Contacts of the helix formed by residues 749 - 761 (chain B) in PDB entry 2VE9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747B ASP* 2.8 9.6 + - - +
748B PRO* 1.3 79.9 - - + +
750B TYR* 1.3 64.1 + - - +
751B ASP 3.4 2.5 - - - -
752B GLU* 3.1 37.9 + - - +
753B ALA* 2.9 22.2 + - - +
772B LEU* 4.0 24.7 - - + +
774B ILE* 3.7 20.9 - - + -
778B ARG* 3.5 30.7 - - - +
782B MET* 3.7 5.2 - - + -
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Residues in contact with TYR 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747B ASP* 3.0 22.1 + - + +
748B PRO 3.3 0.8 - - - -
749B LEU* 1.3 76.5 - - - +
751B ASP* 1.3 72.6 + - - +
753B ALA* 3.1 3.6 + - - +
754B VAL* 2.9 47.9 + - + +
782B MET* 3.5 24.2 - - + -
785B ALA* 3.7 30.2 + - + -
786B MET* 3.7 25.4 - - + -
789B ALA* 3.5 26.9 - - + +
791B VAL* 3.9 5.1 - - + +
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Residues in contact with ASP 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B PRO 4.7 5.2 + - - +
749B LEU 3.4 0.8 - - - -
750B TYR* 1.3 91.4 - - - +
752B GLU* 1.3 56.8 + - + +
754B VAL* 3.4 7.4 + - - +
755B ARG* 2.9 33.8 + - - +
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Residues in contact with GLU 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B PRO 5.3 2.0 - - - +
749B LEU* 3.1 38.8 + - + +
751B ASP* 1.3 76.2 - - + +
753B ALA* 1.3 59.2 + - - +
755B ARG* 3.3 35.7 + - - +
756B PHE* 2.9 27.9 + - - +
771B LYS* 6.0 0.2 - - - -
772B LEU* 3.6 22.1 - - + +
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Residues in contact with ALA 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749B LEU 2.9 7.9 + - - +
750B TYR 3.1 6.0 + - - +
752B GLU* 1.3 72.3 - - - +
754B VAL* 1.3 60.3 + - - +
756B PHE* 3.1 7.0 + - - +
757B VAL* 2.9 34.5 + - - +
768B VAL* 4.2 9.2 - - + -
772B LEU* 3.6 24.6 - - + +
782B MET* 4.1 13.5 - - + -
786B MET* 3.3 22.2 - - + -
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Residues in contact with VAL 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750B TYR* 2.9 58.2 + - + +
751B ASP* 3.7 7.6 - - - +
753B ALA* 1.3 74.8 - - - +
755B ARG* 1.3 63.3 + - - +
757B VAL* 3.4 0.7 + - - +
758B THR* 2.9 45.1 + - + +
786B MET* 3.9 18.2 - - + -
791B VAL* 4.4 13.9 - - + -
805B ALA* 5.8 0.9 - - + -
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Residues in contact with ARG 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751B ASP* 2.9 19.5 + - - +
752B GLU* 3.3 46.6 + - - +
754B VAL* 1.3 76.9 - - - +
756B PHE* 1.3 62.2 + - - +
758B THR* 3.7 6.1 - - - +
759B GLU* 3.1 52.4 + - + +
771B LYS* 5.9 4.9 - - - +
807B ALA 6.1 0.4 - - - +
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Residues in contact with PHE 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752B GLU 2.9 15.7 + - - +
753B ALA* 3.1 9.6 + - - +
755B ARG* 1.3 76.9 - - - +
757B VAL* 1.3 60.8 + - + +
759B GLU* 3.9 2.6 - - - +
760B SER* 2.8 56.1 + - - -
762B ARG* 4.5 15.3 - - - -
767B ALA* 3.8 42.6 - - + -
768B VAL* 3.9 21.1 - - + -
771B LYS* 3.6 44.4 - - + +
772B LEU* 5.6 0.4 - - + -
784C GLU* 5.7 5.4 - - - -
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Residues in contact with VAL 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753B ALA 2.9 17.8 + - - +
754B VAL 3.6 7.0 - - - +
756B PHE* 1.3 76.2 - - + +
758B THR* 1.3 68.6 + - + +
760B SER* 3.6 0.9 - - - -
761B ARG* 2.8 32.1 + - - -
762B ARG 3.3 24.9 - - - +
763B ALA* 4.7 1.3 - - - -
768B VAL* 3.7 25.8 - - + -
783B ILE* 4.5 6.5 - - + -
786B MET* 3.6 30.1 - - - -
791B VAL* 4.2 6.5 - - + -
792B VAL* 4.2 9.2 - - + -
803B VAL* 3.8 8.6 - - + +
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Residues in contact with THR 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754B VAL* 2.9 37.0 + - + +
755B ARG* 3.5 9.5 + - - +
757B VAL* 1.3 86.8 - - + +
759B GLU* 1.3 58.2 + - - +
761B ARG* 2.9 31.7 + - - +
791B VAL* 4.2 2.9 - - + -
803B VAL* 4.1 3.4 - - + -
805B ALA* 3.7 28.5 - - + -
806B PRO 3.5 15.2 + - - +
807B ALA* 3.3 22.2 + - - +
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Residues in contact with GLU 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755B ARG* 3.1 38.7 + - + +
756B PHE* 4.0 2.8 - - + +
758B THR* 1.3 82.3 - - - +
760B SER* 1.3 60.3 + - - +
761B ARG* 3.6 6.8 + - - +
807B ALA* 4.4 22.7 - - + +
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Residues in contact with SER 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B PHE* 2.8 39.3 + - - -
757B VAL* 3.6 4.5 + - - -
759B GLU* 1.3 76.0 - - - +
761B ARG* 1.3 68.3 + - - +
762B ARG* 3.0 49.7 + - - +
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Residues in contact with ARG 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757B VAL 2.8 15.9 + - - -
758B THR* 2.9 28.9 + - - +
759B GLU 4.1 5.6 - - - +
760B SER* 1.3 77.3 - - - +
762B ARG* 1.3 58.8 + - - +
763B ALA 4.0 1.0 + - - -
801B ARG 5.5 1.6 - - - +
802B GLU* 6.1 0.2 - - - -
803B VAL* 3.0 53.6 + - + +
804B ILE 4.2 2.0 + - - -
805B ALA 2.8 28.1 + - - -
806B PRO* 4.1 1.6 - - - +
807B ALA* 3.6 13.3 - - - +
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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