Contacts of the helix formed by residues 735 - 750 (chain A) in PDB entry 2IVF
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 735 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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686A GLU* 3.5 12.6 - - - +
688A TRP* 4.2 3.8 - - - -
689A ASP* 6.2 0.4 - - + -
733A LEU 3.8 0.2 - - - -
734A LEU* 1.3 88.7 - - + +
736A ASN* 1.3 65.8 + - - +
737A GLU* 3.3 10.6 + - - +
738A ASP* 3.0 36.1 + - - +
739A CYS* 3.1 17.3 + - - -
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Residues in contact with ASN 736 (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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198A ILE* 3.4 29.7 - - - +
199A ALA 5.5 1.1 + - - +
658A LYS* 3.7 24.7 - - - +
659A HIS* 2.9 30.3 + - - +
660A GLU* 3.9 7.9 + - - +
686A GLU* 2.9 44.7 + - - +
687A GLU* 4.6 2.9 + - - -
688A TRP* 3.9 8.2 + - - +
735A THR* 1.3 71.4 - - - +
737A GLU* 1.3 57.3 + - - +
739A CYS* 3.1 3.9 + - - -
740A LEU* 2.7 30.8 + - - +
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Residues in contact with GLU 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A HIS* 3.5 39.6 + - + +
686A GLU* 4.8 0.4 + - - -
735A THR* 3.1 8.7 + - - +
736A ASN* 1.3 77.6 - - - +
738A ASP* 1.3 65.3 + - - +
740A LEU* 3.3 2.2 + - - +
741A LYS* 3.0 49.1 + - - +
759A TYR* 2.8 35.7 + - + +
763A LYS* 4.6 5.0 + - - +
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Residues in contact with ASP 738 (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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731A GLY 5.2 0.2 - - - +
732A HIS* 3.6 21.4 + - - +
733A LEU* 3.8 14.8 - - + +
734A LEU* 2.9 27.7 + - - +
735A THR* 3.0 26.7 + - - +
737A GLU* 1.3 78.5 - - - +
739A CYS* 1.3 56.4 - - - +
741A LYS* 3.4 13.5 + - - +
742A GLU* 3.1 21.1 + - - +
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Residues in contact with CYS 739 (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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198A ILE* 3.5 24.7 - - + -
491A LEU* 4.2 7.5 - - + +
688A TRP* 3.4 52.7 - - - -
733A LEU* 4.2 14.8 - - - -
735A THR 3.1 12.5 + - - +
736A ASN 3.1 4.0 + - - +
738A ASP* 1.3 77.7 - - - +
740A LEU* 1.3 54.2 + - - +
742A GLU* 3.2 4.9 + - - +
743A MET* 2.8 38.9 + - - +
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Residues in contact with LEU 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.9 8.2 - - + +
659A HIS* 3.9 14.4 - - + -
660A GLU* 3.6 15.0 - - - +
661A MET* 3.6 42.0 - - + +
673A PHE* 3.5 24.0 - - + -
736A ASN 2.7 20.0 + - - +
737A GLU* 3.7 6.1 - - - +
739A CYS* 1.3 69.3 - - - +
741A LYS* 1.3 60.5 + - - +
743A MET* 3.2 7.7 + - + +
744A VAL* 2.9 33.7 + - + +
759A TYR* 3.4 29.4 - - + +
762A PHE* 4.6 3.4 - - + -
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Residues in contact with LYS 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A GLU* 3.0 31.0 + - + +
738A ASP* 3.5 13.5 + - - +
739A CYS 3.4 0.2 - - - -
740A LEU* 1.3 75.4 - - - +
742A GLU* 1.3 61.5 + - - +
744A VAL* 3.3 9.7 + - - +
745A ASP* 3.1 26.4 + - - +
759A TYR* 3.7 44.4 - - + +
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Residues in contact with GLU 742 (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 LEU* 4.3 13.7 - - + -
494A MET* 3.4 10.8 - - + +
497A PRO* 3.6 21.4 - - - +
498A THR* 2.8 42.2 + - - -
729A MET* 5.1 1.8 - - + -
732A HIS* 4.8 5.2 + - - +
733A LEU* 4.4 13.7 - - + -
738A ASP 3.1 11.0 + - - +
739A CYS* 3.4 11.4 - - - +
740A LEU 3.2 0.2 - - - -
741A LYS* 1.3 77.4 - - - +
743A MET* 1.3 60.7 + - - +
745A ASP* 3.1 13.5 + - - +
746A ILE* 2.8 41.7 + - + +
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Residues in contact with MET 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A SER* 3.4 47.1 - - - +
198A ILE* 3.8 14.1 - - + -
