Contacts of the helix formed by residues 81 - 88 (chain A) in PDB entry 2A5E
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 PRO 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.7 9.2 - - + -
50A GLN* 4.0 35.2 - - + +
54A MET* 4.7 1.9 - - - +
69A GLU 3.3 10.1 - - - +
70A PRO* 3.0 35.2 - - + +
72A CYS 3.5 14.6 - - - +
79A THR 4.4 0.9 - - - +
80A ARG* 1.3 96.7 - - + +
82A VAL* 1.3 61.7 + - - +
83A HIS 3.2 0.6 + - - -
84A ASP* 3.3 16.4 + - + +
85A ALA* 3.4 8.3 + - - +
97A LEU* 4.0 10.7 - - + +
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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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70A PRO 4.5 1.3 - - - +
80A ARG* 4.3 9.0 - - + -
81A PRO* 1.3 79.7 - - - +
83A HIS* 1.3 70.0 + - + +
85A ALA* 3.5 7.0 + - - +
86A ALA* 3.5 17.7 + - - +
94A LEU* 5.1 0.9 - - + -
97A LEU* 4.2 17.5 - - + -
103A ARG 3.3 27.1 - - - +
104A LEU* 3.4 39.5 - - + -
106A VAL* 5.7 0.2 - - + -
114A PRO* 3.3 28.2 - - + +
130A LEU* 3.6 9.2 - - + +
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Residues in contact with HIS 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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79A THR* 4.8 6.7 - - + -
80A ARG* 3.3 18.4 + - + +
81A PRO 3.2 0.4 - - - -
82A VAL* 1.3 74.3 - - + +
84A ASP* 1.3 59.8 + - - +
85A ALA 3.0 0.3 + - - -
86A ALA* 3.1 3.8 + - - -
87A ARG* 2.5 41.6 + - + +
106A VAL* 3.7 24.0 - - + -
108A ASP* 2.9 38.2 + - - +
112A ARG 4.2 2.4 + - - -
113A LEU* 3.5 7.7 - - - -
114A PRO* 3.1 52.6 - - + +
117A LEU* 3.9 18.5 - - + +
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Residues in contact with ASP 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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46A ARG* 5.3 4.7 + - - -
50A GLN* 2.4 61.4 - - + +
54A MET* 2.8 40.0 - - + +
79A THR* 4.3 6.9 - - - +
80A ARG 3.7 3.8 - - - +
81A PRO 3.4 7.2 - - - +
83A HIS* 1.3 76.7 - - - +
85A ALA* 1.3 64.7 + - - +
87A ARG* 3.4 17.2 - - - +
88A GLU 3.4 2.8 + - - -
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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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54A MET* 3.8 6.2 - - - +
81A PRO 3.4 6.2 + - - +
82A VAL 3.7 7.6 - - - +
83A HIS 3.1 0.4 - - - -
84A ASP* 1.3 82.6 - - - +
86A ALA* 1.3 63.4 + - - +
88A GLU 3.2 0.9 + - - -
89A GLY 3.1 3.5 + - - -
90A PHE* 2.9 30.5 + - - +
93A THR* 3.5 28.0 - - + -
94A LEU* 3.1 27.1 - - + -
97A LEU* 4.6 2.5 - - + -
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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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82A VAL 3.5 4.8 + - - +
83A HIS 3.1 5.5 + - - +
85A ALA* 1.3 79.6 - - - +
87A ARG* 1.3 52.5 + - - +
89A GLY 2.8 4.4 + - - +
114A PRO 3.7 11.0 - - - +
117A LEU* 5.6 0.7 - - + -
118A ALA* 3.8 9.0 - - + +
123A HIS* 2.7 36.2 - - - -
126A VAL* 3.2 31.2 - - + +
130A LEU* 3.2 21.8 - - + -
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Residues in contact with ARG 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 MET* 5.6 0.2 - - + -
83A HIS* 2.5 27.6 + - + +
84A ASP* 3.4 12.3 - - - +
85A ALA 3.1 0.2 - - - -
86A ALA* 1.3 73.0 - - - +
88A GLU* 1.3 67.6 + - - +
117A LEU* 3.9 23.0 - - + +
118A ALA 5.7 0.2 - - - +
121A LEU* 4.0 26.3 - - - +
123A HIS* 2.6 24.5 + - - -
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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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53A MET* 2.9 23.0 - - - +
54A MET* 3.2 37.5 - - + +
55A GLY* 4.9 2.5 - - - +
84A ASP 3.4 0.2 + - - -
85A ALA 3.2 5.1 + - - +
86A ALA 3.2 0.2 - - - -
87A ARG* 1.3 94.4 + - - +
89A GLY* 1.3 61.5 + - - +
90A PHE* 4.6 3.6 - - + +
123A HIS* 3.4 9.9 - - - -
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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