Contacts of the helix formed by residues 775 - 789 (chain A) in PDB entry 2VE8
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 775 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A GLN* 3.6 4.7 - - - -
774A ILE* 1.3 80.4 - - - +
776A TYR* 1.4 66.9 + - - -
777A ASN 3.4 2.7 - - - -
778A ARG* 3.4 8.8 + - - +
779A ALA* 3.0 22.5 + - - +
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Residues in contact with TYR 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ILE* 3.6 39.8 - - + +
769A GLN* 3.3 24.0 - - - +
775A GLY* 1.4 70.6 - - - -
777A ASN* 1.3 82.4 + - - +
779A ALA* 3.3 1.9 + - - +
780A ALA* 2.8 35.1 + - + +
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Residues in contact with ASN 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A GLY 3.4 0.6 - - - -
776A TYR* 1.3 97.1 - - - +
778A ARG* 1.3 63.7 + - - +
780A ALA* 3.3 3.7 + - - +
781A ARG* 3.0 47.5 + - - +
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Residues in contact with ARG 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ASP* 2.8 42.7 + - - +
748A PRO* 3.8 6.3 - - - +
749A LEU* 3.5 19.3 - - - +
774A ILE* 4.0 25.8 - - + +
775A GLY* 3.4 14.2 + - - +
776A TYR 3.2 0.2 - - - -
777A ASN* 1.3 80.9 - - - +
779A ALA* 1.3 61.9 + - - +
781A ARG* 3.4 24.2 + - - +
782A MET* 3.2 22.6 + - + +
772D LEU 2.8 22.6 + - - -
773D LYS* 3.0 30.9 + - - +
774D ILE* 4.1 9.3 - - - +
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Residues in contact with ALA 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ILE* 3.9 9.6 - - + +
768A VAL* 3.8 22.3 - - + +
769A GLN* 3.7 22.2 - - + -
774A ILE* 3.8 11.6 - - + +
775A GLY 3.0 18.0 + - - +
776A TYR 3.8 1.8 - - - +
778A ARG* 1.3 76.5 - - - +
780A ALA* 1.3 64.5 + - - +
782A MET* 3.2 5.6 + - - +
783A ILE* 3.0 27.8 + - - +
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Residues in contact with ALA 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ILE* 3.9 30.2 - - + +
776A TYR* 2.8 29.1 + - + +
777A ASN* 3.7 5.2 - - - +
779A ALA* 1.3 77.9 - - - +
781A ARG* 1.3 63.4 + - + +
783A ILE* 3.3 3.2 + - - +
784A GLU* 3.0 25.3 + - - +
801A ARG* 5.7 0.2 + - - -
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Residues in contact with ARG 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A GLU* 3.1 63.9 + - - +
747A ASP* 5.3 4.9 + - + +
777A ASN* 3.0 44.3 + - + +
778A ARG* 3.4 32.9 - - - +
780A ALA* 1.3 77.5 - - + +
782A MET* 1.3 64.4 + - + +
784A GLU* 3.3 16.5 + - - +
785A ALA* 3.0 21.5 + - - +
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Residues in contact with MET 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ASP* 3.8 30.7 - - + +
749A LEU* 3.6 35.7 - - + +
750A TYR* 3.6 14.0 - - + -
753A ALA* 3.9 5.6 - - + -
768A VAL* 4.6 2.2 - - + -
772A LEU* 4.0 13.9 - - + -
774A ILE* 3.4 33.0 - - + -
778A ARG* 3.2 11.3 + - + +
779A ALA* 3.2 8.9 + - - +
781A ARG* 1.3 80.5 - - + +
783A ILE* 1.3 61.0 + - + +
785A ALA* 3.2 9.0 + - - +
786A MET* 2.9 40.8 + - + +
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Residues in contact with ILE 783 (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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763A ALA* 3.5 24.5 - - + +
764A SER 3.7 4.3 - - - +
765A ILE* 3.6 34.3 - - + +
768A VAL* 3.9 19.3 - - + -
779A ALA 3.0 16.2 + - - +
780A ALA* 3.8 5.8 - - - +
782A MET* 1.3 76.4 - - - +
784A GLU* 1.3 62.4 + - - +
786A MET* 3.1 17.4 + - + +
787A GLU* 2.9 20.4 + - - +
792A VAL* 4.0 4.7 - - + +
801A ARG* 3.3 39.5 - - - +
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Residues in contact with GLU 784 (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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780A ALA 3.0 12.0 + - - +
781A ARG* 3.6 21.9 - - - +
783A ILE* 1.3 75.8 - - - +
785A ALA* 1.4 62.5 + - - +
787A GLU* 3.1 8.2 + - - +
788A MET* 3.0 37.5 + - + +
801A ARG* 4.5 12.5 - - - +
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Residues in contact with ALA 785 (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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745A GLU 6.1 1.1 - - - +
746A ASP* 4.8 14.4 - - - +
750A TYR* 3.8 21.4 + - + -
781A ARG 3.0 13.8 + - - +
782A MET* 3.4 10.5 - - - +
784A GLU* 1.4 76.1 - - - +
786A MET* 1.3 63.8 + - - +
788A MET* 3.2 11.9 + - - +
789A ALA* 3.0 23.6 + - - +
771F LYS* 5.9 1.3 - - - +
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Residues in contact with MET 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A TYR* 3.6 20.9 - - + +
753A ALA* 3.4 45.8 - - + +
754A VAL* 3.9 12.3 - - + +
757A VAL* 3.7 31.6 - - + -
768A VAL* 5.0 1.3 - - + -
782A MET* 2.9 27.4 + - + +
783A ILE* 3.1 19.0 + - + +
785A ALA* 1.3 77.7 - - - +
787A GLU* 1.3 60.8 + - - +
789A ALA 3.3 0.9 + - - -
790A GLY 3.1 3.8 + - - -
791A VAL* 2.8 36.4 + - + +
792A VAL* 3.6 15.2 + - + -
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Residues in contact with GLU 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ILE 2.9 8.9 + - - +
784A GLU* 3.1 11.4 + - - +
786A MET* 1.3 76.3 - - - +
788A MET* 1.3 66.5 + - + +
790A GLY* 3.0 12.8 + - - -
792A VAL* 3.6 19.9 - - + +
793A THR 4.1 0.9 - - - +
794A PRO* 3.5 30.8 - - + +
795A MET* 4.7 1.0 + - - +
801A ARG* 2.9 40.2 + - - +
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Residues in contact with MET 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A GLU* 3.0 25.1 + - + +
785A ALA* 3.2 12.5 + - - +
787A GLU* 1.3 78.9 - - + +
789A ALA* 1.3 58.9 + - - +
790A GLY 3.2 0.8 + - - -
771F LYS* 5.5 9.0 - - - +
773F LYS* 5.9 1.4 + - - +
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Residues in contact with ALA 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A TYR* 3.5 25.6 - - + +
785A ALA 3.0 10.6 + - - +
786A MET 3.8 2.9 - - - +
787A GLU 3.1 0.4 - - - -
788A MET* 1.3 75.2 - - - +
790A GLY* 1.3 61.8 + - - +
791A VAL* 3.3 8.8 + - + +
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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