Contacts of the helix formed by residues 749 - 761 (chain E) 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 LEU 749 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747E ASP* 2.8 9.3 + - - +
748E PRO* 1.3 84.2 - - + +
750E TYR* 1.3 64.8 + - - +
751E ASP 3.3 3.6 - - - -
752E GLU* 3.2 12.9 + - + +
753E ALA* 2.9 21.1 + - - +
772E LEU* 4.4 27.0 - - + +
774E ILE* 4.0 22.7 - - + -
778E ARG* 3.9 18.2 - - - +
782E MET* 3.8 11.0 - - + -
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Residues in contact with TYR 750 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744E SER 3.6 20.0 - - - +
745E GLU* 3.5 31.5 - - + +
747E ASP* 3.0 19.8 + - + +
749E LEU* 1.3 77.0 - - - +
751E ASP* 1.3 75.5 + - - +
753E ALA* 3.0 4.6 + - - +
754E VAL* 2.9 40.3 + - + +
782E MET* 3.7 24.2 - - + +
785E ALA* 3.7 21.8 + - + -
786E MET* 3.6 40.2 + - + +
789E ALA* 4.3 10.2 - - - +
791E VAL* 4.5 3.5 - - - +
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Residues in contact with ASP 751 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745E GLU 4.5 4.4 - - - +
747E ASP 4.6 1.7 + - - -
748E PRO 5.4 1.0 + - - -
749E LEU 3.3 1.0 - - - -
750E TYR* 1.3 92.5 - - - +
752E GLU* 1.4 57.6 - - - +
754E VAL* 3.3 6.5 + - - +
755E ARG* 3.0 27.0 + - - +
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Residues in contact with GLU 752 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C ASP* 4.5 1.7 - - - +
749E LEU* 3.2 17.1 + - + +
750E TYR 3.2 0.8 - - - -
751E ASP* 1.4 77.1 - - - +
753E ALA* 1.3 60.2 + - - +
755E ARG* 3.8 25.0 + - - +
756E PHE* 2.8 34.1 + - - +
771E LYS* 3.4 27.6 + - - -
772E LEU* 3.7 22.9 - - + -
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Residues in contact with ALA 753 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749E LEU 2.9 13.7 + - - +
750E TYR* 3.0 8.5 + - - +
752E GLU* 1.3 77.5 - - - +
754E VAL* 1.3 57.5 + - - +
756E PHE* 3.3 2.8 + - - +
757E VAL* 2.9 32.7 + - - +
768E VAL* 4.2 12.1 - - + -
772E LEU* 4.2 12.3 - - + +
782E MET* 3.7 22.2 - - - -
786E MET* 3.6 18.6 - - + -
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Residues in contact with VAL 754 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750E TYR* 2.9 52.1 + - + +
751E ASP* 3.7 8.1 - - - +
752E GLU 3.2 0.2 - - - -
753E ALA* 1.3 73.7 - - - +
755E ARG* 1.3 67.9 + - - +
757E VAL* 3.2 1.0 + - - +
758E THR* 2.9 42.2 + - + +
786E MET* 4.0 17.9 - - + -
791E VAL* 4.3 14.6 - - + -
805E ALA* 6.0 0.2 - - + -
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Residues in contact with ARG 755 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751E ASP 3.0 17.1 + - - +
752E GLU* 3.7 25.2 + - - +
754E VAL* 1.3 77.0 - - - +
756E PHE* 1.3 58.8 + - - +
758E THR* 3.2 7.5 + - - -
759E GLU* 2.9 59.8 + - + +
808E PRO* 4.6 13.4 - - + +
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Residues in contact with PHE 756 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C ASP* 3.4 36.1 - - + -
752E GLU* 2.8 27.8 + - - +
753E ALA* 3.6 4.7 - - - +
755E ARG* 1.3 77.3 - - - +
757E VAL* 1.3 67.7 + - + +
759E GLU* 4.7 2.7 - - - -
760E SER* 2.7 54.9 + - - -
762E ARG* 3.9 26.7 - - - -
767E ALA* 3.5 40.8 - - + -
768E VAL* 4.0 7.4 - - + -
771E LYS* 3.6 27.1 - - + -
772E LEU* 5.1 0.7 - - + -
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Residues in contact with VAL 757 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753E ALA 2.9 20.9 + - - +
754E VAL* 3.9 2.9 - - - +
756E PHE* 1.3 78.2 - - + +
758E THR* 1.3 59.5 + - - +
760E SER* 3.8 5.6 - - - -
761E ARG* 2.8 29.6 + - - -
762E ARG 3.5 17.9 - - - +
763E ALA* 4.2 0.9 - - - -
768E VAL* 3.7 24.7 - - + -
783E ILE* 4.5 4.0 - - + -
786E MET* 4.0 16.2 - - - -
791E VAL* 4.8 3.1 - - + -
792E VAL* 3.8 20.6 - - + -
803E VAL* 3.4 25.8 - - + +
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Residues in contact with THR 758 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754E VAL* 2.9 38.4 + - + +
755E ARG* 3.2 10.7 + - - -
757E VAL* 1.3 79.7 - - - +
759E GLU* 1.3 58.7 + - - +
761E ARG* 2.9 30.2 + - - +
791E VAL* 4.2 6.1 - - + -
803E VAL* 4.1 8.3 - - + -
805E ALA* 3.9 28.3 - - + -
806E PRO 3.6 15.3 - - - +
807E ALA* 3.4 10.7 - - - +
808E PRO* 3.4 13.1 - - - +
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Residues in contact with GLU 759 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B LYS* 2.8 36.8 + - - +
746C ASP* 3.2 41.4 + - + +
748C PRO* 3.8 0.7 - - - +
755E ARG* 2.9 44.2 + - - +
756E PHE 4.0 1.6 - - - +
758E THR* 1.3 78.7 - - - +
760E SER* 1.3 61.7 + - - +
761E ARG 3.5 0.3 + - - -
807E ALA* 4.6 0.9 - - + -
808E PRO* 3.8 24.0 - - + +
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Residues in contact with SER 760 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746C ASP* 4.1 8.1 - - - -
747C ASP 4.0 6.5 - - - -
748C PRO* 3.1 29.0 - - - +
756E PHE* 2.7 47.1 + - - -
757E VAL* 3.8 1.0 + - - -
759E GLU* 1.3 73.3 - - - +
761E ARG* 1.3 69.5 + - - +
762E ARG* 3.1 36.9 + - - +
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Residues in contact with ARG 761 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770B ARG* 3.0 54.4 + - - +
771B LYS* 2.9 57.1 + - + +
773B LYS* 4.1 12.8 - - + -
748C PRO* 4.3 0.2 - - + -
757E VAL 2.8 12.6 + - - -
758E THR 2.9 25.5 + - - -
759E GLU 3.9 7.0 - - - +
760E SER* 1.3 79.9 - - - +
762E ARG* 1.4 58.2 + - - +
763E ALA 3.7 0.7 + - - -
802E GLU* 4.2 2.8 - - - +
803E VAL* 3.2 44.7 + - + +
805E ALA 2.8 20.4 + - - -
807E ALA* 3.5 13.8 - - - +
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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
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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