Contacts of the helix formed by residues 28 - 36 (chain A) in PDB entry 1ML0
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 ARG 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE 3.0 1.6 + - - -
27A LYS* 1.3 83.5 - - - +
29A GLY* 1.3 65.2 + - - +
30A ASP* 3.3 10.5 - - - -
31A GLU* 2.9 46.9 + - + +
32A ILE* 3.0 21.0 + - - +
49A GLY 4.1 3.8 + - - -
50A ILE* 3.5 29.3 - - + +
53A ASP* 2.8 53.9 + - - +
54A VAL* 3.9 15.5 - - + -
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.0 20.9 - - - +
26A ILE* 2.6 34.7 + - - -
27A LYS 2.8 3.1 + - - -
28A ARG* 1.3 70.4 - - - +
30A ASP* 1.3 65.0 + - - +
32A ILE* 3.0 19.1 + - - +
33A GLN* 3.1 14.7 + - - +
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.3 28.2 + - + +
24A SER* 5.1 3.6 - - - -
26A ILE 4.9 0.2 - - - +
28A ARG* 3.7 6.2 + - - -
29A GLY* 1.3 79.5 + - - +
31A GLU* 1.3 63.2 + - + +
33A GLN* 3.5 8.2 + - - +
34A ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 2.9 56.7 + - + +
30A ASP* 1.3 78.2 - - + +
32A ILE* 1.3 67.2 + - - +
34A ALA* 3.2 7.6 + - - +
35A HIS* 2.9 33.7 + - + +
50A ILE* 3.9 18.8 - - + +
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.9 3.1 - - + -
27A LYS 3.7 16.2 - - - +
28A ARG 3.0 15.1 + - - +
29A GLY* 3.0 12.1 + - - +
31A GLU* 1.3 74.7 - - - +
33A GLN* 1.3 61.8 + - - +
34A ALA 2.8 1.0 + - - -
36A CYS* 2.6 61.0 + - + +
37A LEU* 4.3 5.2 - - + -
50A ILE* 4.4 14.8 - - + -
51A LEU* 4.9 5.4 - - + -
54A VAL* 4.6 10.1 - - + -
61A GLU* 4.3 9.4 - - + +
62A LEU* 4.5 17.7 - - + -
65A LEU* 3.7 30.1 - - + -
108A LEU* 5.1 0.7 - - + -
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.1 23.4 - - + +
29A GLY 3.1 11.9 + - - +
30A ASP* 3.5 11.5 + - - +
32A ILE* 1.3 79.4 - - - +
34A ALA* 1.3 66.1 + - - +
37A LEU* 3.6 24.9 - - + +
38A THR* 2.9 39.0 + - - -
65A LEU* 5.3 0.6 - - + +
190A SER* 3.9 35.3 - - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP 2.9 18.2 + - - +
31A GLU* 3.4 9.0 - - - +
32A ILE 2.8 1.8 + - - -
33A GLN* 1.3 85.1 - - - +
35A HIS* 1.3 70.8 + - + +
38A THR* 3.0 28.9 - - - +
40A ALA* 3.9 6.6 - - - +
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Residues in contact with HIS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 2.9 27.7 + - + +
34A ALA* 1.3 84.7 - - + +
36A CYS* 1.3 61.7 + - - +
37A LEU 3.8 0.2 - - - -
38A THR 4.1 2.0 - - - -
40A ALA* 4.2 6.4 - - + +
41A GLU* 2.7 41.5 + - - +
46A GLU* 4.3 14.1 - - + +
47A CYS* 3.8 9.5 - - - +
50A ILE* 3.8 25.6 - - + -
106A ARG* 3.0 26.7 + - - -
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Residues in contact with CYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 2.6 44.3 + - + +
35A HIS* 1.3 73.9 - - - +
37A LEU* 1.3 59.9 + - - +
38A THR 3.5 0.7 - - - -
47A CYS* 2.0 54.1 - - - -
50A ILE* 4.7 4.3 - - - -
51A LEU* 4.1 11.7 - - - -
106A ARG* 2.9 26.1 - - - +
108A LEU* 3.9 22.4 - - + +
155A MET* 4.4 0.4 - - - +
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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