Contacts of the helix formed by residues 3 - 14 (chain M) in PDB entry 6MUO
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 GLU 3 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ARG* 2.8 59.1 + - - +
2M ASP* 1.3 76.0 - - - +
4M THR* 1.3 69.2 + - + +
5M VAL* 3.2 2.6 + - - -
6M ALA* 3.5 14.4 + - + +
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Residues in contact with THR 4 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 3.8 31.1 - - + +
81A GLY* 4.6 13.5 - - - +
2M ASP* 4.8 4.7 - - + +
3M GLU* 1.3 77.8 - - + +
5M VAL* 1.3 64.9 + - - +
6M ALA 3.2 1.3 - - - -
7M GLU* 3.5 3.4 + - - +
8M PHE* 3.1 27.6 + - - +
63M ILE* 4.9 7.9 - - - +
143M LYS* 6.5 1.6 - - - -
147M TYR* 4.9 0.7 + - - -
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Residues in contact with VAL 5 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M ASP* 3.6 35.7 - - + +
4M THR* 1.3 79.0 - - - +
6M ALA* 1.3 61.0 + - + +
8M PHE* 4.3 6.3 - - - -
9M ILE* 3.1 41.5 + - + +
57M GLU* 5.6 3.6 - - - +
61M ALA* 3.4 38.8 - - + +
62M SER 4.2 0.7 - - - -
63M ILE* 3.7 39.5 - - + +
66M ALA* 5.3 1.1 - - + -
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Residues in contact with ALA 6 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.9 14.1 - - - +
2M ASP 5.9 0.4 - - - +
3M GLU* 3.5 12.5 + - + +
4M THR 3.2 0.6 - - - -
5M VAL* 1.3 81.3 - - + +
7M GLU* 1.3 64.1 + - - +
9M ILE* 5.6 0.4 - - - -
10M LYS* 3.2 26.2 + - - +
53M ILE* 3.9 18.6 - - + +
57M GLU* 4.0 20.4 - - - +
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Residues in contact with GLU 7 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 5.0 6.3 - - - -
80A ARG* 3.3 64.1 + - + +
74B GLU* 3.7 12.3 - - - +
3M GLU 4.2 0.8 + - - -
4M THR 3.5 4.2 + - - +
5M VAL 3.5 0.2 - - - -
6M ALA* 1.3 78.7 - - - +
8M PHE* 1.3 62.6 + - - +
10M LYS* 4.0 23.2 + - - +
11M ARG* 2.5 67.6 + - - +
147M TYR* 4.1 2.2 - - - +
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Residues in contact with PHE 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M THR 3.1 18.8 + - - +
5M VAL* 4.0 5.2 - - - +
6M ALA 3.3 0.2 - - - -
7M GLU* 1.3 75.5 - - - +
9M ILE* 1.3 58.7 + - + +
11M ARG* 3.5 1.7 + - - +
12M THR* 2.4 53.6 + - - -
63M ILE* 4.2 21.3 - - + -
66M ALA* 3.4 39.0 - - + -
67M ALA* 4.1 7.2 - - + -
70M ASP* 4.5 17.0 - - + -
134M ARG* 4.3 11.9 - - - -
146M GLN* 3.7 28.7 - - + -
147M TYR* 3.3 34.7 + + - +
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Residues in contact with ILE 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M VAL* 3.1 25.4 + - + +
6M ALA* 5.6 0.2 - - - -
8M PHE* 1.3 77.8 - - + +
10M LYS* 1.3 63.0 + - - +
12M THR* 3.7 6.2 - - - -
13M ILE* 3.1 47.7 + - + +
28M TRP* 5.5 7.9 - - + -
30M PHE* 6.3 1.8 - - + -
52M LEU 5.7 0.7 - - - +
53M ILE* 3.8 17.7 - - + -
56M CYS* 5.0 24.5 - - + -
61M ALA* 5.3 10.3 - - + -
66M ALA* 3.8 31.4 - - + +
69M LEU* 5.0 9.9 - - + -
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Residues in contact with LYS 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 4.9 6.3 + - - -
6M ALA 3.2 18.7 + - - +
7M GLU* 4.0 30.3 + - - +
8M PHE 3.3 0.2 - - - -
9M ILE* 1.3 78.8 - - - +
11M ARG* 1.3 62.1 + - - +
13M ILE* 4.1 3.6 + - - +
14M LEU* 3.5 30.2 + - + +
49M VAL* 4.7 22.4 - - + +
50M GLN* 5.8 6.7 - - + +
53M ILE* 4.1 17.4 - - + +
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Residues in contact with ARG 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 6.4 0.2 - - - -
82A VAL* 3.1 36.6 - - - +
84A PHE* 5.2 8.7 - - - -
74B GLU* 4.0 18.0 + - - +
78B ARG 5.7 2.4 + - - -
79B LYS* 3.7 38.6 - - - +
7M GLU* 2.5 57.6 + - - +
8M PHE 4.2 1.6 - - - +
10M LYS* 1.3 79.4 - - - +
12M THR* 1.3 64.2 + - - +
13M ILE 3.5 0.2 - - - -
14M LEU* 4.0 10.9 + - - +
15M LYS* 3.7 20.4 + - + +
147M TYR* 4.5 14.4 - - + -
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Residues in contact with THR 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 2.4 48.2 + - + -
9M ILE* 3.2 8.3 + - - -
11M ARG* 1.3 77.4 - - - +
13M ILE* 1.3 65.9 + - - +
15M LYS* 3.4 23.2 + - + +
16M ILE* 4.2 7.9 - - + +
69M LEU* 4.1 28.7 - - + +
70M ASP* 4.4 26.9 - - + +
73M TYR* 5.3 6.5 - - + -
147M TYR* 5.5 0.5 - - - -
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Residues in contact with ILE 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M ILE* 3.1 33.5 + - + +
10M LYS* 4.1 2.0 + - - +
11M ARG 3.5 0.2 - - - -
12M THR* 1.3 75.7 - - - +
14M LEU* 1.3 59.2 + - + +
15M LYS 3.1 0.2 - - - -
16M ILE* 2.9 40.9 + - + +
21M LEU* 4.8 17.2 - - + +
25M LEU* 5.8 8.7 - - + -
28M TRP* 6.5 0.4 - - + -
45M LYS* 5.1 2.5 + - - +
48M VAL* 6.1 0.2 - - + -
49M VAL* 3.9 25.8 - - + +
52M LEU* 4.2 34.5 - - + -
53M ILE* 5.6 1.1 - - + -
69M LEU* 4.3 18.8 - - + -
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Residues in contact with LEU 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LYS* 5.6 10.1 - - + -
-32I A 6.1 0.2 - - - +
-31I A 5.7 0.7 + - - -
10M LYS* 3.5 26.6 + - + +
11M ARG* 4.5 6.7 - - - +
12M THR 3.4 0.8 - - - -
13M ILE* 1.3 75.3 - - - +
15M LYS* 1.3 60.2 + - - +
16M ILE 3.2 6.7 + - - +
45M LYS* 4.0 32.2 - - + +
49M VAL* 3.8 30.1 - - + -
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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