Contacts of the strand formed by residues 812 - 817 (chain A) in PDB entry 1HXK
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 GLN 812 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A PRO* 4.0 10.7 - - - +
211A THR* 3.8 16.6 + - - +
249A GLN* 3.0 27.4 + - - +
250A ILE* 3.6 22.1 + - + +
251A TRP* 3.5 18.3 - - + -
807A ASP* 3.0 4.4 - - - +
808A LEU* 2.8 53.3 + - + +
811A LEU* 1.3 86.9 - - + +
813A PHE* 1.3 70.9 + - - +
1034A MET* 3.8 18.6 - - + -
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Residues in contact with PHE 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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250A ILE* 3.9 3.7 - - - +
805A TYR* 4.8 1.8 - - + -
806A THR* 3.5 17.0 - - - +
807A ASP* 3.7 14.8 - - + -
810A GLY 6.2 1.6 - - - -
811A LEU 5.7 1.3 - - - -
812A GLN* 1.3 79.8 - - - +
814A ILE* 1.3 59.0 + - - +
833A SER* 4.7 4.5 - - - -
834A GLY* 3.5 36.6 - - - -
835A MET 4.0 2.2 - - - -
836A PHE* 3.7 25.6 - + + -
847A LEU* 4.8 2.7 - - + -
911A ALA* 3.6 8.7 - - - +
912A GLY* 3.1 46.5 + - - +
913A TYR* 5.4 1.2 - - - -
914A LEU* 3.5 47.8 - - + -
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Residues in contact with ILE 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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44A GLN* 6.0 0.4 - - - +
46A LEU* 6.5 0.9 - - + -
210A PRO* 5.5 0.2 - - + -
250A ILE* 3.9 22.2 - - + -
402A GLY* 4.5 2.7 - - - -
403A ASP* 3.9 35.2 - - - +
805A TYR* 3.5 5.6 - - - -
806A THR 2.9 35.5 + - - +
808A LEU* 3.9 24.7 - - + -
812A GLN 4.0 0.4 + - - -
813A PHE* 1.3 75.8 - - - +
815A LYS* 1.3 73.1 + - - +
816A ARG* 3.4 33.6 + - - +
910A PRO* 3.8 11.4 - - + +
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Residues in contact with LYS 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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46A LEU* 3.6 37.9 - - + +
803A ILE* 3.6 40.2 - - + +
805A TYR* 3.6 35.2 + - + +
814A ILE* 1.3 79.6 - - - +
816A ARG* 1.3 68.9 + - - +
817A ARG* 4.4 9.3 - - - +
906A SER 5.4 0.2 + - - -
907A LYS* 2.9 33.1 + - - +
908A LEU 5.5 0.2 - - - -
909A HIS 3.8 15.8 + - - +
910A PRO 2.9 22.2 + - - +
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Residues in contact with ARG 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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46A LEU* 4.3 2.7 - - - -
403A ASP* 2.8 40.6 + - - -
405A PHE 4.4 0.4 + - - -
803A ILE* 3.4 10.2 - - - +
804A PHE* 2.7 71.9 + - + +
806A THR* 2.8 30.8 + - + +
807A ASP 5.1 0.6 + - - -
808A LEU* 3.9 11.3 - - - +
814A ILE* 3.4 25.0 - - - +
815A LYS* 1.3 81.9 + - - +
817A ARG* 1.3 61.6 + - - +
818A ARG 4.2 0.4 - - - -
829A TYR* 3.3 44.6 - - + +
830A PRO* 4.4 7.7 - - - +
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Residues in contact with ARG 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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46A LEU* 3.5 50.2 + - + +
47A GLU* 5.4 0.8 - - - +
50A ASP* 3.8 39.3 + - - +
802A ASP* 3.2 26.1 + - - +
803A ILE* 3.9 19.1 - - + +
804A PHE* 4.4 2.2 - - - -
815A LYS* 4.4 12.5 - - - +
816A ARG* 1.3 75.5 - - - +
818A ARG* 1.3 76.4 + - - +
819A LEU* 3.3 25.2 + - + +
827A ASN* 4.2 2.4 - - - +
829A TYR* 4.5 9.7 + - - -
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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