Contacts of the helix formed by residues 659 - 666 (chain B) in PDB entry 5J3V
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 ILE 659 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609B TYR* 4.4 15.5 - - + -
648B LEU* 4.5 4.5 - - + +
651B LEU* 4.1 12.8 - - + -
652B ALA* 3.8 31.0 - - + +
655B LEU* 4.6 11.4 - - + +
656B GLY 3.3 16.3 + - - +
657B GLY 3.1 1.0 - - - -
658B ASN* 1.3 76.9 - - - +
660B GLU* 1.3 65.7 + - - +
661B GLN 3.3 2.7 - - - -
662B LEU* 3.2 24.9 + - + -
663B VAL* 3.0 28.1 + - + +
668B ILE* 5.9 0.9 - - + -
694B LEU* 4.1 12.3 - - + -
697B ALA* 4.1 3.8 - - + -
698B CYS* 3.8 23.1 - - + -
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Residues in contact with GLU 660 (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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657B GLY* 3.1 23.2 - - - +
658B ASN 3.2 1.0 - - - -
659B ILE* 1.3 78.2 - - - +
661B GLN* 1.3 65.2 - - + +
663B VAL 3.5 0.2 + - - -
664B ALA* 3.0 21.0 + - - +
697B ALA 3.8 10.7 - - - +
698B CYS* 3.6 16.2 - - + -
700B GLN* 3.1 34.0 + - - +
701B HIS* 3.2 16.9 + - - +
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Residues in contact with GLN 661 (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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658B ASN 4.4 8.2 + - - +
659B ILE 3.3 1.0 - - - -
660B GLU* 1.3 80.4 - - + +
662B LEU* 1.3 65.6 + - + +
664B ALA* 3.6 3.0 + - - +
665B ARG* 3.2 37.9 + - - +
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Residues in contact with LEU 662 (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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605B CYS* 4.1 25.4 - - + +
606B GLU* 3.8 32.3 - - + +
609B TYR* 3.0 62.6 + - + -
651B LEU* 5.5 0.4 - - + -
655B LEU* 5.0 3.4 - - + -
658B ASN 5.1 3.1 + - - +
659B ILE* 3.2 21.2 + - + +
661B GLN* 1.3 82.6 - - + +
663B VAL* 1.3 62.8 + - - +
665B ARG* 3.5 5.7 + - - +
666B SER* 3.1 15.8 + - - -
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Residues in contact with VAL 663 (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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609B TYR* 3.3 14.1 - - + +
659B ILE* 3.0 30.0 + - + +
660B GLU 3.9 2.7 - - - +
662B LEU* 1.3 76.2 - - - +
664B ALA* 1.3 63.9 + - - +
665B ARG 3.2 0.7 + - - -
666B SER* 3.3 18.7 + - - +
667B ASN* 4.4 0.9 + - - -
668B ILE* 4.7 6.7 + - + +
669B LEU* 4.7 14.7 - - + +
694B LEU* 3.9 27.4 - - + -
698B CYS* 3.9 18.2 - - - -
701B HIS* 3.8 28.9 - - + -
702B VAL* 6.4 0.2 - - + -
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Residues in contact with ALA 664 (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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660B GLU 3.0 19.3 + - - +
661B GLN* 4.1 5.2 - - - +
663B VAL* 1.3 78.5 - - - +
665B ARG* 1.3 62.4 + - + +
666B SER 4.0 4.2 - - - +
701B HIS* 3.4 26.2 - - + +
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Residues in contact with ARG 665 (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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661B GLN* 3.2 25.7 + - - +
662B LEU* 4.1 6.3 - - - +
663B VAL 3.2 0.6 - - - -
664B ALA* 1.3 77.7 - - + +
666B SER* 1.3 64.7 + - - +
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Residues in contact with SER 666 (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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609B TYR* 2.3 40.5 + - - -
610B GLN* 5.3 7.2 - - - -
613B VAL* 4.8 7.9 - - - -
662B LEU 3.1 7.5 + - - -
663B VAL 3.3 11.7 + - - +
664B ALA 4.0 4.3 - - - +
665B ARG* 1.3 81.4 - - - +
667B ASN* 1.3 70.8 + - - +
668B ILE* 3.6 8.7 - - - +
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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