Contacts of the strand formed by residues 802 - 812 (chain A) in PDB entry 5J9H
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 LYS 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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728A HIS* 4.5 17.9 + - - +
730A GLY* 3.9 7.2 - - - +
731A HIS* 3.6 35.7 - - + +
801A GLY* 1.3 73.5 - - - -
803A VAL* 1.3 61.4 + - - +
804A PHE* 4.2 30.7 - - + -
856A LEU 3.6 1.0 - - - +
857A LEU* 3.5 3.8 - - - -
858A PHE* 2.9 42.8 + - + +
862A LEU* 5.6 2.9 - - + -
943A ILE* 5.8 1.6 - - - +
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Residues in contact with VAL 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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729A LEU* 3.1 31.6 + - + -
730A GLY 3.0 20.3 + - - +
732A TRP* 4.0 9.6 - - + +
802A LYS* 1.3 81.0 - - - +
804A PHE* 1.3 69.2 + - - +
855A THR* 3.3 33.2 - - + -
856A LEU 3.4 3.8 - - - +
857A LEU* 3.7 20.0 - - + -
872A TRP* 3.8 23.6 - - + +
886A MET* 3.8 16.2 - - + -
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Residues in contact with PHE 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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726A ILE* 3.6 31.0 - - + -
727A GLN 3.3 9.6 - - - +
728A HIS* 3.7 28.7 - + - -
729A LEU* 4.7 0.2 - - - -
802A LYS* 4.2 28.3 - - + -
803A VAL* 1.3 84.2 - - - +
805A LYS* 1.3 59.2 + - - +
855A THR* 3.4 4.7 - - - +
856A LEU* 2.8 46.5 + - + +
858A PHE* 3.7 38.1 - + - -
862A LEU* 4.2 9.6 - - + -
943A ILE* 3.5 24.2 - - + -
948A LEU* 4.3 11.2 - - + -
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Residues in contact with LYS 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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726A ILE* 3.2 5.4 - - - -
727A GLN* 2.9 54.2 + - + +
729A LEU* 3.8 24.1 - - + +
804A PHE* 1.3 72.6 - - - +
806A ILE* 1.3 70.9 + - - +
807A VAL* 3.4 1.2 + - - +
853A SER* 3.3 34.1 + - - +
854A ASP 3.6 8.1 - - - +
855A THR* 3.8 14.3 + - - +
872A TRP* 5.4 5.5 + - + +
874A THR* 4.4 14.6 + - - +
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Residues in contact with ILE 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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724A ALA* 4.4 9.4 - - + -
725A GLU 3.7 4.5 - - - +
726A ILE* 4.6 3.1 - - + -
805A LYS* 1.3 71.1 - - - +
807A VAL* 1.3 62.2 + - - +
808A SER 3.5 24.0 - - - +
809A LEU* 3.8 20.0 - - + -
850A PHE* 4.1 22.2 - - + -
851A GLN 3.6 22.2 - - - +
852A PRO* 4.0 3.4 - - + -
853A SER* 2.8 28.2 + - - -
854A ASP* 2.9 29.4 + - + +
856A LEU* 4.1 28.7 - - + -
950A TRP* 5.6 1.1 - - + -
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Residues in contact with VAL 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A GLU* 2.7 21.0 + - + +
726A ILE 3.9 13.5 - - - +
727A GLN* 3.6 35.2 - - + +
805A LYS* 6.0 0.4 - - + -
806A ILE* 1.3 75.0 - - - +
808A SER* 1.3 59.1 + - - +
852A PRO* 4.2 10.2 - - - +
993A GLY* 4.3 9.0 - - - +
994A SER 3.3 30.3 - - - +
995A GLY* 3.8 11.0 - - - +
1044A LYS* 3.9 29.5 + - + +
1045A GLY* 4.1 2.9 - - - +
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Residues in contact with SER 808 (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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723A HIS* 4.4 0.6 - - - -
724A ALA* 3.3 6.4 - - - -
725A GLU* 3.3 41.8 + - - +
806A ILE* 3.5 9.6 - - - +
807A VAL* 1.3 82.9 - - - +
809A LEU* 1.3 66.0 + - - +
852A PRO* 4.9 7.4 - - - -
1023A MET* 5.7 1.6 - - - +
1044A LYS* 3.9 16.2 + - - -
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Residues in contact with LEU 809 (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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722A ILE* 4.0 22.9 - - + -
723A HIS 3.5 2.7 - - - +
724A ALA* 4.1 13.5 - - + -
806A ILE* 3.8 9.0 - - + -
808A SER* 1.3 83.9 - - - +
810A ARG* 1.3 62.0 + - - +
811A TYR* 3.5 34.1 - - + +
848A SER* 5.3 0.4 - - - -
850A PHE* 3.5 35.9 - - + +
851A GLN* 3.8 17.9 - - - +
852A PRO* 4.1 9.8 - - + +
950A TRP* 5.3 0.9 - - + -
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Residues in contact with ARG 810 (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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721A VAL 3.7 0.9 - - - +
722A ILE* 3.6 2.6 - - - +
723A HIS* 2.8 53.8 + - + +
809A LEU* 1.3 77.1 - - - +
811A TYR* 1.3 66.8 + - - +
812A THR* 3.6 19.7 - - + +
829A ASP* 3.0 45.6 + - - +
1023A MET* 3.8 28.0 - - + +
1024A CYS* 3.3 33.7 + - - +
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Residues in contact with TYR 811 (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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720A GLN* 3.6 31.9 - - - +
721A VAL 3.4 3.8 - - - -
722A ILE* 3.7 35.2 - - + -
809A LEU* 3.5 35.8 - - + +
810A ARG* 1.3 78.1 - - - +
812A THR* 1.3 60.9 + - - +
829A ASP* 3.4 7.4 + - - +
830A SER* 3.0 43.8 + - - +
848A SER* 2.3 39.3 + - - -
850A PHE* 4.3 5.6 - + - +
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Residues in contact with THR 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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719A LYS 3.9 0.9 - - - +
720A GLN* 3.3 4.5 - - - +
721A VAL* 2.9 45.0 + - - +
723A HIS* 6.3 0.4 - - + -
810A ARG* 3.6 31.4 - - + +
811A TYR* 1.3 79.0 - - - +
813A ARG* 1.3 64.7 + - - +
827A THR* 4.9 12.9 - - - +
828A VAL 3.4 12.6 - - - +
829A ASP* 4.2 13.5 - - - +
830A SER* 5.0 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