Contacts of the helix formed by residues 73 - 78 (chain 6) in PDB entry 3J7Y
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 THR 73 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686 PRO 4.2 20.5 + - - +
696 HIS* 4.2 9.6 - - - +
716 TRP* 3.3 17.7 + - - -
726 ARG* 1.3 83.3 + - - +
746 TYR* 1.3 66.1 + - - +
756 ARG* 3.9 14.4 - - + +
766 GLU* 4.0 16.0 - - + +
776 TYR* 3.7 9.4 - - - -
100W THR* 3.2 31.9 - - - +
101W LYS 4.0 3.0 - - - +
102W GLU* 3.8 13.1 + - - -
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Residues in contact with TYR 74 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736 THR* 1.3 75.6 + - - +
756 ARG* 1.3 69.5 + - + +
776 TYR* 3.1 15.5 + - - +
786 PHE* 3.3 46.2 + + + +
796 GLY 5.0 0.2 - - - -
64P GLU* 2.6 34.7 + - - -
67P TRP* 3.2 38.1 + + - -
74P ARG* 3.8 18.4 - - - -
100W THR* 4.8 3.1 - - - -
102W GLU* 2.6 24.9 + - - +
132W HIS* 5.2 5.2 - + - -
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Residues in contact with ARG 75 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656 ALA 2.8 20.0 + - - -
666 GLN* 2.8 32.4 + - - +
676 ALA 3.6 6.7 + - - -
686 PRO* 4.9 6.4 + - - +
736 THR* 3.6 8.1 - - + +
746 TYR* 1.3 81.6 - - - +
766 GLU* 1.3 63.7 + - - +
796 GLY* 3.4 40.3 + - - +
97P ASN 6.0 1.8 - - - -
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Residues in contact with GLU 76 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726 ARG* 3.5 45.1 + - + +
736 THR* 4.0 16.2 - - + +
746 TYR 3.1 0.4 + - - -
756 ARG* 1.3 81.2 - - - +
776 TYR* 1.3 71.4 + - + +
786 PHE 3.7 0.5 + - - -
796 GLY 5.6 0.3 - - - -
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Residues in contact with TYR 77 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726 ARG* 3.8 35.6 - - + +
736 THR 3.7 16.8 - - - -
746 TYR 3.1 6.3 + - - +
766 GLU* 1.3 89.0 - - + +
786 PHE* 1.3 64.9 + - + +
2062A A 3.8 12.0 + - - +
2063A G 5.2 0.5 - - - -
57W GLU* 3.6 20.3 + - - -
98W ARG* 3.5 48.1 + - + -
99W TYR 3.9 6.0 + - - -
100W THR* 3.7 14.6 - - + -
132W HIS* 5.1 2.2 - + + -
134W VAL* 3.8 35.4 - - + +
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Residues in contact with PHE 78 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746 TYR* 3.3 35.9 + + + +
766 GLU 3.5 1.2 - - - -
776 TYR* 1.3 87.6 - - + +
796 GLY* 1.3 67.5 + - - +
64P GLU* 4.3 7.6 - - - +
79W ALA* 3.4 28.7 - - + -
80W HIS* 3.9 9.0 - + - -
132W HIS* 4.0 15.9 - + + -
133W VAL 3.4 22.2 - - - -
134W VAL* 4.0 13.0 - - + -
135W PRO* 3.8 22.2 - - + -
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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