Contacts of the helix formed by residues 81 - 90 (chain A) in PDB entry 1MA3
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 ALA 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.9 23.1 - - + -
79A ASN* 2.6 20.4 + - - +
80A PRO* 1.3 74.8 - - - +
82A HIS* 1.3 55.2 + - - +
84A ALA* 3.3 1.4 + - - +
85A ILE* 3.0 36.3 + - + +
235A ALA* 3.8 28.3 - - + +
236A GLY* 3.8 2.1 - - - +
239A LEU* 4.0 16.3 - - + +
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Residues in contact with HIS 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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26A ILE* 3.8 27.1 - - + +
27A SER* 4.3 1.1 - - - -
78A PRO* 4.0 1.7 - - + +
79A ASN* 3.0 47.6 + - - +
81A ALA* 1.3 76.8 - - - +
83A TYR* 1.3 58.3 + - - +
85A ILE* 3.4 7.5 + - - +
86A ALA* 2.9 28.2 + - - +
101A ASN* 5.2 2.0 + - - -
103A ASP* 5.3 1.0 + - - -
105A LEU* 3.5 45.3 - - + +
106A HIS* 3.6 32.8 + + - +
109A ALA* 3.6 21.6 - - + +
111A SER* 4.6 1.9 + - - -
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Residues in contact with TYR 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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77A GLU* 5.7 0.9 - - - +
78A PRO* 3.6 38.9 + - + +
79A ASN 3.3 19.3 + - - -
80A PRO* 3.8 9.0 - - + +
82A HIS* 1.3 74.0 - - - +
84A ALA* 1.3 61.0 + - - +
86A ALA* 3.2 4.7 + - + +
87A GLU* 2.9 29.3 + - - +
90A ARG* 5.3 2.5 + - - -
108A ARG 4.8 3.3 + - - -
109A ALA* 3.5 34.3 - - + -
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Residues in contact with ALA 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 PRO 2.8 18.5 + - - +
81A ALA 3.6 4.9 - - - +
82A HIS 3.3 0.2 - - - -
83A TYR* 1.3 76.5 - - - +
85A ILE* 1.3 61.6 + - - +
87A GLU* 3.1 8.5 + - - +
88A LEU* 3.0 19.8 + - - +
239A LEU* 3.7 20.2 - - + -
240A PRO* 3.9 10.3 - - + -
243A VAL* 3.5 32.9 - - + +
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Residues in contact with ILE 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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20A VAL* 4.0 33.7 - - + -
22A THR* 4.0 1.6 - - + -
26A ILE* 3.9 26.0 - - + -
81A ALA 3.0 22.0 + - - +
82A HIS* 3.7 4.7 - - - +
84A ALA* 1.3 76.8 - - - +
86A ALA* 1.3 61.6 + - - +
88A LEU* 3.3 11.1 + - + +
89A GLU* 3.3 19.6 + - - +
94A VAL* 4.6 2.3 - - + +
97A VAL* 3.6 31.0 - - + -
106A HIS* 4.0 12.1 - - + +
111A SER* 4.2 5.8 - - - +
190A VAL* 4.6 9.2 - - + -
239A LEU* 4.1 15.9 - - + -
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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 HIS 2.9 17.4 + - - +
83A TYR* 3.2 5.8 + - - +
85A ILE* 1.3 77.5 - - - +
87A GLU* 1.3 57.6 + - - +
89A GLU* 3.4 6.8 + - - +
90A ARG* 3.1 37.3 + - - +
109A ALA 3.8 22.4 - - - +
110A GLY 3.9 4.7 - - - +
111A SER* 3.7 27.8 - - - +
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Residues in contact with GLU 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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83A TYR 2.9 13.1 + - - +
84A ALA* 3.1 13.2 + - - +
86A ALA* 1.3 75.6 - - - +
88A LEU* 1.3 60.0 + - - +
90A ARG* 3.1 35.9 + - - +
91A MET* 2.9 40.3 + - - +
243A VAL* 3.7 18.4 - - + +
247A LYS* 2.9 34.1 + - - -
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Residues in contact with LEU 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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12A LEU* 4.4 11.4 - - + -
84A ALA 3.0 15.0 + - - +
85A ILE* 3.3 11.4 + - + +
87A GLU* 1.3 75.6 - - - +
89A GLU* 1.3 59.4 + - - +
91A MET* 3.4 25.3 + - + +
92A GLY 3.4 2.3 + - - -
93A ILE* 2.9 39.9 + - + +
94A VAL* 3.0 30.1 + - + -
188A MET* 4.3 21.1 - - + -
239A LEU* 4.8 3.6 - - + -
242A ILE* 5.5 0.9 - - + -
243A VAL* 3.8 24.9 - - + -
246A VAL* 4.3 19.5 - - + -
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Residues in contact with GLU 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 ILE 3.3 9.6 + - - +
86A ALA 3.6 7.4 - - - +
87A GLU 3.2 0.4 - - - -
88A LEU* 1.3 75.8 - - - +
90A ARG* 1.3 60.3 + - - +
91A MET 3.1 0.2 - - - -
92A GLY* 2.6 26.0 + - - -
94A VAL* 3.1 32.1 - - + +
95A LYS* 4.9 4.9 - - - +
96A ALA* 5.7 0.4 - - - -
97A VAL* 5.0 4.6 - - + +
110A GLY 4.6 1.1 - - - +
111A SER* 3.3 17.4 + - - -
112A ARG* 3.1 28.7 + - - +
113A ARG* 3.3 29.5 + - - +
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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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83A TYR* 5.3 1.8 + - - -
86A ALA* 3.1 35.2 + - - +
87A GLU* 3.1 40.0 + - - +
89A GLU* 1.3 77.4 - - - +
91A MET* 1.3 59.8 + - + +
92A GLY* 3.0 3.7 + - - -
109A ALA 4.4 7.9 + - - -
110A GLY* 4.7 7.7 + - - -
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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