487A ASN* 3.5 40.6 - - + +
488A MET* 4.2 0.9 - - + -
491A LEU* 3.4 28.9 - - + -
661A MET* 4.1 12.6 - - + -
739A CYS 2.8 18.3 + - - +
740A LEU* 3.2 12.5 + - - +
742A GLU* 1.3 73.0 - - - +
744A VAL* 1.3 58.3 + - - +
746A ILE* 3.3 10.2 + - + +
747A ASN* 2.9 33.2 + - - -
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Residues in contact with VAL 744 (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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661A MET* 4.8 1.8 - - - -
740A LEU* 2.9 23.2 + - + +
741A LYS* 3.6 9.0 - - - +
742A GLU 3.2 0.2 - - - -
743A MET* 1.3 75.9 - - - +
745A ASP* 1.3 59.3 + - - +
747A ASN* 3.2 7.5 + - - +
748A ARG* 2.9 33.1 + - - +
753A PHE* 4.1 13.0 - - + -
757A TYR* 3.5 24.2 - - + +
758A THR* 3.9 0.7 - - - -
759A TYR* 3.6 38.6 - - + +
762A PHE* 4.2 20.4 - - + -
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Residues in contact with ASP 745 (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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498A THR* 3.9 17.0 - - + +
499A ALA* 4.2 19.5 + - - +
741A LYS 3.1 16.3 + - - +
742A GLU* 3.4 17.2 - - - +
744A VAL* 1.3 76.7 - - - +
746A ILE* 1.3 59.6 + - - +
748A ARG* 3.0 33.2 + - - +
749A ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 746 (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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486A ASP* 3.6 33.4 - - + +
487A ASN* 3.6 23.8 - - - +
490A TYR* 3.7 7.9 - - + -
491A LEU* 3.7 20.2 - - + +
494A MET* 3.9 9.9 - - + -
498A THR* 3.3 16.8 - - - +
503A MET* 3.8 19.1 - - + -
742A GLU* 2.8 26.8 + - + +
743A MET* 3.5 11.0 - - - +
745A ASP* 1.3 76.5 - - - +
747A ASN* 1.3 63.3 + - - +
749A ALA* 3.1 4.0 + - - +
750A VAL* 3.0 22.2 + - - +
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Residues in contact with ASN 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A SER* 4.8 2.2 + - - -
487A ASN* 3.8 27.8 + - - +
661A MET* 3.8 15.6 - - - +
671A PHE* 3.8 6.3 - - - -
743A MET 2.9 16.4 + - - +
744A VAL 3.6 2.7 - - - +
746A ILE* 1.3 77.0 - - - +
748A ARG* 1.3 60.4 + - - +
750A VAL* 3.6 5.2 + - - +
751A GLY 3.3 2.1 + - - -
752A VAL* 2.8 51.0 + - - +
753A PHE* 2.9 47.5 + - + +
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Residues in contact with ARG 748 (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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744A VAL* 2.9 24.6 + - - +
745A ASP* 3.0 29.1 + - - +
746A ILE 3.2 0.2 - - - -
747A ASN* 1.3 75.0 - - - +
749A ALA* 1.3 65.0 + - - +
750A VAL 3.5 0.3 + - - -
751A GLY* 3.5 7.4 + - - -
753A PHE* 3.7 15.6 - - + +
754A ALA 3.3 17.3 - - - +
755A LYS* 2.8 38.5 + - - +
756A ASP* 4.4 2.6 - - - +
757A TYR 3.4 22.7 + - - +
758A THR* 3.8 28.2 - - - +
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Residues in contact with ALA 749 (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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498A THR* 3.6 22.7 - - + -
503A MET* 3.8 15.2 - - + +
507A HIS* 5.6 2.8 + - - -
745A ASP 2.9 17.7 + - - +
746A ILE 3.5 4.9 - - - +
748A ARG* 1.3 78.7 - - - +
750A VAL* 1.3 61.3 + - - +
751A GLY 3.7 0.5 + - - -
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Residues in contact with VAL 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASP* 3.5 34.8 - - + +
490A TYR* 4.2 6.1 - - + -
503A MET* 3.8 23.8 - - + -
507A HIS* 4.9 2.0 - - - +
746A ILE 3.0 20.4 + - - +
747A ASN* 3.8 4.9 - - - +
749A ALA* 1.3 78.6 - - - +
751A GLY* 1.3 60.2 + - - +
752A VAL* 3.5 22.6 + - + -
772A SER* 3.6 8.8 + - - -
774A GLY* 3.8 8.8 - - - +
775A THR* 3.7 21.6 - - + +
779A ARG* 4.9 3.6 + - - -
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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
------------------------------------------------------------
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