Contacts of the helix formed by residues 8 - 18 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L LYS* 5.2 2.9 - - - +
6L ALA* 3.1 22.9 + - - +
7L ALA* 1.3 68.7 - - - +
9L ASP* 1.3 59.0 + - - +
10L PHE 3.2 2.0 - - - -
11L LYS* 3.1 44.3 + - - +
12L GLU* 3.2 22.0 + - - +
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Residues in contact with ASP 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ALA* 3.1 4.9 + - + -
8L ASP* 1.3 76.3 - - - +
10L PHE* 1.3 63.4 - - + +
12L GLU* 3.1 25.1 + - - +
13L ALA* 2.9 28.4 + - - +
16L LEU* 6.2 0.2 - - - +
37L LEU* 5.5 0.2 - - - -
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Residues in contact with PHE 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ALA* 3.2 35.6 + - + +
8L ASP 3.2 1.0 - - - -
9L ASP* 1.3 78.7 - - + +
11L LYS* 1.3 58.0 + - - +
13L ALA* 3.3 2.9 + - - +
14L PHE* 3.1 49.3 + - + -
37L LEU* 3.6 47.8 - - + -
65L PHE* 5.7 0.7 - - + -
69L LEU* 4.9 14.8 - - + -
72L LEU* 4.0 21.1 - - + -
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Residues in contact with LYS 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ALA 4.6 0.2 + - - -
8L ASP* 3.1 36.8 + - - +
10L PHE* 1.3 77.6 - - - +
12L GLU* 1.3 68.3 + - - +
14L PHE* 3.2 22.6 + - + +
15L LEU* 3.3 24.7 + - + +
65L PHE* 3.9 31.8 - - + -
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Residues in contact with GLU 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L ASP* 3.2 16.4 - - - +
9L ASP* 3.1 38.5 + - - +
11L LYS* 1.3 87.6 - - + +
13L ALA* 1.3 58.5 + - - +
15L LEU* 3.2 23.4 + - + +
16L LEU* 3.3 20.3 + - + +
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Residues in contact with ALA 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ASP* 2.9 19.1 + - - +
10L PHE 3.6 5.6 - - - +
11L LYS 3.3 0.2 - - - -
12L GLU* 1.3 75.4 - - - +
14L PHE* 1.3 59.6 + - + +
16L LEU* 3.0 29.5 + - + +
17L PHE* 3.0 32.2 + - + -
37L LEU* 3.9 22.0 - - + -
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Residues in contact with PHE 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L PHE* 3.1 26.6 + - + -
11L LYS* 3.2 10.7 + - + +
13L ALA* 1.3 77.2 - - - +
15L LEU* 1.3 61.6 + - + +
17L PHE 3.2 1.2 + - - -
18L ASP* 3.0 31.5 + - - +
23L ALA* 6.4 0.9 - - - -
25L ILE* 3.5 27.9 - - + +
33L ILE* 3.8 7.2 - - + -
37L LEU* 3.6 29.4 - - + -
65L PHE* 3.4 42.0 - + + -
68L PHE* 3.8 44.2 - + + -
69L LEU* 4.8 5.2 - - + -
72L LEU* 5.0 4.0 - - + -
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Residues in contact with LEU 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L LYS* 3.3 24.5 - - + +
12L GLU* 3.2 17.7 + - + +
13L ALA 3.2 0.2 - - - -
14L PHE* 1.3 81.5 - - + +
16L LEU* 1.3 63.0 + - + +
18L ASP* 4.1 16.0 - - + +
21L GLY* 5.8 4.8 - - - +
23L ALA* 4.7 25.8 - - + +
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Residues in contact with LEU 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803J TYR* 5.5 7.0 - - + +
810J ARG* 6.0 4.3 - - - +
12L GLU 3.3 18.6 - - - +
13L ALA* 3.0 18.7 + - + +
15L LEU* 1.3 82.1 - - + +
17L PHE* 1.3 71.3 + - + +
18L ASP 5.1 1.5 - - - -
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Residues in contact with PHE 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803J TYR* 4.0 25.6 - + - -
806J MET* 5.4 13.0 - - + -
13L ALA* 3.0 35.3 + - + +
14L PHE* 3.2 4.0 + - - +
16L LEU* 1.3 89.8 - - + +
18L ASP* 1.3 60.4 - - - +
19L ARG* 3.4 9.8 + - - +
25L ILE* 4.1 2.9 - - + -
29L GLN* 3.0 27.8 + - - +
32L ASP 6.3 0.2 - - - -
33L ILE* 3.5 53.6 - - + -
36L ALA* 3.8 25.6 - - + -
37L LEU* 5.4 1.3 - - + -
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Residues in contact with ASP 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L PHE 3.0 17.4 + - - +
15L LEU* 4.1 14.0 + - + +
16L LEU 3.6 1.3 - - - -
17L PHE* 1.3 75.4 - - - +
19L ARG* 1.3 59.7 + - - +
20L THR* 2.9 27.9 + - - +
21L GLY* 3.2 12.2 + - - -
22L ASP 3.0 9.9 + - - -
23L ALA* 2.9 31.5 + - - +
24L LYS 2.9 26.4 - - - +
25L ILE* 4.0 5.6 - - + -
29L GLN* 5.1 2.0 - - - +
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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