Contacts of the helix formed by residues 733 - 748 (chain A) in PDB entry 2VF8
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 GLY 733 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLN* 3.1 36.0 - - - +
593A PRO* 5.7 1.8 - - - -
731A LEU 3.0 8.4 + - - -
732A SER* 1.3 74.1 - - - +
734A GLY* 1.3 59.7 + - - -
735A GLU 3.4 3.6 - - - +
736A ALA* 3.5 21.3 - - - +
737A GLN* 3.3 16.1 + - - +
762A THR* 4.3 0.2 + - - -
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Residues in contact with GLY 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLN* 3.8 3.8 + - - -
732A SER* 2.6 18.6 + - - -
733A GLY* 1.3 69.9 - - - -
735A GLU* 1.3 60.7 + - - +
737A GLN* 3.2 7.3 + - - +
738A ARG* 3.1 26.4 + - - +
762A THR* 3.3 29.0 - - - +
763A GLY* 4.7 6.1 - - - -
764A LEU* 5.2 3.2 - - - +
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Residues in contact with GLU 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 5.0 4.2 + - - +
46A GLY* 5.8 0.9 - - - -
101A ARG* 4.4 5.9 + - - -
719A LEU* 4.2 12.6 - - + +
721A TYR* 2.9 32.6 + - - +
722A LEU* 3.1 27.7 - - - +
726A GLN* 4.6 0.7 + - - -
730A GLU 4.6 2.4 - - - +
731A LEU* 3.9 16.5 - - + +
732A SER* 2.9 49.6 + - - +
734A GLY* 1.3 71.2 - - - +
736A ALA* 1.3 68.3 + - - +
737A GLN 3.0 1.1 - - - -
738A ARG* 2.8 24.6 + - - +
739A ILE* 3.1 13.3 + - - +
1843A ADP 4.5 10.2 + - - -
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Residues in contact with ALA 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLN 4.0 0.2 - - - +
592A LYS 3.9 15.7 - - - +
593A PRO* 4.1 8.3 - - + -
594A ILE* 3.8 24.1 - - + +
728A ALA 6.2 0.2 - - - +
731A LEU* 4.4 8.7 - - + +
733A GLY* 3.5 24.7 - - - +
734A GLY 3.4 0.4 - - - -
735A GLU* 1.3 78.1 - - - +
737A GLN* 1.3 63.0 + - - +
739A ILE* 3.2 16.3 + - - +
740A LYS* 2.9 20.8 + - - +
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Residues in contact with GLN 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A VAL* 3.6 25.9 - - + +
590A ASP 3.6 19.0 + - - +
591A GLN* 4.9 3.0 - - - +
733A GLY 3.3 10.9 + - - +
734A GLY 3.2 8.7 + - - +
735A GLU 3.0 0.6 - - - -
736A ALA* 1.3 78.4 - - - +
738A ARG* 1.3 71.4 + - - +
739A ILE 3.0 1.4 + - - -
740A LYS* 3.0 17.6 + - - +
741A LEU* 3.0 12.1 + - + +
758A ASP 4.6 3.2 + - - -
759A GLU 3.3 12.3 + - - -
760A PRO* 3.2 23.5 - - - +
762A THR* 3.2 35.4 + - - +
764A LEU* 4.5 3.6 - - - +
772A LEU* 4.9 6.6 - - - +
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Residues in contact with ARG 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 5.9 0.2 - - - +
45A SER* 4.0 26.6 + - - -
717A VAL* 3.0 54.2 + - + +
718A GLY 3.7 15.4 + - - -
719A LEU* 3.7 15.4 - - + +
721A TYR* 4.1 13.3 + - - -
734A GLY 3.1 14.5 + - - +
735A GLU* 2.8 11.6 + - - +
737A GLN* 1.3 86.6 - - - +
739A ILE* 1.3 50.1 + - - +
741A LEU* 3.5 6.8 + - - +
742A ALA* 2.8 26.7 + - - +
764A LEU* 3.7 31.0 - - + +
768A ASP* 4.0 9.5 + - - -
771A ARG* 3.5 22.2 - - - +
772A LEU* 6.4 1.8 - - + -
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Residues in contact with ILE 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ILE* 3.8 24.2 - - + -
602A MET* 3.3 32.5 - - + -
605A TYR* 3.4 32.8 - - + -
606A THR* 4.2 12.1 - - + +
714A LEU* 4.6 6.3 - - + -
719A LEU* 3.9 15.5 - - + -
731A LEU* 4.3 15.9 - - + -
735A GLU 3.1 11.7 + - - +
736A ALA* 3.4 7.9 - - - +
737A GLN 3.0 1.4 + - - -
738A ARG* 1.3 71.1 - - - +
740A LYS* 1.3 61.7 + - - +
741A LEU 2.9 1.1 - - - -
742A ALA* 2.6 28.0 + - - +
743A THR* 3.0 10.8 + - - +
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Residues in contact with LYS 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ARG 5.5 2.9 - - - +
589A VAL* 4.8 17.5 - - + -
590A ASP* 3.3 33.4 + - - +
591A GLN 4.4 0.2 - - - -
592A LYS 2.7 30.6 + - - -
593A PRO 4.5 1.1 + - - -
594A ILE* 3.9 20.9 - - + +
605A TYR* 3.3 27.8 - - + +
736A ALA 2.9 28.8 + - - +
