Contacts of the helix formed by residues 792 - 806 (chain A) in PDB entry 1WER
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 792 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A ARG* 3.6 9.2 - - - +
777A GLU* 3.7 32.5 - - - +
788A PHE* 5.1 3.1 - - - -
790A ALA* 3.4 17.4 + - + +
791A THR* 1.3 78.4 - - - +
793A LEU* 1.3 65.5 + - - +
794A ALA* 3.5 9.1 + - - +
795A SER* 2.9 25.9 + - - -
796A THR* 2.9 26.3 + - - -
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Residues in contact with LEU 793 (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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738A VAL* 4.2 6.7 - - + -
742A SER* 3.5 32.8 - - - -
749A ARG* 3.9 21.2 - - + +
752A LEU* 4.2 9.4 - - + -
753A ALA* 4.0 33.0 - - + +
756A LEU* 4.1 18.6 - - + -
773A LEU* 4.1 19.5 - - + -
792A THR* 1.3 73.2 - - - +
794A ALA* 1.3 57.3 + - - +
797A LEU* 2.8 42.6 + - + +
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Residues in contact with ALA 794 (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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770A LEU* 5.2 0.3 - - - +
773A LEU* 4.0 25.4 - - + +
774A ASN* 3.9 17.3 - - - +
777A GLU* 3.6 32.5 + - + +
788A PHE* 4.5 3.6 - - + -
792A THR* 3.2 3.7 + - - +
793A LEU* 1.3 79.5 - - - +
795A SER* 1.3 57.7 + - - +
797A LEU* 3.6 3.5 - - - +
798A MET* 3.0 33.6 + - - +
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Residues in contact with SER 795 (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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788A PHE* 4.9 7.4 - - - -
790A ALA 3.6 5.3 + - - -
791A THR* 3.8 4.3 - - - +
792A THR* 2.9 36.6 + - - -
794A ALA* 1.3 77.2 - - - +
796A THR* 1.3 57.3 + - - +
798A MET* 3.3 7.4 + - - +
799A GLU* 3.0 36.0 + - - +
899A PHE* 4.5 8.3 - - - -
903A ARG* 3.8 33.3 + - - -
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Residues in contact with THR 796 (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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749A ARG* 3.0 28.0 - - + +
750A THR* 4.6 7.2 - - + +
753A ALA* 3.6 23.1 - - + -
791A THR* 4.1 8.3 - - - +
792A THR 2.9 20.8 + - - -
793A LEU 3.6 3.4 - - - -
795A SER* 1.3 75.0 + - - +
797A LEU* 1.3 64.9 + - - +
799A GLU* 3.3 14.7 + - - +
800A GLN* 3.0 34.7 + - + +
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Residues in contact with LEU 797 (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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753A ALA* 3.5 31.0 - - + +
756A LEU* 4.7 3.6 - - + -
757A LEU* 4.0 25.5 - - + +
769A LEU* 4.0 21.5 - - + -
770A LEU* 3.5 15.9 - - + +
773A LEU* 3.3 34.5 - - + -
793A LEU* 2.8 33.0 + - + +
794A ALA* 3.6 3.6 - - - +
796A THR* 1.3 77.3 - - - +
798A MET* 1.3 57.5 + - - +
800A GLN* 3.3 4.1 + - - +
801A TYR* 2.8 32.1 + - - +
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Residues in contact with MET 798 (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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770A LEU* 4.0 18.6 - - + -
774A ASN* 3.6 28.3 - - - +
794A ALA 3.0 17.4 + - - +
795A SER 3.3 4.7 + - - +
797A LEU* 1.3 75.6 - - - +
799A GLU* 1.3 57.3 + - - +
801A TYR* 3.3 2.7 + - - +
802A MET* 2.9 41.7 + - + +
870A LEU* 4.4 8.3 - - + -
873A ILE* 3.9 20.0 - - + -
874A TYR* 3.9 22.4 - - + -
877A LEU* 4.7 0.9 - - + -
899A PHE* 3.6 51.4 - - + -
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Residues in contact with GLU 799 (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 THR* 6.2 0.3 - - - +
795A SER* 3.0 20.1 + - - +
796A THR* 3.7 15.6 + - + +
797A LEU 3.3 0.2 - - - -
