Contacts of the strand formed by residues 811 - 817 (chain A) in PDB entry 3ZW3
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 LEU 811 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A LEU 4.3 2.0 - - - +
745A VAL* 3.8 18.6 - - + -
746A THR* 3.3 45.8 - - + +
749A ILE* 3.8 30.7 - - + -
767A LEU* 4.4 12.8 - - + -
771A LEU* 5.7 0.2 - - + -
802A LYS 3.7 4.0 - - - -
803A VAL* 4.7 3.8 - - + +
804A MET* 4.8 0.7 - - - -
809A LYS 4.2 2.9 - - - +
810A PRO* 1.3 75.0 - - - +
812A TRP* 1.3 60.5 + - - +
813A LEU* 3.8 25.6 - - + -
830A ILE 3.8 0.7 - - - +
831A ILE* 3.2 8.9 - - - +
832A PHE* 2.9 40.3 + - + +
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Residues in contact with TRP 812 (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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800A LYS 3.5 16.9 + - - -
801A CYS* 3.3 4.7 - - - +
802A LYS* 2.7 72.4 + - + +
804A MET* 4.0 34.1 - - + -
810A PRO 3.8 1.0 + - - -
811A LEU* 1.3 68.9 - - - +
813A LEU* 1.3 61.4 + - - +
814A GLU* 3.0 32.0 + - + +
830A ILE 4.1 2.5 - - - -
831A ILE* 4.3 4.0 - - + -
881A ILE* 3.6 31.9 - - + -
2191A ZW3 3.3 47.8 - + + -
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Residues in contact with LEU 813 (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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742A LEU* 3.9 30.5 - - + -
767A LEU* 5.0 2.9 - - + -
771A LEU* 4.0 20.6 - - + -
796A LEU* 4.1 5.2 - - + -
801A CYS* 3.9 16.8 - - + -
811A LEU* 4.3 26.9 - - + -
812A TRP* 1.3 81.7 - - - +
814A GLU* 1.3 64.1 + - - +
815A PHE* 3.8 16.6 - - + -
829A GLY* 3.4 3.8 - - - -
830A ILE 2.9 39.3 + - - +
832A PHE* 3.8 26.7 - - + -
881A ILE* 4.0 1.6 - - - +
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Residues in contact with GLU 814 (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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796A LEU* 3.6 8.1 - - - +
797A ALA* 2.8 33.2 + - + +
800A LYS* 3.3 43.6 + - + +
801A CYS* 3.7 5.9 - - - -
812A TRP* 3.0 34.6 + - + +
813A LEU* 1.3 80.7 - - - +
815A PHE* 1.3 57.2 + - - +
827A THR* 2.5 33.4 + - - +
828A ILE 3.4 3.4 - - - -
829A GLY* 4.5 7.0 - - - -
883A LYS* 4.3 7.4 + - - -
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Residues in contact with PHE 815 (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* 5.3 0.2 - - + -
742A LEU* 3.8 26.5 - - + -
779A LEU* 4.9 7.2 - - + -
783A PHE* 3.7 23.1 - + - -
793A ALA* 3.9 13.7 - - + -
794A GLY 3.4 19.7 - - - +
795A ALA 3.4 6.1 - - - +
796A LEU* 3.7 32.3 - - + -
797A ALA 4.3 0.9 - - - +
813A LEU* 3.8 21.8 - - + -
814A GLU* 1.3 75.2 - - - +
816A LYS* 1.3 68.8 + - - +
827A THR* 3.3 9.1 - - - -
828A ILE* 2.7 47.4 + - + +
830A ILE* 3.9 27.1 - - + -
832A PHE* 5.5 0.2 - + - -
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Residues in contact with LYS 816 (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 GLN* 5.6 0.2 - - - +
793A ALA* 3.6 3.5 - - - -
794A GLY* 2.6 32.7 + - - -
795A ALA* 2.9 33.8 + - + +
796A LEU 3.9 17.8 + - - -
797A ALA* 4.4 14.6 - - + +
799A GLU* 4.8 6.7 + - - -
815A PHE* 1.3 73.9 - - - +
817A CYS* 1.3 60.8 + - - +
826A GLU 5.5 0.4 - - - -
827A THR* 4.9 8.1 - - + +
828A ILE* 4.5 0.4 - - - -
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Residues in contact with CYS 817 (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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276A GLY 4.2 11.7 - - - -
791A LEU* 4.9 7.6 - - - -
792A LYS 3.6 14.6 - - - -
815A PHE 3.8 2.0 + - - -
816A LYS* 1.3 76.5 - - - +
818A ALA* 1.3 64.8 + - - +
819A ASP* 3.4 31.1 + - - +
822A ALA* 4.4 14.4 - - + -
824A SER 5.9 1.6 - - - +
826A GLU 4.7 12.7 + - - +
828A ILE* 3.8 17.9 - - + +
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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