Contacts of the helix formed by residues 724 - 735 (chain A) in PDB entry 4RH5
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 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A LYS* 4.1 33.2 - - + +
695A TYR 5.9 1.3 - - - +
696A ILE* 5.1 8.1 - - - +
718A GLN* 4.4 5.7 + - - -
720A PRO* 3.4 8.3 - - - +
721A LEU* 2.8 34.0 + - + -
723A HIS* 1.3 98.4 - - + +
725A CYS* 1.3 66.4 + - - +
726A ALA 3.2 2.5 - - - -
727A GLN* 3.2 16.8 + - - +
728A PHE* 3.0 21.7 + - - +
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Residues in contact with CYS 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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720A PRO* 4.2 5.6 - - - -
721A LEU 3.4 15.2 + - - -
722A PRO 3.8 8.5 + - - +
723A HIS 3.6 0.6 - - - -
724A THR* 1.3 78.2 - - - +
726A ALA* 1.3 62.9 + - - +
728A PHE* 3.3 7.5 + - - +
729A TRP* 3.0 31.7 + - - -
755A HIS* 3.5 28.3 - - - -
757A TYR* 3.6 21.5 - - + -
767A HIS* 3.4 30.5 - - + +
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Residues in contact with ALA 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A HIS 5.1 2.8 - - - +
724A THR 3.2 0.6 - - - -
725A CYS* 1.3 78.5 - - - +
727A GLN* 1.3 70.0 + - - +
729A TRP* 3.6 2.3 + - - +
730A GLN* 3.0 28.3 + - - +
767A HIS* 4.3 6.8 + - + +
768A GLY* 3.7 35.3 - - - +
770A PHE* 4.7 4.3 - - - -
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Residues in contact with GLN 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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673A LYS* 5.9 6.0 - - - +
689A LEU* 3.9 10.8 - - + +
694A ASP* 3.1 42.4 + - + +
695A TYR 3.9 14.2 - - - +
696A ILE* 3.8 19.3 - - + -
723A HIS 3.3 8.8 + - - +
724A THR* 3.2 29.6 + - - +
726A ALA* 1.3 84.2 + - - +
728A PHE* 1.3 65.0 + - - +
730A GLN* 3.2 8.0 + - - +
731A VAL* 3.0 26.9 + - - +
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Residues in contact with PHE 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A ILE* 3.7 15.5 - - + +
717A THR* 4.2 13.5 - - + -
718A GLN 4.9 0.4 - - - -
720A PRO* 3.4 27.6 - - + -
724A THR 3.0 13.6 + - - +
725A CYS* 3.3 7.8 + - - +
727A GLN* 1.3 74.5 - - - +
729A TRP* 1.3 77.4 + + - +
731A VAL* 3.2 7.5 + - - +
732A VAL* 3.2 27.5 + - + +
740A ILE* 4.0 16.2 - - + -
757A TYR* 3.4 42.0 - + - -
839A LEU* 3.8 37.6 - - + +
841A HIS* 4.1 9.4 - + - -
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Residues in contact with TRP 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 CYS* 3.0 27.5 + - + +
726A ALA 4.2 1.1 - - - +
728A PHE* 1.3 82.9 - + - +
730A GLN* 1.3 58.0 + - - +
732A VAL* 3.3 26.3 + - + +
733A TRP* 2.8 28.6 + - - +
740A ILE* 4.1 19.3 - - + -
757A TYR* 2.9 51.0 + + + +
767A HIS* 3.8 21.1 - + + +
770A PHE* 4.1 21.9 - - + -
772A ILE* 3.5 34.9 - - + +
788A MET* 3.7 25.8 - - + -
790A VAL* 3.6 25.5 - - + +
801A VAL* 4.6 2.7 - - + -
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Residues in contact with GLN 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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689A LEU* 3.9 25.6 - - + -
690A GLN 5.7 1.7 + - - +
692A ASN* 5.0 12.3 + - + +
726A ALA 3.0 19.3 + - - +
727A GLN* 3.2 6.5 + - - +
729A TRP* 1.3 74.1 - - - +
731A VAL* 1.3 59.4 + - - +
733A TRP* 4.2 7.3 - - - -
734A ASP* 2.8 64.3 + - - +
768A GLY 4.8 3.6 - - - +
770A PHE* 3.3 32.4 - - + -
792A ASN* 6.0 0.2 - - - +
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Residues in contact with VAL 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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687A VAL* 4.1 18.6 - - + -
689A LEU* 3.4 26.0 - - + -
696A ILE* 4.0 16.4 - - + -
698A ALA* 5.6 0.9 - - + -
715A ILE* 3.9 34.3 - - + -
727A GLN 3.0 10.6 + - - +
728A PHE* 3.2 7.8 + - - +
730A GLN* 1.3 72.7 - - - +
732A VAL* 1.3 65.8 + - - +
734A ASP* 3.4 6.2 + - - -
735A GLN* 3.1 30.1 + - - +
737A LEU* 4.2 7.1 - - + +
839A LEU* 4.7 5.8 - - + -
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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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728A PHE* 3.2 15.6 + - + +
729A TRP* 3.5 26.0 - - + +
731A VAL* 1.3 76.4 - - - +
733A TRP* 1.3 59.2 + - - +
736A LYS* 3.1 8.0 + - - -
737A LEU* 3.0 53.2 + - + +
740A ILE* 4.1 16.2 - - + -
790A VAL* 5.0 2.5 - - + -
799A HIS* 4.2 5.9 + - + -
801A VAL* 3.8 20.0 - - + -
839A LEU* 3.8 24.7 - - + -
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Residues in contact with TRP 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 TRP 2.8 11.5 + - - +
730A GLN* 3.7 10.3 - - - +
732A VAL* 1.3 75.5 - - - +
734A ASP* 1.3 71.3 + - - +
736A LYS* 3.0 58.0 + - - +
770A PHE* 3.5 38.8 - + + -
790A VAL* 3.6 27.6 - - + -
792A ASN* 3.4 24.2 - - + +
797A GLU* 3.4 56.0 + - + -
798A GLU 4.0 4.3 - - - -
799A HIS* 3.5 26.9 - + + -
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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
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688A LEU 4.5 1.6 - - - +
689A LEU* 3.5 14.2 - - - +
690A GLN* 2.9 70.5 + - + +
730A GLN* 2.8 49.5 + - - +
731A VAL* 3.8 5.6 - - - +
733A TRP* 1.3 78.3 - - - +
735A GLN* 1.3 66.6 + - + +
736A LYS* 3.7 5.8 + - - +
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Residues in contact with GLN 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A VAL* 4.0 10.3 - - - +
688A LEU 4.7 4.9 + - - -
690A GLN* 4.5 9.4 - - - +
700A TYR* 2.9 36.3 + - - -
715A ILE* 3.6 23.4 - - - +
731A VAL* 3.1 16.0 + - - +
734A ASP* 1.3 86.8 - - + +
736A LYS* 1.3 69.5 + - - +
737A LEU* 3.1 20.4 + - + +
836A GLU* 4.6 5.4 - - - +
837A PRO* 4.2 13.1 - - + +
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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