Contacts of the helix formed by residues 79 - 88 (chain A) in PDB entry 5A5J
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 GLY 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 1.3 82.4 - - - +
80A TYR* 1.3 67.1 + - - -
81A GLU 3.3 3.3 + - - -
82A ALA 3.5 0.2 + - - -
83A VAL* 3.3 18.7 + - - +
393A SER* 2.7 27.8 + - - -
394A VAL* 3.8 5.6 - - - +
397A ASP* 5.8 1.3 - - - -
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY* 1.3 72.2 - - - -
81A GLU* 1.3 80.5 + - + +
83A VAL* 4.8 1.1 - - + -
84A LYS* 2.8 64.4 + - + +
88A ILE* 5.3 3.2 - - + +
393A SER 4.9 1.4 + - - -
394A VAL* 3.9 20.5 - - + +
397A ASP* 5.2 3.4 + - - +
423A LYS* 3.3 64.8 + - + +
424A TYR* 3.0 53.9 - + + +
426A MET* 4.4 11.2 - - + -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY 3.4 1.2 - - - -
80A TYR* 1.3 98.0 - - + +
82A ALA* 1.3 58.3 + - - +
84A LYS* 3.9 9.8 - - - +
85A GLU* 2.9 31.9 + - - +
377A ARG* 3.6 13.5 + - - +
424A TYR* 4.2 8.6 + - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO* 4.8 2.2 - - + -
64A VAL* 4.1 12.1 - - + -
77A LEU* 3.9 22.8 - - + +
78A HIS 3.8 21.5 + - - +
79A GLY 3.5 1.4 + - - +
80A TYR 3.2 0.4 - - - -
81A GLU* 1.3 77.0 - - - +
83A VAL* 1.3 60.5 + - - +
85A GLU* 3.3 3.3 + - - +
86A ALA* 3.0 31.5 + - - +
376A PHE* 4.1 3.9 - - + -
377A ARG* 3.6 17.8 - - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.1 28.9 - - + +
79A GLY 3.3 19.0 + - - +
80A TYR* 4.1 1.6 - - - +
82A ALA* 1.3 73.4 - - - +
84A LYS* 1.3 66.8 + - - +
86A ALA* 4.6 3.1 - - - -
87A LEU* 3.0 49.5 + - + +
88A ILE* 5.2 0.3 - - - +
389A ILE* 4.1 20.2 - - + -
390A SER 5.0 0.9 - - - +
391A LEU* 5.5 0.4 - - + -
394A VAL* 4.0 16.4 - - + -
426A MET* 4.4 22.0 - - + -
430A ALA* 5.1 0.4 - - + +
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 2.8 56.8 + - + +
81A GLU* 3.9 11.4 - - - +
83A VAL* 1.3 74.9 - - - +
85A GLU* 1.3 65.7 + - - +
88A ILE* 3.0 55.0 + - + +
89A ASP* 2.7 38.0 + - - +
423A LYS* 6.1 1.6 - - - +
426A MET* 5.5 2.6 - - - +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 2.9 17.4 + - - +
82A ALA* 3.7 4.9 - - - +
83A VAL 3.2 0.2 - - - -
84A LYS* 1.3 78.1 - - + +
86A ALA* 1.3 57.4 + - - +
89A ASP* 3.2 24.8 + - + +
90A LEU* 3.0 32.0 + - + +
376A PHE* 3.8 15.6 - - + -
377A ARG* 3.1 53.8 + - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.6 25.1 - - + -
82A ALA 3.0 17.7 + - - +
83A VAL 4.0 0.9 - - - +
85A GLU* 1.3 76.8 - - - +
87A LEU* 1.3 63.3 + - + +
90A LEU* 2.8 35.1 + - - +
94A PHE* 3.4 29.4 - - + -
376A PHE* 4.2 9.2 - - + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 5.2 1.3 - - + -
83A VAL* 3.0 32.4 + - + +
86A ALA* 1.3 85.3 - - + +
88A ILE* 1.3 59.5 - - - +
91A GLY* 3.0 20.4 - - - +
94A PHE* 4.1 26.7 - - + +
368A HIS* 4.6 12.3 - - + +
389A ILE* 4.1 30.3 - - + -
391A LEU* 6.0 0.4 - - + -
429A SER* 4.0 9.0 - - - +
430A ALA* 3.4 42.6 - - + +
431A GLY* 3.6 13.8 - - - -
432A LYS 4.4 0.3 + - - -
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TYR* 5.3 2.5 - - - +
84A LYS* 3.0 40.8 + - + +
87A LEU* 1.3 78.3 - - + +
89A ASP* 1.3 77.8 + - - +
90A LEU 3.2 1.3 - - - -
91A GLY* 3.3 11.8 + - - -
426A MET* 4.5 9.6 - - + -
430A ALA* 4.4 22.7 - - + -
431A GLY* 4.5 7.9 - - - +
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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