Contacts of the strand formed by residues 825 - 834 (chain A) in PDB entry 1R4X
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 825 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A LEU* 3.9 3.7 - - - +
819A VAL* 5.4 0.2 - - - +
820A PRO* 5.8 0.2 - - - +
823A LYS* 3.8 35.9 + - - +
824A ASN* 1.3 90.4 + - - +
826A HIS* 1.3 67.3 + - - +
846A LEU 3.4 9.9 - - - +
847A LEU* 3.9 18.2 - - + -
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Residues in contact with HIS 826 (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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797A LEU* 4.1 16.8 - - + -
801A VAL* 3.7 18.6 - - + +
816A SER* 2.7 32.2 + - - -
818A LYS 3.3 17.2 + - - -
819A VAL* 3.9 22.2 - - + +
820A PRO* 4.0 19.3 - - + -
825A THR* 1.3 79.3 - - - +
827A THR* 1.3 85.5 + - - +
828A LEU 4.0 1.6 + - - -
845A ARG* 3.7 0.2 - - - -
846A LEU* 2.8 39.2 + - + +
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Residues in contact with THR 827 (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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816A SER* 3.4 17.3 - - - -
826A HIS* 1.3 88.0 + - - +
828A LEU* 1.3 59.7 + - - +
829A LEU* 3.7 28.2 + - + +
843A ARG* 3.8 16.2 - - + -
844A SER 3.3 8.7 - - - +
845A ARG* 3.9 18.9 + - + +
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Residues in contact with LEU 828 (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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801A VAL* 4.0 13.9 - - + +
804A ILE* 3.8 41.3 - - + -
805A VAL* 4.0 24.9 - - + -
812A PRO* 4.2 2.2 - - + -
816A SER* 3.3 34.3 - - - +
817A ASP 4.2 0.9 - - - +
826A HIS* 4.0 3.2 + - - +
827A THR* 1.3 72.5 - - - +
829A LEU* 1.3 62.4 + - - +
830A LEU* 3.9 23.2 - - + +
842A VAL 3.8 0.9 - - - +
843A ARG* 3.4 4.7 - - - -
844A SER* 2.9 39.7 + - - +
846A LEU* 4.2 9.2 - - + +
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Residues in contact with LEU 829 (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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772A PHE* 3.7 52.0 - - + -
812A PRO* 3.3 4.2 - - - +
813A CYS* 2.8 38.4 + - + +
814A GLU* 4.6 15.3 - - + +
816A SER* 2.9 19.5 + - - +
827A THR* 3.7 27.1 - - + +
828A LEU* 1.3 75.2 - - - +
830A LEU* 1.3 60.8 + - - +
842A VAL 3.5 2.7 - - - -
843A ARG* 4.0 11.0 - - + -
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Residues in contact with LEU 830 (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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772A PHE* 3.4 6.9 - - - -
804A ILE* 4.0 18.8 - - + +
805A VAL* 4.2 15.5 - - + -
808A LEU* 3.8 29.8 - - + -
810A MET* 3.6 27.3 - - + +
811A HIS 3.3 5.6 - - - +
812A PRO* 3.8 28.7 - - + -
828A LEU* 3.9 13.9 - - + +
829A LEU* 1.3 75.8 - - - +
831A ALA* 1.3 60.4 + - - +
841A LEU* 3.4 3.6 - - - -
842A VAL* 2.8 50.4 + - + +
844A SER* 6.2 0.9 - - - -
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Residues in contact with ALA 831 (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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767A VAL* 3.4 29.0 + - + +
769A LYS* 3.7 26.0 - - + -
772A PHE* 4.7 0.9 - - + -
810A MET* 3.7 5.9 - - - +
811A HIS 2.9 29.1 + - - -
813A CYS* 3.8 9.6 - - - -
830A LEU* 1.3 76.2 - - - +
832A GLY* 1.3 58.4 + - - +
840A ILE 3.8 4.0 - - - -
841A LEU* 3.7 11.0 - - + -
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Residues in contact with GLY 832 (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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764A ILE* 4.0 12.8 - - - -
765A GLN 3.2 12.8 - - - -
766A LYS* 4.2 0.2 - - - -
767A VAL* 3.7 7.7 - - - +
810A MET* 3.6 1.2 - - - +
831A ALA* 1.3 76.3 - - - +
833A VAL* 1.3 61.3 + - - +
839A ASP* 3.3 8.1 - - - +
840A ILE* 2.8 38.6 + - - +
841A LEU* 4.9 0.3 - - - +
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Residues in contact with VAL 833 (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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630A PHE* 3.2 17.6 - - + -
764A ILE* 3.4 2.8 - - - +
765A GLN* 2.8 37.6 + - + +
767A VAL* 3.9 21.8 - - + -
832A GLY* 1.3 75.2 - - - -
834A PHE* 1.3 60.4 + - - +
837A GLY* 3.4 41.3 - - - +
838A HIS 3.7 4.7 - - - +
839A ASP* 3.5 19.3 - - - +
840A ILE* 4.2 2.0 - - - -
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Residues in contact with PHE 834 (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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630A PHE* 3.5 3.8 - - - -
763A HIS* 3.4 32.8 - - + -
764A ILE* 4.4 9.0 - - + +
833A VAL* 1.3 74.3 - - - +
835A ARG* 1.3 108.8 + - + +
837A GLY* 2.9 18.0 + - - -
838A HIS 2.9 16.9 + - - +
840A ILE* 4.0 9.6 - - + +
862A GLU* 3.6 24.5 - - - +
864A LEU* 3.8 10.8 - - + -
865A PRO* 3.7 37.0 - - + -
868A ILE* 3.6 35.7 - - + -
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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