Contacts of the helix formed by residues 592 - 598 (chain B) in PDB entry 5M72
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 592 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A TYR* 2.4 31.4 + - - -
89A TYR* 4.4 7.9 - - + +
90A ARG* 3.8 13.3 + - - -
117A GLN* 2.9 25.6 + - - +
201A SO4 5.5 4.3 + - - +
590B PHE 4.0 1.8 + - - -
591B PHE* 1.3 68.6 - - - +
593B LEU* 1.3 61.9 + - - +
594B ALA* 3.3 4.2 + - - +
595B LEU* 3.2 30.9 + - + +
596B ASN* 4.4 3.8 + - - -
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Residues in contact with LEU 593 (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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113A GLU* 3.7 26.7 - - - +
117A GLN* 3.0 7.2 + - - +
143A TYR* 3.9 11.9 - - + +
146A GLU* 3.8 22.7 - - + -
147A ARG* 3.6 52.3 - - + +
150A ASN* 4.3 6.7 - - - +
591B PHE* 3.0 22.2 + - + +
592B ASP* 1.3 71.5 - - - +
594B ALA* 1.3 65.5 + - - +
596B ASN* 3.0 36.4 + - - +
597B HIS* 3.4 11.1 + - - -
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Residues in contact with ALA 594 (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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82A PHE* 3.4 14.4 - - + -
86A TYR* 3.9 18.6 - - + -
113A GLU* 3.8 1.7 - - - +
114A LEU* 4.0 23.3 - - + +
117A GLN* 2.9 19.6 + - - +
592B ASP* 3.2 10.1 - - - +
593B LEU* 1.3 77.0 - - - +
595B LEU* 1.3 62.5 + - - +
597B HIS* 2.9 29.7 + - - +
598B VAL* 3.8 1.0 + - - +
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Residues in contact with LEU 595 (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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56A ILE* 4.4 13.2 - - + +
57A GLN* 4.3 15.4 + - - +
61A PHE* 5.8 0.4 - - + -
86A TYR* 3.3 34.5 - - + +
90A ARG* 4.5 10.1 - - - +
592B ASP* 3.2 23.7 + - + +
593B LEU 3.1 0.2 - - - -
594B ALA* 1.3 76.3 - - - +
596B ASN* 1.3 63.6 + - - +
598B VAL* 3.1 25.6 + - + +
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Residues in contact with ASN 596 (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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143A TYR* 3.4 56.9 + - + +
592B ASP 4.5 3.2 + - - -
593B LEU* 3.0 33.9 + - - +
595B LEU* 1.3 79.7 - - - +
597B HIS* 1.3 62.3 - - + +
598B VAL 3.3 3.3 + - - +
599B ALA* 5.3 3.1 - - - +
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Residues in contact with HIS 597 (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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82A PHE* 3.8 7.7 - - + -
109A ASP* 4.7 7.8 - - + +
110A LYS* 3.2 59.6 + - + +
113A GLU* 2.9 42.2 + - + +
141A ASP* 4.9 9.4 - - - -
147A ARG* 4.6 2.0 + - - -
593B LEU 3.4 23.7 + - - -
594B ALA* 2.9 12.8 + - - +
596B ASN* 1.3 80.2 - - + +
598B VAL* 1.3 57.3 + - - +
599B ALA* 3.1 11.8 + - - +
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Residues in contact with VAL 598 (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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27A PHE* 5.3 0.9 - - - -
53A VAL* 3.9 25.1 - - + +
56A ILE* 3.7 43.7 - - + -
57A GLN* 2.8 32.9 + - - +
82A PHE* 3.8 17.5 - - + -
83A GLU* 5.2 3.1 - - + -
86A TYR* 4.3 9.4 - - + -
594B ALA 3.8 10.8 - - - +
595B LEU* 3.1 23.4 + - + +
596B ASN 3.3 2.5 - - - +
597B HIS* 1.3 73.0 - - - +
599B ALA* 1.3 60.8 + - - +
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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