Contacts of the helix formed by residues 75 - 87 (chain A) in PDB entry 5A2E
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU 3.7 5.7 - - - +
74A TRP* 1.3 81.3 - - - +
76A SER* 1.3 64.5 + - - +
77A ARG* 2.9 44.7 + - + +
78A ALA* 3.4 17.7 + - - +
79A ALA* 3.4 16.3 + - - +
94A ALA* 5.3 2.2 - - - -
127A LEU 5.4 0.7 - - - +
129A CYS* 5.2 4.7 + - - +
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Residues in contact with SER 76 (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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75A ASP* 1.3 71.5 - - - +
77A ARG* 1.4 66.6 + - - +
78A ALA 3.4 0.2 - - - -
79A ALA* 3.7 11.4 - - - +
80A GLU* 3.2 22.2 + - - +
91A ALA* 5.0 2.5 - - - +
94A ALA* 5.2 7.5 - - - +
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Residues in contact with ARG 77 (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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75A ASP* 2.9 25.7 + - - +
76A SER* 1.4 79.6 - - - +
78A ALA* 1.3 62.8 + - - +
80A GLU* 3.4 5.2 + - - +
81A ALA* 3.2 22.2 + - - +
129A CYS* 3.1 22.4 + - + -
130A SER* 2.8 29.5 + - - +
131A GLY* 3.8 26.7 - - - +
132A ALA* 3.9 17.1 - - + +
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Residues in contact with ALA 78 (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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74A TRP* 3.5 28.5 - - + -
75A ASP* 3.4 17.2 + - - +
77A ARG* 1.3 76.4 - - - +
79A ALA* 1.3 60.0 + - - +
81A ALA* 3.5 1.5 + - - +
82A VAL* 3.1 34.9 + - + +
127A LEU* 4.3 10.8 - - + +
129A CYS* 3.9 27.3 - - - -
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Residues in contact with ALA 79 (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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74A TRP* 3.7 25.7 - - + -
75A ASP 3.4 10.1 + - - +
76A SER* 3.7 13.9 - - - +
77A ARG 3.3 0.2 - - - -
78A ALA* 1.3 79.5 - - - +
80A GLU* 1.3 57.0 + - - +
82A VAL* 4.0 1.2 - - - +
83A CYS* 3.0 34.7 + - - -
91A ALA* 3.7 16.8 - - + -
94A ALA* 4.4 9.2 - - + -
153A VAL* 4.0 10.1 - - + -
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Residues in contact with GLU 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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76A SER 3.2 12.1 + - - +
77A ARG 3.7 7.9 - - - +
79A ALA* 1.3 75.9 - - - +
81A ALA* 1.3 60.2 + - - +
83A CYS* 3.4 1.0 + - - +
84A ARG* 2.9 71.1 + - + +
90A GLY* 3.4 9.6 - - - -
91A ALA* 3.0 31.0 + - + +
132A ALA* 4.3 23.3 - - + +
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Residues in contact with ALA 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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77A ARG 3.2 13.1 + - - +
78A ALA 3.8 3.4 - - - +
79A ALA 3.4 0.2 - - - -
80A GLU* 1.3 78.1 - - - +
82A VAL* 1.3 55.8 + - + +
84A ARG* 4.0 3.7 - - - +
85A ALA* 3.1 30.7 + - - +
132A ALA 4.6 1.5 + - - -
133A GLU* 3.5 33.9 - - - +
134A TRP* 3.7 13.2 - - + +
137A CYS* 3.6 22.7 - - - -
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Residues in contact with VAL 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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45A VAL* 3.6 33.9 - - + -
47A LEU* 5.0 6.7 - - + -
58A VAL* 4.8 7.9 - - + -
74A TRP* 4.1 15.9 - - + -
78A ALA* 3.1 21.7 + - + +
79A ALA 4.1 2.2 - - - +
81A ALA* 1.3 74.4 - - + +
83A CYS* 1.4 65.7 + - - +
85A ALA* 3.4 4.4 + - - +
86A LEU* 3.1 39.2 + - + +
127A LEU* 4.2 14.6 - - + -
129A CYS* 6.3 0.2 - - - -
134A TRP* 4.3 15.0 - - + -
137A CYS* 6.0 0.9 - - - -
153A VAL* 5.3 3.8 - - + -
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Residues in contact with CYS 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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47A LEU* 5.5 0.2 - - - -
79A ALA 3.0 22.1 + - - +
80A GLU 3.9 2.0 - - - +
82A VAL* 1.4 76.7 - - - +
84A ARG* 1.3 60.8 + - - +
86A LEU* 3.6 3.1 + - - +
87A GLY 3.3 4.3 + - - -
88A CYS* 2.9 27.9 + - - +
89A GLY 3.3 14.6 - - - +
90A GLY 3.9 6.1 - - - +
91A ALA* 4.1 5.4 - - - -
153A VAL* 4.0 18.6 - - - -
155A CYS* 2.0 55.2 - - + -
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Residues in contact with ARG 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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80A GLU* 2.9 46.4 + - + +
81A ALA* 4.2 4.0 - - - +
83A CYS* 1.3 72.2 - - - +
85A ALA* 1.3 65.2 + - - +
87A GLY* 3.3 12.3 + - - -
89A GLY* 3.3 22.5 - - - +
90A GLY* 3.1 24.7 - - - +
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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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45A VAL* 6.4 3.1 - - + -
81A ALA 3.1 20.6 + - - +
82A VAL* 3.4 5.4 + - - +
84A ARG* 1.3 76.9 - - - +
86A LEU* 1.3 61.5 + - + +
87A GLY* 3.4 0.9 + - - -
134A TRP* 4.0 31.9 - - + -
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Residues in contact with LEU 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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43A LEU 5.2 2.0 - - - +
45A VAL* 3.4 31.4 - - + +
46A ARG* 4.1 7.0 - - + -
47A LEU* 3.5 36.1 - - + +
53A SER 5.1 3.4 - - - +
82A VAL* 3.1 37.3 + - + +
83A CYS* 4.0 3.8 - - - +
85A ALA* 1.3 76.9 - - + +
87A GLY* 1.3 60.3 + - - +
88A CYS* 3.9 17.1 - - - -
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Residues in contact with GLY 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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54A CYS* 4.5 1.9 - - - -
83A CYS 3.3 2.2 + - - -
84A ARG 3.3 9.8 + - - -
85A ALA 3.2 4.6 - - - -
86A LEU* 1.3 79.0 - - - +
88A CYS* 1.3 62.8 + - - +
89A GLY 3.7 2.7 - - - -
157A GLU* 4.7 5.2 - - - +
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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