Contacts of the helix formed by residues 79 - 92 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D PHE* 3.6 34.9 - - + -
42D GLU* 3.0 34.3 + - - +
43D TRP* 2.8 30.0 + - - +
46D PHE* 3.5 10.2 - - - -
68D VAL* 3.6 14.7 - - + +
76D HIS* 2.9 31.2 + - - +
78D ASP* 1.3 84.1 + - - +
80D VAL* 1.3 62.0 + - - +
81D PRO* 3.4 1.6 - - - -
82D TYR* 3.1 6.0 + - - +
83D ILE* 3.1 23.4 + - - +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 5.2 5.6 - - + -
68D VAL* 3.8 22.7 - - + +
69D PHE* 3.7 31.6 - - + -
76D HIS 3.6 0.2 + - - -
77D PRO* 3.3 27.8 - - + +
79D GLN* 1.3 77.6 - - - +
81D PRO* 1.3 71.8 - - + +
82D TYR 3.1 0.3 + - - -
83D ILE* 3.7 2.4 - - - +
84D VAL* 3.0 28.9 + - + +
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Residues in contact with PRO 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 3.6 28.9 - - + +
29D ASP 3.4 26.7 - - - +
30D VAL* 3.8 3.4 - - + -
77D PRO 3.8 4.9 - - - +
78D ASP* 3.7 13.7 - - - +
79D GLN 3.6 2.9 - - - -
80D VAL* 1.3 96.3 - - + +
82D TYR* 1.3 63.0 + - + +
84D VAL* 3.7 0.4 + - + -
85D THR* 2.8 33.3 + - - +
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP 4.5 2.5 + - - -
30D VAL* 3.7 22.0 - - + -
31D LYS* 3.0 34.7 + - - +
34D ARG* 3.4 24.2 + - + +
35D TRP* 3.5 43.9 - + + -
38D PHE* 3.6 17.9 - + + -
43D TRP* 3.8 21.8 - - + -
78D ASP 3.6 24.9 - - - -
79D GLN 3.5 5.6 - - - +
80D VAL 3.1 0.6 - - - -
81D PRO* 1.3 86.6 - - + +
83D ILE* 1.4 65.1 + - - +
85D THR* 3.1 4.2 + - - -
86D TRP* 3.1 26.4 + - - -
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 3.7 24.6 - - + -
50D TRP* 4.5 3.4 - - + -
61D ILE* 3.8 24.2 - - + +
64D VAL* 3.7 22.4 - - + -
65D LYS* 3.8 31.2 - - + +
68D VAL* 3.9 21.5 - - + -
69D PHE* 4.0 13.7 - - + -
79D GLN 3.1 13.4 + - - +
80D VAL 3.7 8.5 - - - +
82D TYR* 1.4 77.2 - - - +
84D VAL* 1.3 59.1 + - - +
86D TRP* 3.4 6.0 + - + +
87D GLU* 2.9 29.0 + - - +
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLN* 3.8 31.2 - - + +
28D VAL* 4.2 15.9 - - + -
65D LYS* 4.4 10.8 - - - +
69D PHE* 3.8 27.8 - - + -
80D VAL* 3.0 27.0 + - + +
81D PRO* 3.9 3.4 - - + +
83D ILE* 1.3 76.4 - - - +
85D THR* 1.4 58.4 + - - +
87D GLU* 3.4 11.0 + - - +
88D ALA* 3.0 26.3 + - - +
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Residues in contact with THR 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.8 18.4 + - - +
22D ILE* 4.5 4.5 - - - +
23D ALA* 3.3 33.4 + - + +
26D GLN* 5.5 0.4 - - + -
28D VAL* 3.5 11.2 - - + -
30D VAL* 3.8 6.1 - - + -
35D TRP* 3.7 19.0 - - - -
81D PRO 2.8 24.2 + - - +
82D TYR 3.1 5.1 + - - -
84D VAL* 1.4 75.2 - - + +
86D TRP* 1.3 66.9 + - - +
88D ALA* 3.2 7.6 + - - +
89D LEU* 3.0 25.4 + - - +
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Residues in contact with TRP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 4.1 1.6 - - + -
9D LEU* 4.3 11.0 - - + -
12D THR* 4.1 11.9 - - + -
35D TRP* 3.3 48.1 + + - -
39D CYS* 3.8 21.1 - - + +
43D TRP* 3.6 25.9 - + - -
50D TRP* 4.0 8.3 - + - -
54D GLY* 4.0 15.7 - - - -
55D THR 3.2 35.7 - - - -
56D PHE* 3.9 26.1 - + - -
61D ILE* 3.6 17.1 - - + +
82D TYR* 3.1 27.3 + - - +
83D ILE* 3.8 12.8 - - + +
85D THR* 1.3 76.8 - - - +
87D GLU* 1.3 62.5 + - - +
89D LEU* 3.2 11.1 + - + +
90D ALA 3.1 17.8 + - - -
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ILE* 3.7 23.4 - - + +
62D THR* 5.0 7.9 + - - +
65D LYS* 2.7 43.9 + - + +
83D ILE 2.9 17.3 + - - +
84D VAL* 3.6 9.1 - - - +
86D TRP* 1.3 76.6 - - - +
88D ALA* 1.3 63.2 + - - +
90D ALA* 3.2 2.7 + - - +
91D PHE* 3.0 55.2 + - + -
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.8 20.6 - - + +
26D GLN* 3.8 27.8 - - + +
84D VAL 3.0 16.8 + - - +
85D THR* 3.2 6.7 + - - +
87D GLU* 1.3 75.0 - - - +
89D LEU* 1.3 63.3 + - - +
91D PHE* 3.3 5.9 + - - +
92D ASP* 3.1 26.5 + - - +
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 4.1 26.2 - - + -
19D VAL* 4.6 6.7 - - + -
22D ILE* 3.5 35.7 - - + -
35D TRP* 4.3 11.7 - - + -
56D PHE* 4.3 18.4 - - + -
85D THR* 3.0 20.1 + - - +
86D TRP* 3.4 15.9 - - + +
88D ALA* 1.3 76.8 - - - +
90D ALA* 1.3 61.0 + - - +
92D ASP 4.4 3.4 - - - -
93D PRO* 3.2 28.8 - - - +
94D PRO* 3.9 17.2 - - + +
96D TRP* 4.0 11.9 - - + -
97D VAL* 4.4 5.4 - - + +
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D PHE* 3.4 31.3 - - - +
58D ARG* 3.6 25.8 - - + +
61D ILE* 3.7 19.5 - - + -
86D TRP 3.1 5.7 + - - -
87D GLU* 3.2 7.8 + - - +
89D LEU* 1.3 78.0 - - - +
91D PHE* 1.3 62.3 + - - +
93D PRO* 3.9 9.2 - - - +
97D VAL* 5.3 2.2 - - - +
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ARG* 2.7 55.6 - - + +
62D THR* 5.8 3.4 - - - -
87D GLU* 3.0 55.3 + - + +
88D ALA* 3.9 5.8 - - - +
90D ALA* 1.3 79.8 - - - +
92D ASP* 1.3 60.1 + - + +
93D PRO* 3.7 4.7 - - - +
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Residues in contact with ASP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 5.5 2.4 - - - +
88D ALA 3.1 13.5 + - - +
89D LEU* 3.4 4.1 - - - +
91D PHE* 1.3 79.5 - - + +
93D PRO* 1.3 72.0 - - - +
94D PRO* 3.3 8.3 - - - +
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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