Contacts of the helix formed by residues 31 - 41 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C TRP* 3.7 4.0 - - - +
29C ASP* 4.8 10.5 - - - +
30C VAL* 1.3 75.3 - - - +
32C LYS* 1.3 63.1 + - - +
33C ARG* 3.4 24.8 - - - +
34C ARG* 2.4 50.1 + - + +
35C TRP* 3.0 20.8 + - - +
82C TYR* 3.0 17.0 + - - +
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Residues in contact with LYS 32 (chain C).
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* 3.6 45.5 - - - +
13C LEU* 3.8 21.7 + - + -
16C TRP* 3.4 62.0 - - + +
31C LYS* 1.3 68.0 - - - +
33C ARG* 1.4 69.5 + - - +
35C TRP* 3.3 2.2 + - - +
36C VAL* 2.9 28.3 + - - +
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Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG* 3.4 60.0 - - - +
32B LYS* 4.4 13.4 - - + +
33B ARG* 5.8 4.0 - - - +
31C LYS* 3.9 21.9 - - + +
32C LYS* 1.4 80.8 - - - +
34C ARG* 1.3 91.7 + - + +
36C VAL* 3.4 7.0 + - - +
37C THR* 2.7 37.8 + - - +
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 2.4 58.6 + - - +
32C LYS 3.1 0.8 - - - -
33C ARG* 1.3 101.0 - - + +
35C TRP* 1.3 58.6 + - - +
37C THR* 4.0 7.0 - - - +
38C PHE* 2.8 49.3 + - + -
82C TYR* 3.3 33.7 - - + +
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Residues in contact with TRP 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.7 16.1 - - + +
12C THR* 2.9 36.9 + - + -
13C LEU* 4.2 8.3 - - + -
16C TRP* 3.6 30.0 - + + -
19C VAL* 3.8 15.5 - - + -
30C VAL* 4.2 4.7 - - + -
31C LYS 3.0 14.7 + - - +
32C LYS 3.4 7.6 - - - +
34C ARG* 1.3 75.8 - - - +
36C VAL* 1.3 56.5 + - - +
38C PHE* 3.5 1.0 + - - +
39C CYS* 3.0 31.9 + - - +
82C TYR* 3.5 30.8 - + + -
85C THR* 3.7 31.4 - - + -
86C TRP* 3.2 57.2 + + - -
89C LEU* 4.1 4.9 - - + -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LYS* 4.0 22.4 - - + -
33B ARG* 3.7 32.5 - - + +
36B VAL* 4.3 10.1 - - + -
9C LEU* 4.4 14.1 - - + -
13C LEU* 4.0 23.8 - - + -
32C LYS 2.9 21.5 + - - +
33C ARG* 3.6 5.6 - - - +
35C TRP* 1.3 70.8 - - - +
37C THR* 1.3 64.7 + - - +
40C SER* 2.5 45.8 + - - +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LYS* 2.8 33.9 + - - +
33C ARG* 2.7 26.6 + - - +
34C ARG* 3.5 12.1 - - + +
36C VAL* 1.3 77.5 - - - +
38C PHE* 1.3 79.2 + - + +
40C SER* 4.2 2.5 - - - -
41C ALA* 3.0 27.0 + - + +
42C GLU* 3.1 10.4 + - + -
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Residues in contact with PHE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 2.8 36.4 + - + +
35C TRP 4.2 1.6 - - - +
37C THR* 1.3 87.7 - - + +
39C CYS* 1.3 60.6 + - - +
42C GLU* 4.0 17.3 - - + -
43C TRP* 2.9 54.6 + - + +
78C ASP* 3.8 24.5 - - + -
79C GLN* 3.6 34.3 - - + -
82C TYR* 3.5 42.8 - + + -
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Residues in contact with CYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.7 20.4 - - + -
35C TRP 3.0 18.4 + - - +
36C VAL 4.1 1.6 - - - +
38C PHE* 1.3 76.5 - - - +
40C SER* 1.3 59.7 + - - +
43C TRP* 4.1 5.2 - - + -
44C PRO* 3.3 12.0 - - - +
50C TRP* 3.1 27.9 + - - +
52C ARG* 3.6 11.8 - - - -
54C GLY* 3.4 37.0 - - - -
86C TRP* 3.8 21.1 - - + +
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER* 5.7 3.8 - - - -
13B LEU* 3.6 29.2 - - - +
32B LYS* 4.9 0.3 - - - +
36B VAL* 4.3 8.7 - - - +
9C LEU* 4.6 6.7 - - - -
36C VAL* 2.5 45.6 + - - +
37C THR* 4.1 1.9 + - - -
39C CYS* 1.3 75.3 - - - +
41C ALA* 1.3 60.0 + - - +
44C PRO* 3.9 5.6 - - - +
52C ARG* 3.5 35.1 - - - +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER* 5.7 1.6 - - - +
13B LEU* 3.8 33.2 - - + +
14B GLY* 5.1 1.3 - - - +
32B LYS* 5.8 1.8 - - + +
37C THR* 3.0 19.0 + - + +
40C SER* 1.3 83.6 - - - +
42C GLU* 1.3 64.9 + - - +
43C TRP 3.7 0.2 - - - -
44C PRO* 3.6 7.1 - - - +
45C THR* 3.3 19.4 + - - +
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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