Contacts of the helix formed by residues 74 - 86 (chain A) in PDB entry 3M8V
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 ARG 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.9 0.7 - - - -
39A GLU* 3.8 22.8 + - - +
72A PHE 6.2 0.2 - - - -
73A ILE* 1.3 79.0 - - - +
75A ALA* 1.3 66.9 + - - +
76A GLU* 2.8 43.6 + - - +
77A ILE* 3.1 14.8 + - + +
78A PHE* 3.0 18.9 + - - +
97A LEU* 3.4 26.3 - - - +
100A GLU* 2.9 28.7 + - - +
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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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38A VAL* 3.9 18.9 - - - +
39A GLU* 3.0 22.0 + - + +
41A ARG* 3.9 31.6 - - + -
43A PHE* 3.7 6.0 - - + -
73A ILE 3.8 1.0 + - - -
74A ARG* 1.3 71.6 - - - +
76A GLU* 1.3 59.7 + - - +
78A PHE* 3.0 3.8 + - - +
79A ALA* 2.8 28.4 + - - +
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Residues in contact with GLU 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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39A GLU* 5.0 0.2 + - - -
74A ARG* 2.8 44.6 + - - +
75A ALA* 1.3 78.0 - - - +
77A ILE* 1.3 66.6 + - + +
79A ALA* 3.4 10.4 - - - +
80A GLU* 3.3 20.6 + - - +
97A LEU* 4.1 19.4 - - + +
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Residues in contact with ILE 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 ILE* 4.2 4.5 - - + -
74A ARG* 3.1 26.6 + - + +
75A ALA 3.1 0.4 - - - -
76A GLU* 1.3 76.6 - - + +
78A PHE* 1.3 66.1 + - - +
80A GLU* 3.1 18.1 + - + +
81A ILE* 3.2 11.1 + - - +
97A LEU* 4.1 36.8 - - + +
100A GLU* 3.8 32.8 - - + +
101A LEU* 4.1 16.8 - - + +
104A SER* 3.6 31.4 - - - +
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Residues in contact with PHE 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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36A VAL* 3.9 25.1 - - + -
38A VAL* 3.7 13.2 - - + -
43A PHE* 3.6 36.1 - + + -
50A LEU* 5.6 0.2 - - + -
57A PHE* 4.0 14.8 - + - -
70A LEU* 3.9 15.3 - - + -
73A ILE* 4.1 11.7 - - + -
74A ARG 3.0 12.4 + - - +
75A ALA 3.6 6.3 - - - +
77A ILE* 1.3 75.7 - - - +
79A ALA* 1.3 63.5 + - - +
81A ILE* 2.9 22.1 + - + +
82A LEU* 3.0 44.2 + - + +
108A LEU* 3.8 30.5 - - + -
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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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26A ARG* 4.9 0.9 + - - +
43A PHE* 3.8 23.7 - - + -
75A ALA 2.8 17.1 + - - +
76A GLU* 3.4 15.5 - - - +
78A PHE* 1.3 73.8 - - - +
80A GLU* 1.3 56.3 + - - +
82A LEU* 3.3 5.0 + - - +
83A ASN* 2.9 37.3 + - - +
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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 GLU 3.3 9.6 + - - +
77A ILE* 3.1 14.0 + - + +
79A ALA* 1.3 75.1 - - - +
81A ILE* 1.3 66.4 + - - +
82A LEU 3.1 1.1 - - - -
83A ASN* 2.9 35.3 + - - +
84A TYR* 3.0 23.0 + - - +
89A LYS 4.7 0.2 - - - +
90A ILE* 3.7 29.4 - - + +
91A VAL 4.0 5.8 + - - +
93A VAL* 3.9 23.0 - - + +
101A LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 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 ILE 3.5 12.3 - - - +
78A PHE* 2.9 18.1 + - + +
80A GLU* 1.3 77.3 - - - +
82A LEU* 1.3 59.9 + - - +
84A TYR* 3.4 5.6 + - - +
85A ILE* 2.9 35.3 + - + +
101A LEU* 3.7 15.5 - - + -
104A SER* 2.9 30.5 - - - +
105A GLY* 3.9 7.9 - - - +
108A LEU* 4.3 14.6 - - + -
110A VAL* 4.0 26.5 - - + -
113A ILE* 3.9 19.5 - - + -
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Residues in contact with LEU 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 ARG* 3.5 34.3 - - - +
36A VAL* 6.4 0.2 - - + -
43A PHE* 3.9 20.0 - - + -
44A ARG 5.0 0.2 - - - +
45A ALA* 4.9 9.9 - - + -
50A LEU* 3.9 28.3 - - + -
57A PHE* 5.5 0.4 - - + -
78A PHE* 3.0 47.7 + - + +
79A ALA* 3.5 8.7 - - - +
81A ILE* 1.3 76.3 - - - +
83A ASN* 1.3 68.0 + - - +
85A ILE* 2.9 13.9 + - + +
86A TYR* 2.7 29.1 + - + -
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Residues in contact with ASN 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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23A ASN* 4.9 4.7 + - - +
26A ARG* 3.0 22.6 + - - +
79A ALA* 2.9 23.8 + - - +
80A GLU* 2.9 34.9 + - - +
82A LEU* 1.3 75.7 - - - +
84A TYR* 1.3 56.9 + - - +
86A TYR* 3.3 3.0 + - - +
87A SER* 2.8 33.8 + - - +
89A LYS 4.1 3.1 - - - +
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Residues in contact with TYR 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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53A SER* 5.7 3.6 - - - -
80A GLU 3.0 11.7 + - - +
81A ILE 3.5 7.4 - - - +
83A ASN* 1.3 72.9 - - - +
85A ILE* 1.3 86.4 + - + +
86A TYR 2.9 1.6 - - - -
87A SER* 2.8 0.7 + - - -
88A SER* 2.7 61.2 + - - -
89A LYS 3.4 19.4 + - - +
90A ILE* 4.1 9.2 - - + -
110A VAL* 3.5 32.7 - - + +
112A PHE* 3.2 46.5 - + + +
113A ILE* 4.1 11.7 - - + -
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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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19A LEU* 4.1 10.7 - - - +
49A ILE* 3.6 30.2 - - + +
50A LEU* 3.9 27.4 - - + -
53A SER* 4.1 27.7 + - - -
54A SER* 4.7 8.7 - - - -
57A PHE* 5.3 4.5 - - + -
81A ILE* 2.9 31.4 + - + +
82A LEU* 2.9 15.1 + - + +
84A TYR* 1.3 90.9 - - + +
86A TYR* 1.3 62.9 + - + +
87A SER 3.8 0.2 + - - -
88A SER 4.9 0.3 + - - -
110A VAL* 4.6 11.4 - - + -
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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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19A LEU* 3.6 29.9 - - + +
20A ASN* 5.1 0.3 - - - -
22A LEU* 3.8 21.8 - - + -
23A ASN* 3.3 42.8 + - - +
26A ARG* 3.4 28.0 - - - +
45A ALA* 3.8 6.2 - - + +
46A HIS* 2.8 51.2 + - - +
49A ILE* 4.0 19.6 - - + +
50A LEU* 4.5 9.1 - - + +
82A LEU* 2.7 23.8 + - + +
83A ASN 3.4 2.2 - - - +
85A ILE* 1.3 90.5 - - + +
87A SER* 1.3 60.2 + - - +
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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