798A MET* 1.3 76.6 - - - +
800A GLN* 1.3 57.2 + - + +
802A MET* 3.4 8.7 + - + +
803A LYS* 2.9 30.6 + - - +
903A ARG* 2.7 64.8 + - + +
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Residues in contact with GLN 800 (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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750A THR* 3.3 32.7 + - - +
753A ALA* 3.4 19.8 - - - +
754A SER* 3.3 28.3 + - - -
757A LEU* 3.9 11.9 - - + +
796A THR* 3.0 25.8 + - + +
797A LEU* 3.7 4.0 - - - +
799A GLU* 1.3 77.0 - - + +
801A TYR* 1.3 58.2 + - - +
803A LYS* 3.0 40.1 + - + +
804A ALA* 3.0 25.5 + - - +
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Residues in contact with TYR 801 (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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757A LEU* 3.8 22.6 - - + +
761A LEU* 4.4 11.9 - - + -
766A GLU* 3.8 21.2 + - + -
770A LEU* 3.5 25.6 - - + -
797A LEU 2.8 17.9 + - - +
798A MET* 3.7 5.2 - - - +
800A GLN* 1.3 78.3 - - - +
802A MET* 1.3 62.3 + - - +
804A ALA* 3.2 5.5 + - + +
805A THR* 2.9 57.3 + - + +
867A PRO* 5.8 1.2 - - - +
869A THR* 3.4 30.3 - - - +
870A LEU* 4.0 26.7 + - + +
873A ILE* 3.8 19.7 - - + -
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Residues in contact with MET 802 (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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798A MET* 2.9 32.9 + - + +
799A GLU* 3.9 6.5 - - - +
801A TYR* 1.3 72.8 - - + +
803A LYS* 1.3 61.2 - - - +
805A THR* 4.0 5.6 - - - -
806A ALA* 2.8 38.7 + - + +
870A LEU* 4.0 22.2 - - + -
874A TYR* 3.2 26.7 - - - -
899A PHE* 3.6 43.1 - - + +
903A ARG* 3.9 17.5 - - + +
904A LEU* 4.2 24.7 - - + -
915A PHE* 4.5 1.6 - - - -
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Residues in contact with LYS 803 (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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757A LEU* 4.8 4.0 - - - +
799A GLU 2.9 14.7 + - - +
800A GLN* 3.0 54.1 + - + +
802A MET* 1.3 77.8 - - - +
804A ALA* 1.3 72.5 + - - +
805A THR 3.3 0.2 + - - -
806A ALA 4.2 0.2 + - - -
807A THR* 3.5 19.6 + - - -
904A LEU* 5.1 0.6 - - - +
914A MET* 5.9 9.9 - - + -
915A PHE* 3.9 22.6 - - + -
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Residues in contact with ALA 804 (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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757A LEU* 5.2 4.9 - - + -
761A LEU* 5.4 7.6 - - + -
800A GLN 3.0 16.9 + - - +
801A TYR* 3.2 9.2 + - + +
803A LYS* 1.3 89.7 - - - +
805A THR* 1.3 65.9 + - + +
807A THR* 5.1 2.7 + - - -
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Residues in contact with THR 805 (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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761A LEU* 5.5 6.5 - - + -
801A TYR* 2.9 56.6 + - + +
802A MET* 4.0 2.6 - - - -
804A ALA* 1.3 87.1 - - + +
806A ALA* 1.3 60.5 + - - +
807A THR* 3.4 6.0 + - - -
808A GLN* 4.9 8.7 + - - +
867A PRO* 3.3 28.9 - - - +
870A LEU* 4.7 4.2 - - - +
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Residues in contact with ALA 806 (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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802A MET* 2.8 27.0 + - - +
805A THR* 1.3 71.7 + - - +
807A THR* 1.3 58.5 + - - +
808A GLN 3.3 2.5 - - - -
809A PHE* 3.2 5.1 + - - +
810A VAL* 2.9 32.2 + - + +
866A LEU* 4.4 8.7 - - + -
867A PRO* 4.5 6.3 - - + -
870A LEU* 4.2 22.2 - - + -
904A LEU* 4.3 19.3 - - + -
915A PHE* 4.7 0.4 - - - -
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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