Contacts of the helix formed by residues 739 - 755 (chain A) in PDB entry 4REA
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 739 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A GLY* 5.6 0.2 - - - -
737A GLU 3.3 4.6 + - - -
738A VAL* 1.3 77.9 - - - +
740A THR* 1.3 67.6 + - - +
741A GLY 3.3 3.0 + - - +
742A HIS* 3.4 10.9 + - + +
743A ARG* 3.1 19.4 + - - +
950A ASP* 3.5 4.0 - - - +
953A HIS* 3.0 54.2 - - + +
986A LYS* 5.8 1.3 - - - -
990A TRP* 6.2 0.7 - - + -
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Residues in contact with THR 740 (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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739A ARG* 1.3 74.8 - - - +
741A GLY* 1.3 53.8 + - - +
743A ARG* 3.2 17.7 - - + +
744A LEU* 2.7 37.4 + - - +
772A MET* 5.9 8.7 - - + -
989A ILE* 3.5 38.2 - - + +
990A TRP* 4.0 13.1 - - - -
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Residues in contact with GLY 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A ARG* 3.4 1.8 - - - +
740A THR* 1.3 77.9 - - - +
742A HIS* 1.3 60.4 + - - +
745A SER 3.1 6.4 + - - -
985A HIS* 2.7 32.4 - - - +
986A LYS* 3.6 42.2 - - - +
989A ILE* 3.8 3.0 - - - +
990A TRP* 5.3 1.8 - - - -
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Residues in contact with HIS 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ASP 5.8 3.3 + - - -
705A GLY* 3.4 38.8 + - - +
706A ARG* 3.6 35.0 + - + +
709A ASP* 4.1 15.0 + - + +
738A VAL* 3.8 9.2 - - + -
739A ARG* 3.4 10.7 + - + +
741A GLY* 1.3 69.3 - - - +
743A ARG* 1.3 57.2 + - - +
745A SER* 3.0 9.5 - - - -
746A LEU* 2.8 38.2 + - + +
953A HIS* 5.9 3.4 - + - -
985A HIS* 5.1 3.7 - + - -
986A LYS* 4.3 23.4 + - + -
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Residues in contact with ARG 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A GLY 4.6 0.8 + - - -
733A LEU* 3.2 45.4 + - + +
734A ALA 5.0 1.6 + - - -
735A ASP 3.1 23.6 + - - -
736A PRO* 4.4 11.0 + - - +
738A VAL* 2.6 44.9 + - + +
739A ARG 3.1 10.2 + - - +
740A THR* 3.2 26.2 - - + +
742A HIS* 1.3 76.7 - - - +
744A LEU* 1.3 56.9 + - - +
746A LEU* 3.1 5.1 + - - +
747A TYR* 2.9 30.5 + - - +
772A MET* 5.8 8.0 - - - -
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Residues in contact with LEU 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A THR* 2.7 20.1 + - + +
741A GLY 3.7 3.4 - - - +
743A ARG* 1.3 72.2 - - - +
745A SER* 1.3 57.0 + - - +
747A TYR* 3.8 22.8 - - + -
748A GLN* 3.0 39.6 + - + +
772A MET 4.9 4.0 - - - +
774A VAL* 3.7 26.5 - - + -
985A HIS* 3.5 34.1 - - + +
988A MET* 3.8 24.9 - - + -
989A ILE* 3.7 19.3 - - + -
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Residues in contact with SER 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A ASP* 2.7 30.2 + - - +
741A GLY 3.1 7.4 + - - -
742A HIS* 3.0 14.1 - - - -
744A LEU* 1.3 78.0 - - - +
746A LEU* 1.3 63.0 + - - +
748A GLN* 3.8 6.1 + - - +
749A ARG* 3.3 22.2 + - - +
985A HIS* 2.7 48.3 + - - -
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Residues in contact with LEU 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A GLY 4.8 1.8 - - - +
708A TRP* 3.7 28.0 - - + +
709A ASP* 3.6 32.5 - - - +
712A ALA* 4.2 14.6 - - + -
728A CYS* 4.7 1.1 - - - +
729A ILE* 3.5 27.9 - - + +
732A GLY* 4.4 16.4 - - - -
733A LEU* 4.3 9.0 - - + +
738A VAL* 4.4 13.9 - - + -
742A HIS 2.8 27.2 + - - +
743A ARG* 3.1 5.6 + - - +
745A SER* 1.3 74.0 - - - +
747A TYR* 1.3 66.1 + - - +
749A ARG* 3.1 16.2 + - - +
750A ALA 3.1 9.2 + - - -
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Residues in contact with TYR 747 (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* 4.6 1.1 - - - -
