Contacts of the helix formed by residues 747 - 754 (chain E) in PDB entry 6V3O
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 PRO 747 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746E THR* 1.3 85.5 - - - +
748E GLU* 1.3 62.6 + - - +
749E THR 3.2 2.7 - - - -
750E GLU* 3.1 12.8 + - - +
751E TYR* 2.9 22.5 + - - +
779E PHE* 5.4 2.5 - - + -
780E SER* 3.9 13.0 - - - +
783E GLN* 4.0 16.2 - - + -
784E THR* 3.9 12.6 - - + -
905E GLN* 4.0 20.9 - - - +
909E LEU* 4.1 20.9 - - + -
913E ARG* 4.2 2.0 - - - +
959E MET* 3.9 20.4 - - + -
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Residues in contact with GLU 748 (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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742E PHE* 3.6 23.6 - - + +
743E ARG* 3.8 24.9 + - - +
746E THR* 3.1 17.8 + - - +
747E PRO* 1.3 75.7 - - - +
749E THR* 1.3 64.1 + - - +
751E TYR* 3.3 7.1 + - - +
752E GLY* 3.2 16.8 + - - -
761E ALA* 3.8 16.3 - - - +
772E LEU* 3.5 21.6 - - - +
776E PRO* 3.3 23.1 - - - +
780E SER* 2.6 37.0 + - - +
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Residues in contact with THR 749 (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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743E ARG* 3.3 51.4 + - - +
746E THR 4.7 0.8 + - - -
747E PRO 3.2 0.6 - - - -
748E GLU* 1.3 78.3 - - - +
750E GLU* 1.3 75.0 + - - +
752E GLY* 3.3 2.8 + - - -
753E ARG* 3.1 65.5 + - + +
913E ARG* 5.0 0.9 - - - -
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Residues in contact with GLU 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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747E PRO* 3.1 10.3 + - - +
749E THR* 1.3 81.5 - - - +
751E TYR* 1.3 66.3 + - - +
753E ARG* 4.5 7.5 + - - +
754E MET* 3.0 39.4 + - + +
909E LEU* 3.6 20.8 - - + +
912E ILE* 4.6 11.5 - - + +
913E ARG* 3.0 47.4 + - - +
947E TYR* 5.8 2.2 - - + +
955E LEU* 3.9 24.2 - - + -
959E MET* 4.3 4.9 - - + -
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Residues in contact with TYR 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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178E PRO* 4.4 4.5 + - - +
747E PRO* 2.9 14.3 + - + +
748E GLU* 3.3 16.4 - - - +
750E GLU* 1.3 77.7 - - - +
752E GLY* 1.3 63.8 + - - +
755E ASN 3.3 0.5 + - - -
756E ILE* 3.1 79.3 + - + +
757E GLY* 3.8 11.4 - - - -
759E ARG 5.9 1.6 - - - -
761E ALA* 4.6 6.1 - - + -
775E ILE* 3.8 21.8 - - - +
776E PRO* 3.9 35.4 - - + +
779E PHE* 3.4 45.7 - + + -
780E SER* 4.8 1.3 - - - +
959E MET* 4.2 6.1 - - + +
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Residues in contact with GLY 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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748E GLU* 3.2 9.5 + - - -
749E THR 3.3 2.4 + - - -
750E GLU 3.2 0.6 - - - -
751E TYR* 1.3 85.8 - - - +
753E ARG* 1.3 64.5 + - - +
755E ASN* 3.1 15.1 + - - +
756E ILE 5.4 0.7 - - - -
759E ARG 5.5 3.9 - - - +
761E ALA* 4.5 16.6 - - - -
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Residues in contact with ARG 753 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743E ARG* 6.0 0.6 - - - +
749E THR* 3.1 43.7 + - + +
750E GLU* 3.4 7.5 + - - +
752E GLY* 1.3 77.2 - - - +
754E MET* 1.3 60.9 + - - +
755E ASN* 3.2 2.3 + - - +
947E TYR* 4.5 15.6 + - - +
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Residues in contact with MET 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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234E GLN* 4.5 8.4 + - - +
750E GLU* 3.0 27.0 + - + +
753E ARG* 1.3 73.6 - - - +
755E ASN* 1.3 69.8 + - - +
756E ILE* 3.5 15.5 + - + +
912E ILE* 4.0 13.9 - - + -
947E TYR* 3.8 42.0 - - + +
952E GLU* 4.6 17.5 - - - +
955E LEU* 3.7 32.5 - - + -
956E ILE* 4.5 22.0 - - + -
959E MET* 5.1 4.3 - - - -
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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