Contacts of the helix formed by residues 723 - 731 (chain A) in PDB entry 1RS0
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 VAL 723 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A HIS* 4.0 13.9 - - + +
550A TYR* 3.9 26.2 - - + -
552A VAL* 4.3 7.0 - - + -
654A ARG* 4.5 3.8 - - + -
718A ILE* 4.2 20.4 - - + -
719A ASN 4.2 0.4 - - - +
720A LEU* 3.1 35.4 + - + +
722A GLN* 1.3 82.6 - - - +
724A LEU* 1.3 65.6 + - - +
725A PRO* 3.3 3.8 - - - -
726A TRP* 3.0 20.8 + - + +
727A LEU* 3.1 20.8 + - + +
740A IOD 3.9 6.5 - - - -
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Residues in contact with LEU 724 (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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573A PRO* 3.6 24.5 - - + +
574A CYS* 3.5 13.0 - - + -
590A CYS* 3.5 32.3 - - - -
720A LEU 3.3 14.2 + - - +
721A PHE* 3.9 21.3 - - + +
722A GLN 3.7 0.2 - - - -
723A VAL* 1.3 76.7 - - - +
725A PRO* 1.3 64.5 - - + +
727A LEU* 3.8 12.7 - - + +
728A LYS* 2.8 36.7 + - + +
738A PHE* 4.1 21.5 - - + -
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Residues in contact with PRO 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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721A PHE 5.1 1.1 - - - +
722A GLN 4.8 2.7 - - - +
723A VAL* 3.3 6.1 - - - +
724A LEU* 1.3 93.4 - - + +
726A TRP* 1.3 59.1 - - - +
728A LYS* 3.9 8.4 - - + +
729A GLU* 3.2 22.3 + - - +
740A IOD 3.9 18.8 - - + -
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Residues in contact with TRP 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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497A LEU* 4.1 3.4 - - + -
529A LEU* 3.4 21.9 - - + +
530A PHE 4.0 3.2 + - - -
531A HIS* 3.5 40.9 - - + +
532A PRO* 3.6 27.5 - - + +
552A VAL* 3.4 23.1 - - + -
553A ALA* 3.7 25.4 - - - -
554A LEU* 3.7 20.9 - - + -
723A VAL* 3.0 14.4 + - + +
725A PRO* 1.3 77.7 - - - +
727A LEU* 1.3 98.3 + - + +
729A GLU* 3.1 5.1 + - - +
730A LYS* 2.9 53.0 + - + +
740A IOD 4.0 2.6 - - + +
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Residues in contact with LEU 727 (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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491A VAL* 6.4 0.2 - - + -
497A LEU* 4.2 17.0 - - + -
554A LEU* 4.1 13.0 - - + -
572A LEU* 4.8 8.7 - - + -
573A PRO* 5.3 2.2 - - + -
720A LEU* 4.2 38.6 - - + +
723A VAL* 3.1 16.6 + - + +
724A LEU* 3.8 15.5 - - + +
726A TRP* 1.3 104.5 - - + +
728A LYS* 1.3 58.6 + - - +
730A LYS* 4.9 2.0 - - - -
731A LEU* 2.8 47.4 + - + +
738A PHE* 4.1 15.5 - - + -
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Residues in contact with LYS 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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724A LEU* 2.8 23.2 + - + +
725A PRO* 3.9 8.3 - - + +
727A LEU* 1.3 73.6 - - - +
729A GLU* 1.3 56.5 + - - +
731A LEU 3.9 0.2 - - - -
732A GLN* 3.0 31.8 + - + +
738A PHE* 3.9 39.3 - - + -
739A LEU* 3.3 32.3 + - - +
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Residues in contact with GLU 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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725A PRO 3.2 17.3 + - - +
726A TRP* 3.1 7.9 + - + +
728A LYS* 1.3 78.0 - - - +
730A LYS* 1.3 82.6 + - - +
732A GLN* 2.6 58.5 + - - +
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Residues in contact with LYS 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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495A PHE* 4.0 20.5 - - + -
529A LEU* 4.0 26.6 - - + +
532A PRO* 5.7 2.7 - - - -
554A LEU* 3.7 21.1 - - + -
726A TRP* 2.9 54.8 + - + +
727A LEU 4.2 0.2 - - - +
729A GLU* 1.3 94.6 + - + +
731A LEU* 1.3 60.6 + - - +
732A GLN* 3.5 1.2 - - - +
733A ASP 5.2 0.2 + - - -
734A GLU* 4.9 0.5 - - - +
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Residues in contact with LEU 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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491A VAL* 4.4 7.2 - - + -
492A SER* 4.1 3.4 - - - +
495A PHE* 3.7 42.0 - - + -
554A LEU* 4.2 10.3 - - + -
572A LEU* 3.8 20.2 - - + -
727A LEU* 2.8 33.6 + - + +
728A LYS 3.9 1.1 - - - -
730A LYS* 1.3 78.8 - - - +
732A GLN* 1.3 52.8 + - - +
733A ASP 2.7 18.8 + - - -
734A GLU* 2.8 29.0 + - + +
735A ASP 4.4 0.3 + - - -
736A LEU* 4.0 8.2 + - + +
738A PHE* 3.7 31.4 - - + -
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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