Contacts of the helix formed by residues 747 - 754 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746D THR* 1.3 86.2 - - - +
748D GLU* 1.3 62.0 + - - +
749D THR 3.3 2.5 - - - -
750D GLU* 3.3 13.7 + - + +
751D TYR* 2.9 22.8 + - + +
779D PHE* 5.4 2.0 - - + -
780D SER* 3.8 15.9 - - - +
783D GLN* 4.0 17.7 - - + +
784D THR* 4.0 9.0 - - + -
844D TYR* 5.1 0.7 - - + -
905D GLN* 4.0 22.0 - - + +
909D LEU* 4.0 24.2 - - + -
913D ARG* 4.1 3.1 - - - +
955D LEU* 5.5 2.2 - - + -
959D MET* 5.0 11.4 - - - -
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Residues in contact with GLU 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742D PHE* 3.6 21.3 - - + +
743D ARG* 3.3 27.9 + - - +
746D THR* 3.1 20.4 + - - +
747D PRO* 1.3 77.8 - - - +
749D THR* 1.3 63.3 + - - +
751D TYR* 3.3 10.4 - - - +
752D GLY* 3.2 16.5 + - - -
761D ALA* 3.9 14.2 - - - +
762D LYS* 5.6 0.2 - - - +
772D LEU* 3.6 21.5 - - - +
776D PRO* 3.4 21.9 - - - +
780D SER* 3.3 23.7 + - - +
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Residues in contact with THR 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743D ARG* 3.4 49.8 + - + +
746D THR 4.8 0.6 + - - -
748D GLU* 1.3 75.7 - - - +
750D GLU* 1.3 85.7 + - - +
752D GLY* 3.2 3.5 + - - -
753D ARG* 2.9 47.2 + - - +
913D ARG* 4.3 4.5 + - - -
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Residues in contact with GLU 750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747D PRO* 3.3 13.3 + - + +
749D THR* 1.3 87.1 + - - +
751D TYR* 1.3 59.4 + - - +
753D ARG* 4.2 13.5 + - + +
754D MET* 2.8 39.4 + - + +
909D LEU* 3.7 16.2 - - + -
912D ILE* 4.7 4.5 - - + +
913D ARG* 2.8 43.6 + - - +
947D TYR* 4.0 23.1 - - + +
955D LEU* 4.2 21.1 - - + -
959D MET* 5.6 0.9 - - - -
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Residues in contact with TYR 751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D PRO* 4.7 3.4 + - - +
747D PRO* 2.9 14.3 + - + +
748D GLU* 3.3 26.0 - - - +
750D GLU* 1.3 75.7 - - - +
752D GLY* 1.3 63.8 + - - +
755D ASN* 3.3 1.9 + - - -
756D ILE* 3.1 77.6 + - + +
757D GLY* 3.8 10.6 - - - -
759D ARG 5.9 1.8 - - - -
761D ALA* 4.7 6.3 - - + -
775D ILE* 3.8 22.0 - - - +
776D PRO* 3.9 25.7 - - + +
779D PHE* 3.4 48.7 - + + -
780D SER* 5.8 0.2 - - - -
959D MET* 4.9 6.3 - - - -
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Residues in contact with GLY 752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D GLU* 3.2 6.3 + - - -
749D THR 3.2 7.2 + - - -
751D TYR* 1.3 84.5 - - - +
753D ARG* 1.3 59.1 + - - +
755D ASN* 3.0 24.0 + - - +
756D ILE 5.6 0.2 - - - -
759D ARG 5.7 2.5 - - - +
761D ALA* 4.6 15.9 - - - -
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Residues in contact with ARG 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749D THR* 2.9 35.8 + - - +
750D GLU* 3.4 7.0 + - - +
752D GLY* 1.3 76.4 - - - +
754D MET* 1.3 60.5 + - - +
755D ASN* 3.4 2.4 + - - +
946D GLU* 4.2 22.0 - - - +
947D TYR* 3.8 21.5 + - - +
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Residues in contact with MET 754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ARG* 5.6 4.0 + - - -
750D GLU* 2.8 22.0 + - + +
753D ARG* 1.3 75.0 - - - +
755D ASN* 1.3 69.8 + - - +
756D ILE* 3.4 17.4 + - + +
912D ILE* 4.4 0.9 - - + -
946D GLU* 5.5 1.1 - - - -
947D TYR* 3.7 37.9 - - + +
952D GLU* 3.6 47.9 - - + +
955D LEU* 3.7 24.7 - - + -
956D ILE* 4.1 9.3 - - + +
959D MET* 4.1 23.3 - - - -
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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