Contacts of the helix formed by residues 725 - 734 (chain A) in PDB entry 1SC7
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 ASP 725 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A TYR* 3.6 20.5 - - + +
595A SER* 3.2 12.0 + - - +
598A LEU* 4.6 0.3 - - - +
724A LEU* 1.3 72.7 - - - +
726A PRO* 1.3 74.5 - - - +
727A ARG* 3.1 40.7 + - - +
728A ILE* 3.3 35.3 + - + +
729A THR* 4.0 5.0 + - - -
754A TRP* 4.0 2.3 - - - -
763A TYR* 3.0 23.8 + - - -
765A PHE* 3.4 14.2 - - + -
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Residues in contact with PRO 726 (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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444A TYR* 3.8 14.6 - - + -
724A LEU 3.4 9.8 - - - +
725A ASP* 1.3 86.7 - - - +
727A ARG* 1.3 59.7 + - - +
728A ILE 3.3 0.4 - - - -
729A THR* 3.3 5.1 + - - +
730A VAL* 3.0 30.1 + - - +
744A TYR* 3.4 19.4 + - + +
752A PHE* 3.6 39.3 - - + -
754A TRP* 3.7 17.3 - - + -
755A ALA* 3.6 18.6 - - + -
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Residues in contact with ARG 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TRP* 3.6 17.2 - - - +
444A TYR* 3.9 17.4 - - - +
445A GLU* 3.0 30.5 + - - -
448A ARG* 3.7 14.6 - - - +
725A ASP* 3.1 27.4 + - - +
726A PRO* 1.3 74.3 - - - +
728A ILE* 1.3 56.6 + - - +
730A VAL* 3.2 5.1 + - - +
731A ALA* 2.8 36.9 + - - +
754A TRP* 3.7 18.1 - - + -
755A ALA* 4.0 22.7 - - + -
758A MET* 5.4 7.1 - - - +
759A ALA* 3.9 22.8 - - + +
763A TYR* 3.1 33.8 + - + +
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Residues in contact with ILE 728 (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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595A SER* 3.4 42.8 - - - +
598A LEU* 4.0 11.4 - - + -
599A GLN* 4.0 30.7 - - + +
602A LEU* 4.0 14.7 - - + +
725A ASP* 3.3 23.1 + - + +
727A ARG* 1.3 75.6 - - - +
729A THR* 1.3 60.8 + - - +
731A ALA* 3.6 5.2 + - - +
732A TRP* 3.3 21.0 + - - +
763A TYR* 4.3 17.3 - - + -
765A PHE* 4.0 17.9 - - + -
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Residues in contact with THR 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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598A LEU* 4.0 12.1 - - - +
602A LEU* 5.0 1.1 - - - -
619A TYR* 3.2 43.8 + - + +
724A LEU* 5.8 0.7 - - - +
725A ASP 4.2 3.1 + - - -
726A PRO 3.3 2.3 + - - -
727A ARG 3.2 0.4 - - - -
728A ILE* 1.3 75.4 - - - +
730A VAL* 1.3 59.4 + - - +
731A ALA 3.1 1.6 - - - -
732A TRP* 3.0 7.2 + - + +
733A CYS* 2.8 41.4 + - - -
743A ILE* 3.9 16.4 - - + -
744A TYR* 3.3 29.5 + - + +
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Residues in contact with VAL 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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726A PRO 3.0 16.6 + - - +
727A ARG* 3.8 4.7 - - - +
729A THR* 1.3 74.4 - - - +
731A ALA* 1.3 57.4 - - - +
733A CYS* 3.9 7.2 - - + +
734A LYS* 3.1 50.5 + - + +
740A ILE* 4.7 9.6 - - + -
744A TYR* 4.6 11.0 - - + -
755A ALA* 3.6 34.8 - - + +
756A ILE* 3.9 26.2 - - + +
759A ALA 4.0 8.5 - - - +
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Residues in contact with ALA 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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727A ARG 2.8 17.8 + - - +
728A ILE* 3.7 7.2 - - - +
729A THR 3.1 0.2 - - - -
730A VAL* 1.3 75.0 - - - +
732A TRP* 1.3 58.1 + - - +
734A LYS 4.3 1.3 - - - -
735A LYS* 3.3 21.8 - - - +
759A ALA 5.0 1.1 + - - +
760A ASP 3.4 25.1 - - - +
761A GLU* 3.6 16.2 - - - +
763A TYR* 3.8 25.1 - - + +
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Residues in contact with TRP 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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602A LEU* 3.7 40.0 - - + +
606A THR* 3.1 31.2 + - + -
615A LYS* 3.3 46.0 - - + -
616A ILE* 4.5 1.1 - - - -
619A TYR* 3.9 26.7 - + + -
728A ILE 3.3 12.3 + - - +
729A THR* 3.0 8.2 + - - +
731A ALA* 1.3 78.3 - - - +
733A CYS* 1.3 74.2 + - - +
734A LYS 3.4 0.4 - - - -
735A LYS* 3.7 7.9 - - + +
736A TRP* 3.1 49.8 + + - +
738A VAL* 4.0 26.0 - - + -
743A ILE* 4.5 4.9 - - + -
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Residues in contact with CYS 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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729A THR* 2.8 28.3 + - - +
730A VAL* 3.9 7.2 - - + +
732A TRP* 1.3 95.0 - - - +
734A LYS* 1.3 57.1 - - + +
737A GLY* 3.2 8.5 + - - -
738A VAL 3.1 46.9 + - - +
740A ILE* 4.4 25.1 - - + -
743A ILE* 4.1 22.7 - - - -
744A TYR* 6.3 0.4 - - - -
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Residues in contact with LYS 734 (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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730A VAL* 3.1 31.9 + - + +
733A CYS* 1.3 76.8 - - + +
735A LYS* 1.3 62.0 + - - +
737A GLY* 4.2 4.6 + - - +
740A ILE* 5.9 8.8 - - + +
756A ILE* 3.9 24.5 + - - +
757A ASP 5.7 1.1 - - - -
758A MET 5.6 0.2 - - - -
759A ALA 4.9 3.1 - - - -
760A ASP* 4.3 20.2 - - + +
761A GLU* 3.9 31.7 - - + +
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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