Contacts of the helix formed by residues 31 - 41 (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 LYS 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TRP* 4.9 1.0 - - - +
20A GLU* 2.9 25.1 + - - -
29A ASP* 3.7 7.4 + - - +
30A VAL 2.7 36.7 + - - -
31A LYS* 3.8 26.7 - - + +
32A LYS 5.0 0.6 - - - +
33A ARG* 6.1 0.7 - - - +
16B TRP* 3.9 1.8 - - - -
30B VAL* 1.3 73.4 - - - +
32B LYS* 1.3 66.2 + - - +
33B ARG* 4.3 20.6 - - + +
34B ARG* 3.2 38.5 + - + +
35B TRP* 2.9 22.5 + - - +
82B TYR* 2.9 14.6 + - - +
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Residues in contact with LYS 32 (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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31A LYS* 5.4 0.2 - - - +
13B LEU* 3.7 31.1 + - + -
16B TRP* 3.5 60.8 - - + +
31B LYS* 1.3 72.2 - - - +
33B ARG* 1.3 64.8 + - - +
35B TRP* 3.2 1.2 + - - +
36B VAL* 3.0 27.5 + - - +
33C ARG* 4.4 12.7 - - + +
36C VAL* 4.0 18.6 - - + -
37C THR* 2.8 42.2 + - - +
40C SER* 4.9 0.7 - - - +
41C ALA* 5.8 2.1 - - + +
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Residues in contact with ARG 33 (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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20A GLU* 4.4 4.2 + - - -
31B LYS* 4.3 22.3 - - + +
32B LYS* 1.3 79.5 - - - +
34B ARG* 1.3 102.5 + - + +
36B VAL* 3.4 2.8 + - - +
37B THR* 3.0 31.6 + - - -
13C LEU* 4.5 16.0 - - + +
32C LYS* 3.6 50.0 - - - +
33C ARG* 5.8 4.9 - - - +
36C VAL* 3.7 29.3 - - + +
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Residues in contact with ARG 34 (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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17A LYS* 4.6 2.8 - - - +
20A GLU* 2.8 26.5 + - - -
24A HIS* 3.7 12.5 + - - -
29A ASP* 2.9 40.8 + - - -
31B LYS* 3.2 14.9 + - + +
33B ARG* 1.3 112.3 - - + +
35B TRP* 1.3 66.1 + - - +
36B VAL 3.2 0.4 - - - -
37B THR* 4.3 6.5 - - - +
38B PHE* 2.8 51.9 + - + -
78B ASP* 5.9 0.4 - - - -
82B TYR* 3.6 21.8 - - + +
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Residues in contact with TRP 35 (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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9B LEU* 3.7 15.0 - - + +
12B THR* 2.9 33.5 + - + -
13B LEU* 4.3 6.7 - - + -
16B TRP* 3.5 30.3 - + + -
19B VAL* 3.8 18.6 - - + -
30B VAL* 4.5 4.0 - - + -
31B LYS 2.9 14.0 + - - +
32B LYS 3.4 7.9 - - - +
34B ARG* 1.3 76.5 - - - +
36B VAL* 1.3 63.5 + - - +
38B PHE* 4.4 1.1 - - - +
39B CYS* 3.1 26.3 + - - +
43B TRP* 5.8 0.7 - - - -
82B TYR* 3.5 33.5 - + + -
85B THR* 3.7 28.5 - - + -
86B TRP* 3.2 61.3 + + - +
89B LEU* 4.6 4.3 - - + -
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Residues in contact with VAL 36 (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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9B LEU* 4.5 10.5 - - + -
13B LEU* 3.9 34.8 - - + -
32B LYS 3.0 17.2 + - - +
33B ARG* 3.6 8.1 - - - +
35B TRP* 1.3 76.4 - - - +
37B THR* 1.3 61.8 + - - +
39B CYS* 3.4 0.9 + - - +
40B SER* 2.7 46.5 + - - +
9C LEU* 4.5 21.1 - - + -
36C VAL* 4.3 12.8 - - + -
40C SER* 4.3 5.4 - - - +
52C ARG* 4.1 11.4 - - - +
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Residues in contact with THR 37 (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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33B ARG 3.0 18.2 + - - -
34B ARG* 4.2 6.3 - - - -
36B VAL* 1.3 79.6 - - - +
38B PHE* 1.3 63.1 + - + +
40B SER* 4.8 1.3 - - - -
41B ALA* 2.9 39.7 + - + +
42B GLU* 3.1 18.0 + - + +
9C LEU* 6.0 0.9 - - - +
10C SER* 5.0 13.8 - - - -
13C LEU* 4.7 12.8 - - - +
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Residues in contact with PHE 38 (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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34B ARG* 2.8 47.5 + - + +
35B TRP 4.4 1.3 - - - +
37B THR* 1.3 79.5 - - + +
39B CYS* 1.3 62.7 + - - +
40B SER 3.4 0.2 + - - -
42B GLU* 3.7 23.3 - - + -
43B TRP* 2.9 50.7 + - + +
78B ASP* 3.7 19.3 - - + -
79B GLN* 3.7 35.7 - - + -
82B TYR* 3.5 44.6 - + + -
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Residues in contact with CYS 39 (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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9B LEU* 4.2 11.9 - - + -
35B TRP 3.1 20.0 + - - +
36B VAL 3.8 2.7 - - - +
38B PHE* 1.3 77.3 - - - +
40B SER* 1.3 58.8 + - - +
43B TRP* 4.0 6.8 - - + -
44B PRO* 3.4 8.0 - - - +
50B TRP* 3.1 36.6 + - - +
52B ARG* 3.5 9.9 - - - -
53B ASP 4.1 1.8 - - - -
54B GLY* 3.4 37.0 - - - -
86B TRP* 3.9 21.8 - - + +
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Residues in contact with SER 40 (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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9B LEU* 3.5 8.3 - - - +
36B VAL* 2.7 24.0 + - - -
37B THR* 4.5 1.8 - - - -
39B CYS* 1.3 78.3 - - - +
41B ALA* 1.3 59.0 + - - +
44B PRO* 3.7 6.0 - - - +
52B ARG* 3.4 38.9 + - - +
5C VAL* 3.4 8.2 - - - +
52C ARG* 2.8 39.1 + - - -
53C ASP* 5.0 0.4 - - - -
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Residues in contact with ALA 41 (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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37B THR* 2.9 27.5 + - + +
39B CYS 3.6 0.2 - - - -
40B SER* 1.3 80.3 - - - +
42B GLU* 1.3 71.5 + - - +
44B PRO* 3.6 7.8 - - - +
45B THR* 3.5 14.6 + - - -
5C VAL* 4.0 31.0 + - + +
10C SER* 6.1 3.6 - - - -
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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