* 3.8 20.0 - - + -
421A SER* 2.9 32.7 + - - +
422A ARG 5.7 0.2 + - - -
724A SER* 4.1 0.8 - - - -
725A GLY 2.7 22.0 + - - -
726A ALA* 3.5 0.6 + - - +
728A LEU 3.0 25.1 + - - -
729A PHE* 3.9 2.8 - - - +
782A ILE* 4.1 0.9 - - - -
788A THR 3.4 6.1 - - - -
789A GLU* 2.8 52.4 + - + +
865A MET* 5.2 0.2 - - + -
867A ASP* 1.3 85.5 + - - +
869A ARG* 1.3 60.7 + - - +
870A LEU* 3.5 16.8 - - + +
882A VAL* 3.7 12.3 - - + +
885A ASN* 2.9 16.2 + - - -
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Residues in contact with ARG 869 (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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782A ILE* 3.9 13.4 - - + +
783A GLY 3.5 27.9 + - - -
784A SER* 3.8 10.5 - - - +
785A LEU 3.6 25.1 - - - +
786A ASP* 2.9 23.3 + - - +
787A ASN* 2.8 26.7 + - - -
788A THR 2.9 16.7 + - - -
868A ARG* 1.3 74.1 - - - +
870A LEU* 1.3 57.5 + - - +
882A VAL 3.4 8.1 - - - +
883A LEU* 3.0 44.3 + - + +
885A ASN* 3.0 32.9 + - - +
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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