Contacts of the helix formed by residues 740 - 755 (chain A) in PDB entry 2VGE
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 740 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A ASN* 3.6 11.6 - - - +
706A THR* 4.6 0.2 + - - -
739A GLU* 1.3 74.4 - - - +
741A TYR* 1.3 63.9 + - - +
742A ALA 3.5 2.0 - - - -
743A ASP* 3.5 11.6 + - - +
744A CYS* 3.1 25.1 + - - +
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Residues in contact with TYR 741 (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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704A ASN* 3.4 9.4 - - - +
731A PHE* 5.8 3.5 - - - -
734A CYS* 3.6 33.7 - - + -
735A ASP 3.5 17.3 - - - +
736A PRO* 3.4 39.7 - - + +
738A ARG 3.7 6.5 - - - +
739A GLU 3.3 3.0 - - - -
740A GLY* 1.3 77.7 - - - +
742A ALA* 1.3 72.0 + - + +
744A CYS* 3.3 0.9 + - - +
745A ALA* 2.9 36.6 + - + +
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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
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740A GLY 3.5 0.4 - - - -
741A TYR* 1.3 90.7 - - + +
743A ASP* 1.3 62.4 + - - +
745A ALA* 4.1 1.6 - - - +
746A THR* 3.0 33.5 + - - +
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Residues in contact with ASP 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A THR* 2.8 29.0 + - - +
740A GLY* 3.5 12.9 + - - +
741A TYR 3.3 0.4 - - - -
742A ALA* 1.3 78.2 - - - +
744A CYS* 1.3 58.0 + - - +
746A THR* 3.8 5.2 - - - +
747A TYR* 3.1 27.5 + - - +
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Residues in contact with CYS 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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701A ALA* 4.2 2.2 - - - -
704A ASN* 3.6 30.1 - - + +
705A ASP 4.1 0.2 - - - -
706A THR* 3.2 19.2 + - - +
709A CYS* 3.6 31.4 - - - -
734A CYS* 4.0 14.8 - - - -
740A GLY 3.1 16.1 + - - +
741A TYR 3.9 2.0 - - - +
743A ASP* 1.3 76.0 - - - +
745A ALA* 1.3 66.4 + - - +
747A TYR* 3.2 3.5 + - - +
748A LEU* 3.0 30.3 + - - +
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Residues in contact with ALA 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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731A PHE* 3.3 24.2 - - + +
734A CYS* 3.7 18.9 - - + -
741A TYR* 2.9 38.5 + - + +
742A ALA* 4.1 2.9 - - - +
744A CYS* 1.3 75.5 - - - +
746A THR* 1.3 59.2 + - - +
748A LEU 3.3 0.5 + - - -
749A ALA* 2.8 32.6 + - - +
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Residues in contact with THR 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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742A ALA* 3.0 23.4 + - - +
743A ASP* 3.8 4.9 - - - +
745A ALA* 1.3 77.1 - - - +
747A TYR* 1.3 59.1 + - - +
749A ALA* 3.4 6.4 + - - +
750A ASP* 2.9 30.5 + - + +
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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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706A THR* 4.0 16.6 - - + -
709A CYS* 3.9 15.0 - - + -
710A MET* 3.3 57.5 + - + +
713A VAL* 3.5 18.8 - - + +
714A GLN* 4.9 3.8 + - - +
743A ASP* 3.1 19.3 + - - +
744A CYS 3.2 4.2 + - - +
746A THR* 1.3 77.6 - - - +
748A LEU* 1.3 72.3 + - + +
750A ASP* 3.1 9.0 + - + +
751A VAL* 2.8 51.6 + - + +
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Residues in contact with LEU 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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697A LEU* 4.5 17.5 - - + -
