Contacts of the helix formed by residues 721 - 735 (chain A) in PDB entry 4REC
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 ARG 721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684A GLU* 3.0 33.7 + - - -
687A VAL* 5.6 2.8 - - - +
715A LEU* 2.8 16.9 + - + +
719A LEU* 3.5 45.1 + - + +
720A LYS* 1.3 75.0 - - - +
722A LEU* 1.3 57.5 + - - +
724A PRO* 3.5 26.2 - - + +
725A THR* 2.5 34.0 + - - -
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Residues in contact with LEU 722 (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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716A HIS* 4.8 12.8 - - + +
720A LYS* 3.6 16.6 + - + +
721A ARG* 1.3 74.5 - - - +
723A GLU* 1.3 61.9 + - - +
724A PRO* 3.9 0.2 - - - +
725A THR* 3.3 7.2 - - - +
726A ILE* 3.1 31.5 + - - +
752A ARG* 6.1 0.9 - - - +
753A LEU* 4.1 14.1 - - + -
758A SER* 3.1 41.1 - - - +
759A CYS* 3.7 21.5 - - - -
761A LYS* 5.8 1.6 - - - -
762A PHE* 3.9 12.3 - - + -
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Residues in contact with GLU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A LEU* 1.3 76.3 - - - +
724A PRO* 1.4 69.9 - - + +
725A THR 3.2 1.1 - - - -
726A ILE* 3.4 9.6 + - - +
727A LYS* 3.2 39.4 + - + +
762A PHE* 3.2 33.2 - - + -
764A HIS* 5.3 2.8 + - - -
765A LEU* 3.7 23.3 - - + +
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Residues in contact with PRO 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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715A LEU* 3.9 18.2 - - + +
721A ARG* 3.3 36.6 - - + +
722A LEU 3.9 0.2 - - - +
723A GLU* 1.4 94.3 - - + +
725A THR* 1.3 50.0 + - - +
727A LYS* 3.1 23.7 + - - +
728A CYS* 2.8 35.7 + - - +
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Residues in contact with THR 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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712A ALA* 4.0 12.6 - - + +
715A LEU* 3.2 21.1 - - - +
716A HIS* 3.2 25.4 + - + -
721A ARG 2.5 21.5 + - - -
722A LEU* 3.3 10.9 - - - -
724A PRO* 1.3 79.5 - - - +
726A ILE* 1.3 62.5 + - - +
728A CYS* 3.2 3.6 + - - +
729A ILE* 3.0 31.0 + - + +
749A ARG* 4.6 0.4 - - - -
753A LEU* 3.4 25.8 - - + -
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Residues in contact with ILE 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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722A LEU 3.1 21.1 - - - +
723A GLU* 3.8 11.0 - - - +
724A PRO 3.3 0.2 - - - -
725A THR* 1.3 76.2 - - - +
727A LYS* 1.3 63.4 + - - +
729A ILE* 3.4 8.1 + - + +
730A THR* 2.9 34.2 + - + +
750A ALA* 6.5 0.2 - - + -
753A LEU* 3.6 22.9 - - + -
759A CYS* 4.7 7.2 - - - -
762A PHE* 4.8 4.0 - - + -
765A LEU* 3.7 41.1 - - + +
766A PHE* 3.4 43.1 - - + -
768A GLN* 5.8 0.2 - - - +
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Residues in contact with LYS 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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723A GLU* 3.2 33.7 + - + +
724A PRO* 3.1 28.1 + - - +
726A ILE* 1.3 79.7 - - + +
728A CYS* 1.3 56.3 + - - +
730A THR* 2.5 22.1 + - - -
731A GLU* 2.9 31.1 + - + +
765A LEU* 5.8 6.1 - - + -
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Residues in contact with CYS 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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708A TRP* 3.6 19.5 - - - +
711A LEU* 3.6 26.2 - - + -
712A ALA* 3.6 33.0 - - - -
715A LEU* 4.0 11.0 - - + -
724A PRO 2.8 16.0 + - - +
725A THR* 3.2 6.3 + - - +
727A LYS* 1.3 76.1 - - - +
729A ILE* 1.3 54.1 + - - +
731A GLU* 3.3 9.9 + - - -
732A GLY* 2.8 33.3 + - - -
746A LEU* 5.7 0.4 - - - -
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Residues in contact with ILE 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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712A ALA* 4.2 15.5 - - + -
725A THR* 3.0 27.1 + - + +
726A ILE* 3.8 7.0 - - + +
728A CYS* 1.3 74.8 - - - +
730A THR* 1.3 61.0 + - + +
732A GLY 3.7 0.2 - - - -
733A LEU* 2.8 47.1 + - + +
746A LEU* 3.8 36.0 - - + +
749A ARG* 3.7 32.1 - - + +
750A ALA* 3.9 23.1 - - + +
753A LEU* 4.4 4.9 - - + -
766A PHE* 6.5 0.2 - - + -
768A GLN* 5.1 1.1 - - - +
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Residues in contact with THR 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 ILE* 2.9 18.5 + - + +
727A LYS* 2.5 27.0 + - - -
729A ILE* 1.3 76.8 - - + +
731A GLU* 1.3 63.1 + - - +
733A LEU* 3.5 6.3 + - - +
734A ALA* 3.1 22.9 + - - +
765A LEU 4.2 9.9 - - - +
768A GLN* 3.2 45.4 - - + +
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Residues in contact with GLU 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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708A TRP* 3.5 28.9 - - + -
727A LYS* 2.9 32.7 + - + +
728A CYS* 3.7 5.8 - - - +
730A THR* 1.3 73.8 - - - +
732A GLY* 1.3 66.4 + - - +
734A ALA* 3.0 17.8 + - - +
735A ASP* 3.0 13.9 + - - +
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Residues in contact with GLY 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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708A TRP* 3.5 32.4 - - - -
728A CYS 2.8 14.5 + - - -
729A ILE 3.7 0.9 - - - -
731A GLU* 1.3 75.8 - - - +
733A LEU* 1.3 62.7 + - - +
735A ASP* 3.0 18.2 + - - +
738A VAL* 3.5 11.8 - - - +
746A LEU* 3.9 12.6 - - - -
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Residues in contact with LEU 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 ILE* 2.8 38.9 + - + +
730A THR* 3.8 5.8 - - - +
731A GLU 3.3 0.2 - - - -
732A GLY* 1.3 73.4 - - - +
734A ALA* 1.3 54.8 + - - +
743A ARG* 2.8 74.7 + - + +
746A LEU* 4.1 10.0 - - + +
747A TYR* 4.5 16.8 - - + +
768A GLN* 4.6 11.0 - - + +
769A LEU* 4.8 2.9 - - + -
770A PRO* 4.0 34.3 - - + -
772A MET* 5.2 4.3 - - - -
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Residues in contact with ALA 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 THR 3.1 13.5 + - - +
731A GLU* 3.0 14.0 + - - +
733A LEU* 1.3 76.2 - - - +
735A ASP* 1.3 62.9 + - - +
736A PRO* 3.3 10.4 - - - +
743A ARG* 4.5 1.7 + - - +
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Residues in contact with ASP 735 (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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697A ARG* 5.6 4.0 + - - -
704A ARG* 2.9 28.1 + - - -
708A TRP* 2.7 31.6 + - + +
731A GLU 3.0 8.2 + - - +
732A GLY 3.0 13.4 + - - +
734A ALA* 1.3 72.7 - - - +
736A PRO* 1.3 71.6 - - - +
737A GLU* 3.0 26.2 + - - +
738A VAL* 3.1 19.6 + - + +
743A ARG* 3.3 13.0 + - - -
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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