Contacts of the helix formed by residues 71 - 81 (chain A) in PDB entry 2M10
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 THR 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY 4.1 1.6 - - - -
27A VAL* 3.6 28.7 - - + -
36A ILE* 3.8 0.4 - - - +
69A GLY 4.7 3.4 - - - +
70A ALA* 1.3 80.4 - - - +
72A HIS* 1.4 61.9 + - - +
73A LYS* 3.6 11.3 + - - +
74A GLN* 3.1 29.6 + - + +
75A ALA* 2.8 26.7 + - - +
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Residues in contact with HIS 72 (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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23A VAL* 3.4 14.7 - - + +
24A THR* 4.1 20.4 - - - -
25A GLY 3.4 28.1 + - - +
27A VAL* 4.8 3.3 - - + +
29A THR* 6.1 2.5 - - + -
36A ILE* 4.5 1.6 - - - -
71A THR* 1.4 74.4 - - - +
73A LYS* 1.4 85.4 + - + +
75A ALA* 3.1 20.8 - - - +
76A VAL* 3.4 5.4 + - - +
101A 33B 2.8 37.8 + - - -
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 3.4 7.9 + - - +
72A HIS* 1.4 92.9 + - + +
74A GLN* 1.3 63.8 + - - +
76A VAL* 3.0 16.7 - - - +
77A CYS* 3.0 18.9 + - - +
101A 33B 3.4 60.4 + - + +
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Residues in contact with GLN 74 (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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67A LEU* 4.8 0.4 - - - -
70A ALA* 4.1 9.6 - - + -
71A THR* 3.1 32.7 + - + +
73A LYS* 1.3 75.3 - - - +
75A ALA* 1.3 57.8 + - - +
77A CYS* 3.5 16.1 - - - +
78A THR* 2.6 36.9 + - - +
101A 33B 2.9 28.5 + - - +
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Residues in contact with ALA 75 (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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23A VAL* 3.9 9.6 - - + -
36A ILE* 3.2 37.0 - - + -
62A VAL* 4.8 1.7 - - - +
67A LEU* 3.7 16.1 - - + +
71A THR 2.8 11.4 + - - +
72A HIS 3.1 12.6 - - - +
73A LYS 3.1 0.2 - - - -
74A GLN* 1.3 76.5 - - - +
76A VAL* 1.3 61.6 + - - +
78A THR* 3.3 4.2 + - - -
79A LEU* 3.1 26.5 + - + +
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Residues in contact with VAL 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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19A LEU* 5.7 3.6 - - + -
21A ILE 4.0 20.9 - - - +
22A CYS* 4.7 1.3 - - - -
23A VAL* 3.7 24.9 - - + -
72A HIS 3.8 5.2 - - - +
73A LYS 3.0 16.4 + - - +
75A ALA* 1.3 77.8 - - - +
77A CYS* 1.4 65.9 + - - +
79A LEU* 3.0 18.5 + - + +
80A ARG* 2.8 33.2 + - + +
101A 33B 3.2 44.2 - - + +
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Residues in contact with CYS 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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73A LYS 3.0 10.1 + - - +
74A GLN* 3.5 21.8 - - - +
76A VAL* 1.4 79.0 - - - +
78A THR* 1.4 58.7 + - - +
80A ARG* 3.6 3.6 - - - +
81A ASN* 3.0 38.2 + - - -
101A 33B 1.8 83.0 - - + +
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Residues in contact with THR 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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62A VAL* 3.7 31.2 - - + +
63A ASN* 5.9 1.1 - - + -
65A VAL* 4.6 13.7 - - + -
67A LEU* 3.5 21.7 - - + +
74A GLN* 2.6 24.1 + - - +
75A ALA 3.5 5.4 - - - -
77A CYS* 1.4 80.3 - - - +
79A LEU* 1.4 60.4 + - - +
80A ARG 3.3 0.5 + - - -
81A ASN* 3.5 12.9 + - + +
82A THR* 3.2 17.0 - - - +
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Residues in contact with LEU 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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14A LYS* 4.0 0.9 - - - +
19A LEU* 3.7 35.8 - - + +
21A ILE* 5.2 13.0 - - + -
23A VAL* 4.7 13.2 - - + -
36A ILE* 6.2 0.2 - - + -
59A VAL* 5.3 6.1 - - + -
62A VAL* 3.7 22.9 - - + -
75A ALA* 3.1 18.6 + - + +
76A VAL* 3.0 23.1 + - + +
78A THR* 1.4 77.2 - - - +
80A ARG* 1.4 55.6 + - - +
82A THR* 2.8 24.9 + - - +
86A VAL* 4.1 8.9 - - + +
88A LEU* 3.5 31.0 - - + -
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Residues in contact with ARG 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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14A LYS* 2.8 23.4 + - - +
17A ASN 6.0 0.7 - - - -
18A SER* 5.6 6.7 + - - +
19A LEU* 3.3 44.0 + - - +
20A GLY* 4.3 9.3 - - - -
76A VAL* 2.8 24.8 + - - +
77A CYS* 3.6 10.8 - - - +
79A LEU* 1.4 73.8 - - - +
81A ASN* 1.4 57.0 + - - +
82A THR 2.6 19.0 + - - +
101A 33B 5.1 18.7 - - + -
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Residues in contact with ASN 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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63A ASN* 5.4 4.5 + - - +
77A CYS* 3.0 38.3 + - - +
78A THR* 3.5 8.2 + - + +
80A ARG* 1.4 74.6 - - - +
82A THR* 1.3 63.1 + - - +
101A 33B 3.9 6.8 + - - +
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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