Contacts of the helix formed by residues 80 - 91 (chain A) 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 LEU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A VAL* 5.4 0.9 - - + -
49A HIS* 3.5 50.0 - - + +
52A VAL* 4.0 25.6 - - + -
68A ILE* 4.1 10.5 - - + +
75A LEU* 3.8 34.5 - - + -
78A ASN 3.9 9.6 - - - +
79A SER* 1.3 89.1 + - - +
81A SER* 1.3 58.9 + - - +
82A PHE 3.2 2.5 - - - -
83A GLU* 3.2 24.1 + - + +
84A LYS* 2.8 29.4 + - - +
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Residues in contact with SER 81 (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 SER* 3.6 4.6 + - - -
80A LEU* 1.3 74.9 - - - +
82A PHE* 1.3 57.3 + - - +
84A LYS* 4.4 2.7 - - - -
85A ALA* 2.9 33.3 + - - +
100A THR* 3.4 20.6 + - - +
103A SER 5.1 0.5 + - - -
104A ALA* 3.7 24.6 - - - -
111A LEU* 4.2 6.3 - - - -
202A SO4 2.6 36.3 + - - -
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Residues in contact with PHE 82 (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 LEU 3.2 0.2 - - - -
81A SER* 1.3 78.7 - - - +
83A GLU* 1.3 78.6 + - + +
85A ALA* 3.7 2.0 - - - +
86A TYR* 2.8 36.2 + - + +
108A THR* 5.1 1.8 - - - +
110A LYS* 3.4 49.4 - - + -
111A LEU* 3.6 23.4 - - + +
114A LEU* 4.1 20.0 - - + -
202A SO4 4.9 0.2 + - - -
594B ALA* 3.4 30.1 - - + -
597B HIS* 3.8 20.4 - - + -
598B VAL* 3.8 23.8 - - + -
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Residues in contact with GLU 83 (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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49A HIS* 2.7 34.3 + - + +
52A VAL* 3.7 30.1 - - + -
53A VAL* 4.4 9.7 - - + +
56A ILE* 4.0 11.2 - - + -
68A ILE* 4.1 2.2 - - + -
80A LEU* 3.2 26.4 + - + +
82A PHE* 1.3 99.0 - - + +
84A LYS* 1.3 63.2 + - - +
86A TYR* 3.3 6.6 + - - +
87A CYS* 3.0 29.6 + - - -
110A LYS* 4.6 9.2 + - - +
598B VAL* 5.2 2.5 - - + -
599B ALA 4.7 2.3 + - - +
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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
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65A LEU* 3.8 13.1 - - + +
68A ILE* 3.6 29.3 - - + +
69A ASN* 3.7 22.0 - - - +
80A LEU 2.8 21.2 + - - +
81A SER* 3.9 4.7 - - - +
83A GLU* 1.3 74.1 - - - +
85A ALA* 1.3 62.4 + - - +
87A CYS* 3.3 2.3 + - - +
88A GLU* 2.8 51.9 + - - +
100A THR* 2.9 24.3 + - + +
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Residues in contact with ALA 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 SER 2.9 19.0 + - - +
82A PHE* 4.6 0.4 - - - -
84A LYS* 1.3 76.9 - - - +
86A TYR* 1.3 58.2 + - - +
88A GLU* 3.3 10.9 + - - -
89A TYR* 2.8 30.7 + - - +
97A ALA* 3.5 15.8 - - - +
100A THR* 3.7 7.1 - - + +
101A ILE* 3.7 29.8 - - + -
114A LEU* 3.7 10.7 - - + +
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Residues in contact with TYR 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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56A ILE* 3.8 33.4 - - + -
61A PHE* 4.3 2.0 - + - -
82A PHE* 2.8 26.8 + + + +
83A GLU* 3.6 8.1 - - - +
84A LYS 3.2 0.2 - - - -
85A ALA* 1.3 76.8 - - - +
87A CYS* 1.3 60.8 + - - +
89A TYR* 3.3 13.6 + + - +
90A ARG* 2.9 61.8 + - + +
114A LEU* 3.5 15.4 - - + +
592B ASP* 2.4 40.1 + - - -
594B ALA* 3.9 21.3 - - + -
595B LEU* 3.3 20.9 - - + +
598B VAL* 4.3 7.4 - - + -
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Residues in contact with CYS 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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52A VAL* 5.3 0.9 - - - -
56A ILE* 3.7 18.6 - - - -
61A PHE* 3.6 35.9 - - + +
64A ALA* 3.7 21.1 - - - -
65A LEU* 4.1 16.8 - - + -
68A ILE* 5.3 0.7 - - - -
83A GLU 3.0 22.2 + - - +
84A LYS* 3.7 4.5 - - - +
86A TYR* 1.3 76.8 - - - +
88A GLU* 1.3 58.3 + - - +
90A ARG* 3.1 4.2 + - - +
91A LEU* 2.9 36.1 + - + +
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Residues in contact with GLU 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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65A LEU* 4.1 18.0 - - + +
69A ASN* 5.7 0.2 + - - -
84A LYS* 2.8 50.3 + - - +
85A ALA* 3.3 3.7 + - - +
87A CYS* 1.3 75.0 - - - +
89A TYR* 1.3 61.0 + - - +
91A LEU* 3.2 10.2 + - - -
93A ARG* 2.9 51.4 + - + +
96A ASN* 3.3 28.2 + - + +
97A ALA* 3.5 4.4 - - - +
100A THR* 2.8 26.5 + - - -
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Residues in contact with TYR 89 (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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85A ALA 2.8 18.1 + - - +
86A TYR* 3.3 11.0 - + - +
87A CYS 3.2 0.2 - - - -
88A GLU* 1.3 75.7 - - - +
90A ARG* 1.3 79.4 + - - +
91A LEU 3.3 0.7 + - - -
92A ASN* 3.3 10.4 + - - -
93A ARG 4.8 2.9 - - - +
94A ILE* 3.8 21.1 + - + +
97A ALA* 3.8 10.2 - - + +
114A LEU* 3.9 13.9 - - + -
117A GLN* 3.2 54.8 + - + +
118A VAL* 3.9 7.6 - - + -
121A ARG* 3.5 56.0 + - - -
201A SO4 4.6 3.7 + - - -
590B PHE* 5.0 6.4 - - - -
592B ASP* 4.4 11.9 - - - +
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Residues in contact with ARG 90 (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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61A PHE* 3.4 56.6 - - + -
86A TYR* 2.9 61.5 + - + +
87A CYS 3.1 4.0 + - - +
89A TYR* 1.3 88.1 - - - +
91A LEU* 1.3 60.2 + - - +
92A ASN* 3.3 3.3 + - - +
121A ARG* 5.5 0.2 - - - +
201A SO4 4.5 30.2 + - - -
592B ASP* 3.8 8.6 + - - -
595B LEU* 4.5 11.9 - - - +
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Residues in contact with LEU 91 (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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61A PHE* 4.0 21.8 - - + -
62A LYS* 3.9 40.4 - - + +
65A LEU* 3.9 25.8 - - + -
87A CYS 2.9 20.2 + - - +
88A GLU 3.2 4.4 + - - +
90A ARG* 1.3 79.2 - - - +
92A ASN* 1.3 70.3 + - - +
93A ARG* 3.2 23.6 + - - +
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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