701A ALA* 3.7 30.7 - - + -
709A CYS* 4.2 11.7 - - + -
713A VAL* 4.9 4.0 - - + -
719A ILE* 5.0 2.9 - - + +
730A ALA* 3.7 16.8 - - + +
731A PHE* 3.8 16.6 - - + +
734A CYS* 3.7 13.7 - - - -
744A CYS* 3.0 19.7 + - - +
745A ALA 3.8 2.9 - - - +
747A TYR* 1.3 96.2 - - + +
749A ALA* 1.3 57.7 + - - +
751A VAL* 3.5 7.4 - - + +
752A GLU* 2.9 35.4 + - + +
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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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731A PHE* 3.7 21.9 - - + -
745A ALA 2.8 22.9 + - - +
746A THR* 3.7 6.7 - - - +
748A LEU* 1.3 72.2 - - - +
750A ASP* 1.3 62.7 + - - +
752A GLU* 3.3 9.2 + - - +
753A GLN* 3.0 29.6 + - + +
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Residues in contact with ASP 750 (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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746A THR* 2.9 19.0 + - + +
747A TYR* 3.5 10.5 - - + +
749A ALA* 1.3 74.2 - - - +
751A VAL* 1.3 67.7 + - - +
753A GLN* 3.4 7.1 + - - +
754A SER* 2.9 28.4 + - - -
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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
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713A VAL* 4.3 6.7 - - + -
719A ILE* 3.5 40.6 - - + -
747A TYR* 2.8 57.1 + - + +
748A LEU* 3.2 11.6 + - + +
750A ASP* 1.3 76.4 - - + +
752A GLU* 1.3 63.0 + - - +
754A SER* 2.8 23.6 + - - -
755A MET* 3.5 8.1 + - - +
817A LEU* 4.0 17.0 - - + -
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Residues in contact with GLU 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A ILE* 3.6 26.7 - - + +
720A PHE* 3.7 38.7 - - + -
729A THR* 3.6 24.6 + - - +
731A PHE* 3.8 24.7 + - + +
748A LEU* 2.9 21.8 + - + +
749A ALA* 3.6 7.0 - - - +
750A ASP 3.3 0.2 - - - -
751A VAL* 1.3 77.2 - - - +
753A GLN* 1.3 68.8 + - + +
755A MET* 3.5 17.4 + - - +
790A ARG* 4.6 2.1 + - - -
799A TRP* 5.5 0.7 - - - -
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Residues in contact with GLN 753 (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 PHE* 5.9 0.7 - - - -
749A ALA* 3.0 19.9 + - + +
750A ASP* 3.9 8.7 - - - +
751A VAL 3.3 0.2 - - - -
752A GLU* 1.3 81.8 - - + +
754A SER* 1.3 60.9 + - - +
755A MET 3.2 0.7 - - - -
757A LEU* 4.0 7.3 - - + +
790A ARG* 2.9 47.8 + - - +
791A ASP* 5.5 1.6 + - - -
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Residues in contact with SER 754 (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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750A ASP* 2.9 21.1 + - - -
751A VAL* 2.8 17.0 + - - -
753A GLN* 1.3 75.4 - - - +
755A MET* 1.3 59.6 + - - +
756A GLY 3.3 0.3 + - - -
757A LEU* 3.2 4.7 + - - -
758A MET* 2.8 56.4 + - - +
817A LEU* 3.6 23.9 - - - +
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Residues in contact with MET 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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719A ILE* 3.6 31.0 - - + -
720A PHE* 4.0 15.3 - - + -
751A VAL 3.5 13.2 - - - +
752A GLU 3.7 9.1 - - - +
753A GLN 3.2 1.6 - - - -
754A SER* 1.3 75.4 + - - +
756A GLY* 1.3 57.4 + - - +
757A LEU 3.2 0.7 - - - -
763A VAL* 3.5 26.7 - - + -
787A VAL* 5.0 1.6 - - - -
790A ARG* 3.1 26.0 + - - +
799A TRP* 4.1 19.9 - - + -
815A PHE* 3.7 20.9 - - + +
816A GLY 3.6 26.2 - - - +
817A LEU* 3.7 17.7 - - + +
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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