Contacts of the helix formed by residues 79 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.7 38.2 - - + -
42A GLU* 4.3 14.3 + - - +
43A TRP* 2.8 34.8 + - - +
46A PHE* 3.5 8.7 - - - -
68A VAL* 3.6 11.7 - - + +
76A HIS* 2.9 44.0 + - + +
78A ASP* 1.3 83.2 + - - +
80A VAL* 1.3 65.2 + - - +
81A PRO* 3.4 1.8 - - - -
82A TYR* 3.1 19.2 + - - +
83A ILE* 3.1 14.6 + - - +
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Residues in contact with VAL 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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68A VAL* 3.7 24.7 - - + +
69A PHE* 3.8 33.4 - - + -
76A HIS 3.5 3.6 + - - +
77A PRO* 3.2 22.4 + - + +
79A GLN* 1.3 76.9 - - - +
81A PRO* 1.3 69.1 - - + +
83A ILE* 3.4 2.0 + - - +
84A VAL* 3.0 33.4 + - + +
27B SER* 3.7 26.2 - - - +
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Residues in contact with PRO 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.7 26.1 - - + +
29A ASP 3.6 20.2 - - - +
30A VAL* 3.7 2.1 - - + +
77A PRO 3.9 2.2 - - - +
78A ASP 3.7 8.1 - - - +
79A GLN 3.6 2.5 - - - -
80A VAL* 1.3 95.8 - - + +
82A TYR* 1.3 62.4 + - + +
84A VAL* 3.8 3.1 - - + +
85A THR* 2.8 34.1 + - - -
27B SER 3.5 10.1 - - - +
28B VAL* 3.8 6.7 - - - -
29B ASP* 3.8 30.7 - - + +
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Residues in contact with TYR 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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30A VAL* 3.7 18.4 - - + -
31A LYS* 2.9 49.8 + - - +
34A ARG* 3.5 7.7 - - + +
35A TRP* 3.6 32.0 - + + -
38A PHE* 3.5 22.7 - + + -
43A TRP* 3.9 19.7 - - + -
78A ASP 3.6 18.4 - - - -
79A GLN 3.4 6.3 - - - +
80A VAL 3.1 0.4 - - - -
81A PRO* 1.3 81.2 - - + +
83A ILE* 1.4 64.8 + - - +
85A THR* 3.2 4.0 + - - -
86A TRP* 3.0 26.7 + - - -
29B ASP* 2.6 36.8 + - + -
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Residues in contact with ILE 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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43A TRP* 3.7 22.8 - - + -
50A TRP* 4.6 2.7 - - + -
61A ILE* 3.7 27.6 - - + +
64A VAL* 3.6 25.1 - - + -
65A LYS* 3.8 27.1 - - + +
68A VAL* 3.9 21.5 - - + -
69A PHE* 4.0 15.3 - - + -
79A GLN 3.1 10.6 + - - +
80A VAL 3.6 8.3 - - - +
82A TYR* 1.4 77.2 - - - +
84A VAL* 1.4 60.1 + - - +
86A TRP* 3.4 6.6 + - + -
87A GLU* 2.9 28.8 + - - +
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Residues in contact with VAL 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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26A GLN* 3.9 31.6 - - + +
28A VAL* 4.6 10.5 - - + -
65A LYS* 5.9 2.2 - - + -
69A PHE* 4.0 26.0 - - + -
80A VAL* 3.0 27.8 + - + +
81A PRO* 3.8 6.3 - - + +
83A ILE* 1.4 76.9 - - + +
85A THR* 1.3 57.6 + - - +
87A GLU* 3.4 15.9 + - - +
88A ALA* 2.9 26.7 + - - +
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.9 25.8 - - + +
22A ILE* 4.0 5.7 - - + +
23A ALA* 3.3 31.4 - - + +
26A GLN* 5.4 0.7 - - - -
28A VAL* 3.6 5.2 - - - +
30A VAL* 3.8 3.6 - - + +
35A TRP* 3.6 22.7 - - + -
81A PRO 2.8 22.4 + - - -
82A TYR 3.7 3.6 - - - -
84A VAL* 1.3 73.8 - - - +
86A TRP* 1.4 65.6 + - - +
88A ALA* 3.8 5.1 - - - +
89A LEU* 2.8 27.0 + - + +