733A LEU* 4.2 18.7 - - + +
743A ARG 2.9 15.2 + - - +
744A LEU* 3.8 22.4 - - + -
746A LEU* 1.3 74.0 - - - +
748A GLN* 1.3 73.7 + - + +
750A ALA* 2.7 30.1 + - - +
751A VAL* 3.0 35.3 + - + +
769A LEU* 5.2 11.4 - - + -
770A PRO* 4.1 21.1 - - + -
771A GLU* 5.1 5.8 + - - +
772A MET* 3.3 35.1 + - + -
773A ALA* 4.6 9.5 - - - +
774A VAL* 6.3 0.2 - - + -
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Residues in contact with GLN 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A LEU* 3.0 22.4 + - + +
745A SER 3.8 4.6 + - - +
747A TYR* 1.3 87.2 - - + +
749A ARG* 1.3 64.7 + - - +
751A VAL* 3.5 6.5 + - - +
752A ARG* 3.2 21.8 + - + +
985A HIS* 3.0 40.5 + - - -
988A MET* 5.3 5.2 - - - +
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Residues in contact with ARG 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A ASP* 4.6 11.5 + - - -
712A ALA* 3.4 36.1 - - - +
713A LEU* 3.7 37.1 - - - +
716A HIS* 3.4 36.9 + - + +
717A GLN* 4.3 8.5 + - - +
725A THR* 4.5 0.2 - - - -
729A ILE* 3.8 9.4 - - + -
745A SER* 3.3 11.2 + - - +
746A LEU* 3.1 11.2 + - - +
747A TYR 3.1 0.6 - - - -
748A GLN* 1.3 80.1 - - + +
750A ALA* 1.3 65.5 + - - +
752A ARG* 3.5 10.4 + - + +
753A LEU* 3.1 30.1 + - + +
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Residues in contact with ALA 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A ILE* 6.1 2.9 - - + -
729A ILE* 3.7 33.4 - - + +
746A LEU 3.1 4.6 + - - -
747A TYR* 2.7 17.4 + - + +
749A ARG* 1.3 69.4 - - - +
751A VAL* 1.3 54.5 + - + +
753A LEU* 2.9 6.9 + - - +
754A ARG* 2.8 36.8 + - - +
766A PHE* 4.5 5.9 - - + -
769A LEU* 3.7 27.8 - - + -
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Residues in contact with VAL 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A TYR* 3.0 43.5 + - + +
748A GLN* 3.7 10.3 - - - +
750A ALA* 1.3 75.3 - - + +
752A ARG* 1.3 63.4 + - - +
753A LEU 3.3 0.3 + - - -
754A ARG* 3.3 13.0 + - - +
755A GLU* 3.4 40.3 + - - +
769A LEU* 5.6 6.5 - - + -
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Residues in contact with ARG 752 (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* 3.2 40.7 + - + +
748A GLN* 3.2 11.7 + - + +
749A ARG* 3.5 13.5 - - + +
750A ALA 3.2 0.2 - - - -
751A VAL* 1.3 82.2 - - - +
753A LEU* 1.3 60.9 + - - +
755A GLU* 3.6 12.7 + - - +
756A SER* 3.6 24.0 + - - -
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Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A HIS* 2.7 45.3 - - + +
722A LEU* 4.3 24.7 - - + -
725A THR* 3.3 29.8 - - + -
726A ILE* 4.0 18.6 - - + -
729A ILE* 3.9 8.3 - - + -
749A ARG* 3.1 22.0 + - + +
750A ALA* 2.9 7.8 + - - +
752A ARG* 1.3 73.2 - - - +
754A ARG* 1.3 57.5 + - - +
755A GLU 3.0 9.2 + - - -
756A SER* 3.8 9.4 + - - +
758A SER* 6.0 1.3 - - - -
759A CYS* 2.9 32.7 - - - +
766A PHE* 4.6 0.9 - - - -
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Residues in contact with ARG 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ALA 2.8 13.7 + - - +
751A VAL* 3.3 6.4 + - - +
753A LEU* 1.3 75.7 - - - +
755A GLU* 1.3 67.1 + - + +
756A SER 3.8 1.5 + - - +
759A CYS* 4.6 4.3 - - - +
763A LYS* 2.8 66.3 + - - +
766A PHE* 3.0 63.2 + - + +
767A GLN* 4.3 6.9 - - - +
769A LEU* 5.2 5.7 - - + +
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Residues in contact with GLU 755 (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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751A VAL* 3.4 37.7 + - - +
752A ARG* 3.6 5.4 + - - +
753A LEU 3.0 1.8 - - - -
754A ARG* 1.3 90.7 - - + +
756A SER* 1.3 59.9 + - - +
763A LYS* 5.8 0.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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