Contacts of the helix formed by residues 675 - 683 (chain B) in PDB entry 3JUE
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 ASP 675 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645B HIS* 4.1 2.2 - - - -
666B LEU 3.9 9.7 - - - +
667B GLY* 4.4 8.8 - - - -
668B ALA 3.3 13.0 - - - +
669B ARG* 3.4 29.3 + - - +
674B ARG* 1.3 75.3 - - - +
676B PRO* 1.3 77.2 - - + +
677B LEU* 3.8 16.6 - - - +
678B THR* 2.8 42.4 + - - -
679B ILE* 3.3 11.1 + - - +
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Residues in contact with PRO 676 (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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644B LEU* 3.5 41.1 - - + -
645B HIS* 3.7 20.0 - - + +
648B THR* 3.6 12.3 - - - +
665B ASP 4.6 1.8 - - - +
666B LEU 3.2 22.0 - - - +
668B ALA 3.6 10.3 - - - +
675B ASP* 1.3 83.3 - - + +
677B LEU* 1.3 61.3 + - - +
679B ILE* 3.3 6.0 + - + -
680B ALA* 3.0 20.1 + - - +
692B LEU* 3.4 23.0 - - + +
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Residues in contact with LEU 677 (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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666B LEU* 5.1 2.1 + - + +
675B ASP* 3.2 15.9 + - - +
676B PRO* 1.3 77.1 - - - +
678B THR* 1.3 63.9 + - - +
680B ALA* 3.2 2.8 + - - +
681B MET* 3.0 32.8 + - + +
689B VAL* 4.1 39.0 - - + +
692B LEU* 3.5 16.8 - - + +
693B ARG* 4.3 27.8 - - + +
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Residues in contact with THR 678 (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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669B ARG* 4.0 9.9 + - - -
674B ARG* 4.1 16.8 - - + -
675B ASP* 2.8 32.5 + - - -
677B LEU* 1.3 76.4 - - - +
679B ILE* 1.3 57.6 + - - +
681B MET* 3.4 5.0 + - - +
682B GLU* 3.0 54.9 + - + +
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Residues in contact with ILE 679 (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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645B HIS* 3.6 43.7 - - + +
648B THR* 3.8 13.5 - - + -
649B ILE* 3.8 35.9 - - + +
670B ASP* 4.3 0.2 - - - +
674B ARG* 4.0 35.9 - - + +
675B ASP 3.5 8.7 - - - +
676B PRO* 3.3 6.9 + - + +
677B LEU 3.2 0.8 - - - -
678B THR* 1.3 76.0 - - - +
680B ALA* 1.3 57.7 + - - +
682B GLU* 3.3 8.4 + - + +
683B THR* 2.8 39.7 + - + +
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Residues in contact with ALA 680 (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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648B THR* 3.4 14.7 - - + +
676B PRO 3.0 16.5 + - - +
677B LEU 3.2 2.9 + - - +
679B ILE* 1.3 76.7 - - - +
681B MET* 1.3 59.8 + - - +
683B THR* 3.2 6.5 + - - -
684B ALA 3.2 2.3 + - - -
685B ASN* 2.8 33.2 + - - +
688B ILE* 3.9 10.8 - - + -
689B VAL* 3.6 32.0 - - + +
692B LEU* 4.0 4.3 - - + -
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Residues in contact with MET 681 (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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677B LEU* 3.0 25.0 + - + +
678B THR* 3.7 8.5 - - - +
680B ALA* 1.3 74.4 - - - +
682B GLU* 1.3 61.0 + - + +
684B ALA* 2.9 22.7 + - - +
689B VAL* 3.7 36.7 - - + +
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Residues in contact with GLU 682 (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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674B ARG* 4.0 20.4 + - - +
678B THR* 3.0 44.0 + - + +
679B ILE* 3.8 6.5 - - - +
681B MET* 1.3 76.8 - - + +
683B THR* 1.3 61.7 + - + +
684B ALA* 3.2 1.7 + - - +
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Residues in contact with THR 683 (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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648B THR 4.4 7.3 + - - +
649B ILE* 4.6 15.5 - - + +
679B ILE* 2.8 32.2 + - + +
680B ALA* 3.2 12.3 + - - -
682B GLU* 1.3 77.1 - - + +
684B ALA* 1.3 69.0 + - - +
685B ASN* 3.3 10.0 + - - +
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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