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Residues in contact with TRP 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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8A PRO* 4.5 0.9 - - + -
9A LEU* 4.3 9.9 - - + -
12A THR* 4.1 13.5 - - + -
35A TRP* 3.2 49.7 + + - -
39A CYS* 3.8 22.4 - - + +
43A TRP* 3.6 24.1 - + - -
50A TRP* 3.8 11.9 - + - -
54A GLY* 4.1 15.9 - - - -
55A THR 3.4 32.8 - - - -
56A PHE* 4.1 23.1 - + - -
61A ILE* 3.6 10.4 - - + +
82A TYR 3.0 26.6 + - - -
83A ILE* 3.8 14.4 - - + +
85A THR* 1.4 74.8 - - - +
87A GLU* 1.3 62.8 + - - +
89A LEU* 3.3 10.6 + - + +
90A ALA* 3.0 24.4 + - - +
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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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58A ARG* 4.4 22.9 + - - +
61A ILE* 3.7 21.9 - - + +
62A THR* 4.8 7.6 + - - -
65A LYS* 2.8 44.0 + - + +
83A ILE 2.9 17.7 + - - +
84A VAL* 3.6 14.9 - - - +
86A TRP* 1.3 77.2 - - - +
88A ALA* 1.3 57.1 + - - +
90A ALA* 3.2 3.0 + - - +
91A PHE* 2.9 33.5 + - + +
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Residues in contact with ALA 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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22A ILE* 3.8 17.1 - - + +
26A GLN* 3.7 35.2 - - + +
84A VAL 2.9 18.2 + - - +
85A THR 3.8 0.9 - - - +
87A GLU* 1.3 76.7 - - - +
89A LEU* 1.3 61.8 + - - +
91A PHE* 4.4 6.1 - - - +
92A ASP* 3.1 30.0 + - + +
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Residues in contact with LEU 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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12A THR* 3.9 27.4 - - + -
19A VAL* 4.6 6.5 - - + -
22A ILE* 3.8 25.6 - - + +
35A TRP* 4.4 17.9 - - + -
56A PHE* 3.5 31.9 - - + -
85A THR 2.8 15.5 + - - +
86A TRP* 3.4 10.1 - - + +
88A ALA* 1.3 78.3 - - - +
90A ALA* 1.3 60.1 + - - +
92A ASP 4.8 0.7 - - - -
93A PRO* 3.0 29.6 - - - +
94A PRO* 4.9 2.2 - - + -
96A TRP* 4.2 12.3 - - + -
97A VAL 4.3 11.0 - - - +
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Residues in contact with ALA 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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56A PHE* 3.5 31.0 - - - +
58A ARG* 4.0 17.9 - - + +
61A ILE* 3.6 23.8 - - + -
86A TRP 3.0 6.9 + - - +
87A GLU* 3.8 2.7 - - - +
89A LEU* 1.3 82.1 - - + +
91A PHE* 1.3 61.9 + - - +
93A PRO* 3.5 12.5 - - - +
97A VAL 5.6 1.1 - - - -
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Residues in contact with PHE 91 (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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58A ARG* 3.2 50.5 - - - +
87A GLU* 2.9 20.7 + - + +
88A ALA* 4.2 4.9 - - - +
90A ALA* 1.3 76.5 - - - +
92A ASP* 1.3 66.2 + - + +
93A PRO* 3.4 5.0 - - - +
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Residues in contact with ASP 92 (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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21A ARG* 5.4 10.8 + - - -
22A ILE* 5.3 3.3 - - - +
25A ASN* 5.2 7.8 + - - -
88A ALA* 3.1 16.0 + - - +
89A LEU* 4.8 0.5 - - - -
91A PHE* 1.3 87.4 - - + +
93A PRO* 1.3 67.1 - - - +
94A PRO* 3.7 2.9 - - - +
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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