Contacts of the strand formed by residues 722 - 734 (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 CYS 722 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A PRO* 3.5 32.1 - - - -
684A THR* 3.8 5.8 - - - -
685A GLU* 3.6 15.0 - - + -
687A TYR* 3.5 33.0 - - + -
720A VAL 4.3 0.2 - - - +
721A ALA* 1.3 77.1 - - - +
723A THR* 1.3 66.7 + - - +
724A PHE* 3.7 16.2 - - + -
756A LEU 3.9 0.5 - - - +
757A GLU* 3.7 2.9 - - - +
758A VAL* 2.9 35.6 + - + +
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Residues in contact with THR 723 (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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682A GLU 3.7 0.3 - - - +
683A PRO* 3.4 1.7 - - - +
684A THR* 2.9 52.1 + - + +
722A CYS* 1.3 73.1 - - - +
724A PHE* 1.3 64.5 + - - +
725A SER* 4.1 0.8 + - - +
755A ASP* 3.8 28.3 - - + +
756A LEU 3.6 3.6 - - - +
757A GLU* 2.4 38.2 + - - +
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Residues in contact with PHE 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A PHE* 3.9 11.2 - + - -
681A MET* 3.5 40.4 - - + -
682A GLU 3.4 4.7 - - - +
683A PRO* 3.6 31.9 - - + -
687A TYR* 3.8 25.8 - + + -
689A VAL* 5.4 1.3 - - + -
710A VAL* 4.5 11.7 - - + -
722A CYS* 3.7 22.2 - - + -
723A THR* 1.3 77.6 - - - +
725A SER* 1.3 62.3 + - - +
726A CYS* 3.7 6.1 + - - -
755A ASP* 3.3 5.8 - - - -
756A LEU* 2.8 41.2 + - + +
758A VAL* 3.7 27.1 - - + -
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Residues in contact with SER 725 (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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680A GLN 3.5 1.0 - - - +
681A MET* 3.3 5.7 - - - -
682A GLU* 2.9 52.7 + - - +
684A THR* 6.0 1.6 - - - +
723A THR* 4.1 2.1 + - - +
724A PHE* 1.3 71.8 - - - +
726A CYS* 1.3 58.3 + - - +
755A ASP* 3.7 15.9 + - - -
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Residues in contact with CYS 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A LEU* 4.7 7.2 - - + -
663A PHE* 5.0 1.1 - - - -
679A VAL* 4.0 13.7 - - + -
680A GLN 3.2 4.7 - - - -
681A MET* 4.2 23.1 - - - -
724A PHE 3.7 15.2 + - - -
725A SER* 1.3 76.8 - - - +
727A MET* 1.3 61.5 + - - +
752A VAL* 4.1 4.5 - - - +
753A LEU* 3.1 34.6 + - + +
754A GLU 3.7 18.6 + - - +
755A ASP* 4.6 1.8 + - - -
756A LEU* 4.0 20.9 - - - -
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Residues in contact with MET 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A VAL* 4.3 3.5 - - - +
680A GLN* 2.9 54.6 + - - +
726A CYS* 1.3 75.8 - - - +
728A MET* 1.3 73.8 + - - +
729A LYS* 3.5 7.5 + - + -
750A GLU* 3.4 44.6 - - + +
751A TYR 3.5 9.6 - - - -
752A VAL* 3.6 30.5 - - + -
753A LEU 4.5 0.4 - - - +
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Residues in contact with MET 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A TYR* 3.7 40.6 - - + -
648A ILE* 3.7 26.5 - - + -
665A CYS* 5.6 0.2 - - + -
674A LEU* 4.2 9.2 - - + -
677A VAL* 4.3 12.3 - - + -
678A THR 3.3 7.6 - - - +
679A VAL* 4.4 8.5 - - + +
698A LEU* 5.2 3.4 - - + -
727A MET* 1.3 72.5 - - - +
729A LYS* 1.3 58.1 + - - +
730A PHE* 3.8 25.1 - - + -
750A GLU* 3.1 9.2 - - - +
751A TYR* 2.8 35.4 + - - +
753A LEU* 4.0 28.0 - - + +
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Residues in contact with LYS 729 (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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676A ASN 3.4 2.8 - - - +
677A VAL* 3.2 2.3 - - - +
678A THR* 2.8 44.8 + - - +
680A GLN* 3.6 31.9 + - + +
727A MET* 4.1 15.3 - - + +
728A MET* 1.3 77.7 - - - +
730A PHE* 1.3 64.8 + - - +
749A ASP 3.7 6.5 - - - +
750A GLU* 3.9 21.3 + - + -
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Residues in contact with PHE 730 (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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646A TYR* 4.0 14.4 - + - -
672A GLN* 5.5 0.2 - - - -
674A LEU* 3.7 24.0 - - + -
675A GLU 3.7 11.2 - - - +
676A ASN* 3.7 4.7 - - - -
677A VAL* 3.8 15.0 - - + -
728A MET* 3.8 40.2 - - + -
729A LYS* 1.3 79.9 - - - +
731A THR* 1.3 62.6 + - - +
732A VAL* 3.5 25.1 - - + -
748A GLU* 3.5 6.3 - - - +
749A ASP* 2.9 42.2 + - + +
750A GLU* 3.9 28.5 - - - -
751A TYR* 3.9 8.3 - + + -
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Residues in contact with THR 731 (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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673A THR 3.8 0.3 - - - +
674A LEU* 3.2 8.3 - - - +
675A GLU* 2.8 47.9 + - + +
676A ASN* 4.5 10.2 + - - +
730A PHE* 1.3 74.1 + - - +
732A VAL* 1.3 65.4 + - - +
733A LYS* 4.0 20.8 + - + +
746A GLY* 4.1 2.2 - - - -
747A TYR 3.4 22.7 - - - +
748A GLU* 4.3 13.1 + - + +
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Residues in contact with VAL 732 (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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672A GLN* 3.8 23.1 - - + +
673A THR 3.9 2.7 - - - -
674A LEU* 4.0 5.2 - - + -
730A PHE* 3.5 30.3 - - + -
731A THR* 1.3 72.1 - - - +
733A LYS* 1.3 72.9 + - - +
734A ASP* 4.3 6.5 - - - +
745A GLU 4.7 0.2 - - - +
746A GLY* 3.1 5.5 - - - -
747A TYR* 2.8 67.2 + - + +
749A ASP* 3.9 16.6 - - + +
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Residues in contact with LYS 733 (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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672A GLN* 3.3 2.3 - - - -
673A THR* 2.9 44.9 + - - +
675A GLU* 3.2 39.2 + - + +
731A THR* 4.1 9.6 - - + +
732A VAL* 1.3 80.6 - - - +
734A ASP* 1.3 63.3 + - - +
735A CYS* 4.6 0.2 - - - +
742A THR* 3.9 18.6 - - + -
743A ASP 3.6 19.5 - - - +
744A ASP* 3.3 39.6 + - - +
745A GLU 5.4 0.4 - - - -
746A GLY* 3.7 15.3 - - - +
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Residues in contact with ASP 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ASP 3.7 10.7 - - - +
672A GLN* 4.5 1.1 - - - +
732A VAL* 4.2 12.5 + - - +
733A LYS* 1.3 73.1 - - - +
735A CYS* 1.3 61.1 + - - +
742A THR* 3.6 0.7 - - - +
743A ASP* 2.9 46.4 + - + +
745A GLU 5.7 2.0 + - - +
747A TYR* 4.5 18.2 + - - -
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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