Contacts of the helix formed by residues 8 - 18 (chain R) in PDB entry 1MVW
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 ASP 8 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4R LYS* 5.2 2.6 - - - +
6R ALA* 3.1 23.4 + - - +
7R ALA* 1.3 69.1 - - - +
9R ASP* 1.3 57.7 + - - +
10R PHE 3.2 1.8 - - - -
11R LYS* 3.1 44.9 + - - +
12R GLU* 3.2 21.7 + - - +
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Residues in contact with ASP 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R ALA* 3.1 5.1 + - + +
8R ASP* 1.3 76.9 - - - +
10R PHE* 1.3 62.9 + - + +
12R GLU* 3.1 26.2 + - - +
13R ALA* 2.9 27.6 + - - +
37R LEU* 5.5 0.2 - - - -
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Residues in contact with PHE 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R ALA* 3.2 34.9 + - + +
8R ASP 3.2 0.6 - - - -
9R ASP* 1.3 78.2 - - + +
11R LYS* 1.3 57.1 + - - +
13R ALA* 3.3 2.8 + - - +
14R PHE* 3.1 50.7 + - + -
37R LEU* 3.6 45.3 - - + -
65R PHE* 5.6 1.6 - - + -
69R LEU* 4.9 14.6 - - + -
72R LEU* 4.0 21.3 - - + -
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Residues in contact with LYS 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R ASP* 3.1 36.1 + - - +
10R PHE* 1.3 75.9 - - - +
12R GLU* 1.3 71.3 + - - +
14R PHE* 3.2 21.9 + - + +
15R LEU* 3.3 24.8 + - + +
65R PHE* 3.9 31.6 - - + -
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Residues in contact with GLU 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R ASP* 3.2 15.3 - - - +
9R ASP* 3.1 39.3 + - - +
11R LYS* 1.3 86.8 - - - +
13R ALA* 1.3 59.4 + - - +
15R LEU* 3.2 24.0 + - + +
16R LEU* 3.3 20.0 + - + +
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Residues in contact with ALA 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803P TYR* 5.0 3.6 - - - +
9R ASP* 2.9 19.5 + - - +
10R PHE 3.6 5.8 - - - +
11R LYS 3.3 0.2 - - - -
12R GLU* 1.3 75.8 - - - +
14R PHE* 1.3 58.8 + - + +
16R LEU* 3.0 28.6 + - + +
17R PHE* 3.0 33.1 + - + -
37R LEU* 3.9 21.8 - - + -
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Residues in contact with PHE 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R PHE* 3.1 26.3 + - + -
11R LYS* 3.2 11.6 + - + +
13R ALA* 1.3 76.2 - - - +
15R LEU* 1.3 61.4 + - + +
17R PHE* 3.2 1.3 + - - -
18R ASP* 3.0 31.8 + - - +
23R ALA* 6.4 0.7 - - - -
25R ILE* 3.5 27.2 - - + +
33R ILE* 3.8 7.9 - - + -
37R LEU* 3.6 29.2 - - + -
65R PHE* 3.4 42.8 - + + -
68R PHE* 3.8 44.0 - + + -
69R LEU* 4.8 5.4 - - + -
72R LEU* 5.0 4.3 - - + -
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Residues in contact with LEU 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R LYS* 3.3 23.8 - - + +
12R GLU* 3.2 18.4 + - + +
13R ALA 3.2 0.4 - - - -
14R PHE* 1.3 80.7 - - + +
16R LEU* 1.3 62.3 + - + +
17R PHE 3.4 0.2 - - - -
18R ASP* 4.1 15.6 - - - +
21R GLY* 5.8 6.0 - - - +
23R ALA* 4.7 25.1 - - + +
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Residues in contact with LEU 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803P TYR* 3.3 29.4 - - + +
810P ARG* 5.5 9.0 - - - +
12R GLU* 3.3 17.9 - - + +
13R ALA* 3.0 14.7 + - + +
15R LEU* 1.3 81.6 - - + +
17R PHE* 1.3 67.5 + - + +
18R ASP 3.6 0.8 - - - -
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Residues in contact with PHE 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803P TYR* 2.8 48.5 - + - -
806P MET* 5.1 12.3 - - + -
13R ALA* 3.0 35.2 + - + +
14R PHE* 3.2 3.8 + - - +
16R LEU* 1.3 84.3 - - - +
18R ASP* 1.3 61.2 + - - +
19R ARG* 3.4 10.1 + - - +
25R ILE* 4.1 2.9 - - + -
29R GLN* 3.0 27.2 + - - +
32R ASP 6.3 0.2 - - - -
33R ILE* 3.5 54.3 - - + -
36R ALA* 3.8 18.6 - - + -
37R LEU* 5.4 1.6 - - + -
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Residues in contact with ASP 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R PHE 3.0 17.4 + - - +
15R LEU* 4.1 14.6 + - + +
16R LEU 3.6 1.5 - - - -
17R PHE* 1.3 75.8 - - - +
19R ARG* 1.3 60.6 + - - +
20R THR* 2.9 28.3 + - - +
21R GLY* 3.2 12.6 + - - -
22R ASP* 3.0 9.5 + - - +
23R ALA* 2.9 31.7 + - - -
24R LYS 2.9 28.8 - - - +
25R ILE* 4.0 5.8 - - + +
29R GLN* 5.1 1.8 - - - +
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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