Contacts of the helix formed by residues 79 - 92 (chain B) in PDB entry 1MN8
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 GLN 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.7 44.5 - - + -
42B GLU* 4.3 14.6 + - - +
43B TRP* 2.8 35.0 + - - +
46B PHE* 3.5 7.9 - - - -
68B VAL* 3.7 11.2 - - + +
76B HIS* 2.9 44.0 + - + +
78B ASP* 1.3 83.3 + - - +
80B VAL* 1.3 64.6 - - - +
81B PRO 3.4 1.6 - - - -
82B TYR* 3.1 14.2 + - - +
83B ILE* 3.1 14.2 + - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.7 25.4 - - - +
28B VAL* 6.0 2.5 - - + -
68B VAL* 3.8 23.3 - - + +
69B PHE* 3.7 35.0 - - + -
76B HIS 4.0 3.4 - - - +
77B PRO* 3.2 19.9 + - + +
79B GLN* 1.3 76.7 - - - +
81B PRO* 1.4 72.4 - - + +
82B TYR 3.1 0.2 + - - -
83B ILE* 3.3 2.0 + - - +
84B VAL* 3.0 33.0 + - + +
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Residues in contact with PRO 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 3.4 17.5 - - - +
28A VAL* 3.8 15.0 - - - -
29A ASP 3.9 9.2 - - - +
28B VAL* 3.8 25.8 - - + +
29B ASP 3.7 20.0 - - - +
30B VAL* 3.7 1.6 - - + +
77B PRO 3.9 2.0 - - - +
78B ASP 3.7 9.4 - - - +
79B GLN 3.6 3.1 - - - -
80B VAL* 1.4 95.0 - - + +
82B TYR* 1.3 64.9 + - + +
84B VAL* 3.9 2.6 - - + +
85B THR* 2.8 33.8 + - - -
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 2.6 37.1 + - + -
30B VAL* 3.7 18.6 - - + -
31B LYS* 2.9 48.4 + - - +
34B ARG* 3.6 7.7 - - + +
35B TRP* 3.5 32.2 - + + -
38B PHE* 3.5 22.0 - + + -
43B TRP* 3.9 19.3 - - + -
78B ASP 3.6 19.1 - - - -
79B GLN 3.1 6.9 + - - +
81B PRO* 1.3 83.0 - - + +
83B ILE* 1.3 63.0 + - - +
85B THR* 3.2 3.5 + - - -
86B TRP* 3.0 26.9 + - - -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 3.7 25.2 - - + -
50B TRP* 4.7 2.9 - - + -
61B ILE* 3.8 25.8 - - + +
64B VAL* 3.6 22.9 - - + -
65B LYS* 3.8 28.5 - - + +
68B VAL* 4.0 21.5 - - + -
69B PHE* 4.0 15.5 - - + -
79B GLN 3.1 12.6 + - - +
80B VAL 3.6 8.5 - - - +
82B TYR* 1.3 76.5 - - - +
84B VAL* 1.4 59.4 + - - +
86B TRP* 3.4 6.0 + - + -
87B GLU* 2.9 29.2 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 4.0 31.2 - - + +
28B VAL* 4.7 9.9 - - + -
65B LYS* 5.4 3.6 - - - +
69B PHE* 3.9 28.0 - - + -
80B VAL* 3.0 26.1 + - + +
81B PRO* 3.9 6.3 - - + +
83B ILE* 1.4 75.8 - - + +
85B THR* 1.3 58.3 + - - +
87B GLU* 3.4 12.9 + - - +
88B ALA* 2.9 26.5 + - - +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 4.0 13.0 - - + +
22B ILE* 4.2 4.9 - - + -
23B ALA* 3.3 45.2 - - + +
26B GLN* 5.3 0.6 - - - +
28B VAL* 3.6 5.4 - - - +
30B VAL* 3.9 3.3 - - + +
35B TRP* 3.7 22.9 - - + -
81B PRO 2.8 22.1 + - - -
82B TYR 3.2 4.7 + - - -
84B VAL* 1.3 74.4 - - - +
86B TRP* 1.4 65.7 + - - +
88B ALA* 3.2 6.0 + - - +
89B LEU* 2.9 26.6 + - + +
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Residues in contact with TRP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 4.4 0.9 - - + -
9B LEU* 4.3 11.0 - - + -
12B THR* 4.1 13.5 - - + -
35B TRP* 3.2 51.2 + + - +
39B CYS* 3.9 21.2 - - + +
43B TRP* 3.6 25.6 - + - -
50B TRP* 4.2 10.1 - + - -
54B GLY* 3.9 16.2 - - - -
55B THR 3.3 35.4 - - - -
56B PHE* 4.2 20.3 - + - -
61B ILE* 3.7 11.7 - - + +
82B TYR 3.0 27.1 + - - -
83B ILE* 3.8 13.2 - - + +
85B THR* 1.4 75.3 - - - +
87B GLU* 1.3 63.1 + - - +
89B LEU* 3.3 8.3 + - + +
90B ALA* 3.0 23.9 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG* 6.0 0.7 - - + -
61B ILE* 3.8 21.0 - - + +
62B THR* 4.4 10.7 + - - -
65B LYS* 3.0 45.0 + - + +
83B ILE 2.9 18.5 + - - +
84B VAL* 3.6 10.4 - - - +
86B TRP* 1.3 77.4 - - - +
88B ALA* 1.3 57.3 + - - +
90B ALA* 3.2 2.9 + - - +
91B PHE* 2.9 54.4 + - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.8 13.5 - - + +
26B GLN* 3.7 35.7 - - + +
84B VAL 2.9 17.1 + - - +
85B THR 3.7 4.7 - - - +
87B GLU* 1.3 76.9 - - - +
89B LEU* 1.3 62.8 + - - +
91B PHE* 3.9 4.9 - - - +
92B ASP* 3.0 27.9 + - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 3.8 29.2 - - + -
19B VAL* 4.9 4.3 - - + -
22B ILE* 3.4 36.0 - - + +
35B TRP* 4.6 13.5 - - + -
56B PHE* 3.9 16.6 - - + -
85B THR* 2.9 17.4 + - + +
86B TRP* 3.5 9.4 - - + +
88B ALA* 1.3 77.3 - - - +
90B ALA* 1.3 57.3 + - - +
92B ASP 4.8 0.9 - - - -
93B PRO* 3.0 34.0 - - - +
94B PRO* 3.4 18.8 - - + -
96B TRP* 3.8 10.1 - - + -
97B VAL* 3.6 14.2 - - + +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.3 34.6 - - + +
58B ARG* 3.9 21.5 + - + +
61B ILE* 3.6 15.7 - - + -
86B TRP 3.0 16.4 + - - +
87B GLU 3.2 3.6 + - - +
89B LEU* 1.3 78.7 - - - +
91B PHE* 1.3 61.2 + - - +
93B PRO* 3.8 10.2 - - - +
97B VAL* 5.8 0.9 - - - -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG* 3.6 44.6 + - + +
62B THR* 6.0 0.9 - - - -
87B GLU* 2.9 48.8 + - + +
88B ALA* 3.4 6.5 + - - +
90B ALA* 1.3 79.0 - - - +
92B ASP* 1.3 64.1 + - + +
93B PRO* 3.4 5.4 - - - +
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 5.6 3.6 + - - -
22B ILE* 5.2 4.2 - - - +
88B ALA 3.0 14.2 + - - +
89B LEU* 3.7 2.7 - - - +
91B PHE* 1.3 80.8 - - + +
93B PRO* 1.3 67.6 - - - +
94B PRO* 3.8 3.8 - - - +
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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