737A GLN* 3.0 9.1 + - - +
739A ILE* 1.3 80.1 - - - +
741A LEU* 1.3 63.2 + - - +
743A THR* 3.2 21.5 - - - -
744A GLU* 3.6 14.9 - - - +
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Residues in contact with LEU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A VAL* 4.0 26.6 - - + +
717A VAL* 4.3 7.9 - - + -
737A GLN* 3.0 12.6 + - + +
738A ARG* 3.5 11.7 - - - +
739A ILE 2.9 0.8 - - - -
740A LYS* 1.3 78.0 - - - +
742A ALA* 1.3 65.5 + - - +
743A THR 2.9 1.4 + - - -
744A GLU* 3.1 15.9 + - + +
745A LEU* 3.1 32.3 + - + +
755A TYR* 5.1 7.0 - - + -
757A LEU* 5.2 3.8 - - + -
772A LEU* 4.1 25.8 - - + -
775A GLN* 4.9 5.4 - - + -
776A LEU* 4.9 16.2 - - + -
779A LEU* 5.1 13.5 - - + -
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Residues in contact with ALA 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A THR* 5.9 0.4 - - + -
713A THR* 2.6 58.2 - - - +
714A LEU* 3.7 24.0 - - + -
717A VAL* 3.8 8.2 - - + +
738A ARG 2.8 16.1 + - - +
739A ILE* 2.6 18.4 + - - +
741A LEU* 1.3 71.3 - - - +
743A THR* 1.3 57.9 + - - +
745A LEU* 4.5 0.7 - - - -
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Residues in contact with THR 743 (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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605A TYR* 4.4 11.5 + - + -
606A THR* 4.6 22.8 - - - +
739A ILE 3.0 10.9 + - - -
740A LYS* 3.2 16.1 + - - -
741A LEU 2.9 0.2 + - - -
742A ALA* 1.3 79.6 - - - +
744A GLU* 1.3 79.3 + - - +
745A LEU 3.0 1.7 + - - -
746A ARG* 3.3 8.8 + - - +
747A ARG* 3.6 12.6 + - + +
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Residues in contact with GLU 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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585A ARG* 3.6 15.6 + - - -
587A VAL* 3.4 42.0 - - + +
589A VAL* 5.3 2.2 - - + -
740A LYS* 3.6 16.2 - - - +
741A LEU* 3.1 7.2 + - + +
743A THR* 1.3 88.7 - - - +
745A LEU* 1.3 57.6 + - - +
746A ARG 2.8 7.5 + - - -
747A ARG* 3.8 10.1 - - - +
748A SER* 3.2 26.3 + - - -
755A TYR* 3.5 23.9 + - + +
779A LEU* 5.2 1.5 - - + +
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Residues in contact with LEU 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A THR* 3.7 16.5 - - + +
716A GLU* 4.7 2.5 - - + +
717A VAL* 3.8 25.1 - - + +
741A LEU* 3.1 21.4 + - + +
743A THR 3.0 1.8 + - - -
744A GLU* 1.3 74.9 - - - +
746A ARG* 1.3 67.0 + - - +
748A SER* 4.4 7.8 + - - -
775A GLN* 3.3 61.0 - - + +
778A LYS* 4.0 18.5 - - + +
779A LEU* 4.7 18.1 - - + +
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Residues in contact with ARG 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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709A ARG* 3.8 45.0 + - + +
712A ASP* 3.4 28.8 + - - +
713A THR* 3.3 31.9 + - + +
716A GLU* 2.8 36.6 + - - -
743A THR 3.3 5.1 + - - +
744A GLU 3.0 0.4 - - - -
745A LEU* 1.3 87.4 + - - +
747A ARG* 1.3 63.0 + - - +
748A SER* 3.1 5.2 + - - +
749A GLY* 3.9 6.1 + - - -
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Residues in contact with ARG 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ARG* 3.3 63.2 - - - +
743A THR* 3.6 15.2 + - + +
744A GLU* 3.2 14.2 + - - +
746A ARG* 1.3 71.5 - - - +
748A SER* 1.3 50.9 + - - +
749A GLY* 2.3 25.1 + - - -
750A ARG 4.2 2.3 + - - +
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Residues in contact with SER 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ARG* 5.4 2.2 - - - +
744A GLU 3.2 12.3 + - - -
745A LEU* 4.4 10.2 + - - +
746A ARG* 3.1 3.4 - - - -
747A ARG* 1.3 73.6 - - - +
749A GLY* 1.3 51.4 + - - +
750A ARG* 2.7 19.1 + - - -
751A GLY* 3.1 14.6 + - - -
753A THR* 5.9 1.6 - - - -
755A TYR* 3.7 22.0 - - - -
779A LEU* 5.2 10.2 - - - +
782A ALA* 5.1 13.0 - - - +
784A ASN* 4.4 10.5 - - - -
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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