Contacts of the helix formed by residues 34 - 41 (chain A) in PDB entry 1M4M
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 THR 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PHE 4.3 0.7 - - - -
29A GLU* 3.8 17.7 - - - +
30A ASP* 3.6 24.0 - - - +
31A CYS* 2.9 25.1 + - - +
32A ALA 3.5 2.4 + - - -
33A CYS* 1.3 75.8 - - - +
35A PRO* 1.3 75.1 - - - +
36A GLU* 2.9 12.0 - - - +
37A ARG* 2.8 37.1 + - + +
38A MET* 2.9 10.7 + - - +
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Residues in contact with PRO 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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19A ILE* 4.5 10.8 - - + +
22A PHE* 3.8 34.6 - - + -
25A TRP* 3.4 27.8 - - + -
27A PHE 3.8 13.2 - - - +
28A LEU* 4.4 14.4 - - + -
29A GLU* 4.2 10.1 - - - +
33A CYS 3.8 0.2 - - - -
34A THR* 1.3 86.8 - - - +
36A GLU* 1.3 54.8 + - - +
38A MET* 3.9 2.1 - - + +
39A ALA* 3.0 30.7 + - - +
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Residues in contact with GLU 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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15A LYS* 4.5 8.1 + - - +
19A ILE* 4.5 22.7 - - + +
29A GLU* 5.5 3.1 + - - +
34A THR* 2.9 16.0 - - - +
35A PRO* 1.3 79.7 - - - +
37A ARG* 1.3 92.9 + - + +
39A ALA* 4.3 0.9 - - - +
40A GLU* 3.0 34.4 + - - +
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Residues in contact with ARG 37 (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 CYS 4.5 2.5 - - - -
32A ALA* 3.2 39.1 + - - +
34A THR* 2.8 22.0 + - - +
36A GLU* 1.3 110.2 + - + +
38A MET* 1.3 69.9 + - - +
40A GLU* 3.1 28.4 + - - +
41A ALA* 3.0 18.9 + - - +
72A ASN* 5.4 9.3 + - - +
73A PRO* 4.0 7.1 - - + +
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Residues in contact with MET 38 (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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22A PHE* 3.7 16.4 - - + -
25A TRP* 3.6 33.0 - - + +
33A CYS* 3.5 20.6 - - - -
34A THR 2.9 16.2 + - - +
35A PRO 3.9 0.2 - - - +
37A ARG* 1.3 77.0 - - - +
39A ALA* 1.3 56.6 + - - +
41A ALA* 2.6 32.1 + - - +
42A GLY 3.3 3.3 + - - -
43A PHE* 3.5 18.2 + - + -
55A ALA* 3.5 31.9 - - + -
67A TRP* 3.6 20.4 - - + -
73A PRO* 3.4 30.3 - - + -
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Residues in contact with ALA 39 (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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15A LYS* 4.5 3.6 - - + +
18A ARG* 2.6 46.4 + - + +
19A ILE* 3.7 37.7 - - + +
22A PHE* 4.1 2.6 - - + -
35A PRO 3.0 16.0 + - - +
36A GLU 4.3 0.9 - - - +
38A MET* 1.3 79.6 - - - +
40A GLU* 1.3 55.3 + - - +
42A GLY 3.0 2.6 + - - -
43A PHE 3.5 15.7 - - - +
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Residues in contact with GLU 40 (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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15A LYS* 3.1 40.8 + - - +
18A ARG* 4.2 5.0 + - - +
36A GLU* 3.0 30.0 + - - +
37A ARG* 3.1 30.5 + - - +
38A MET 2.9 0.4 + - - -
39A ALA* 1.3 78.6 - - - +
41A ALA* 1.3 59.0 + - - +
42A GLY 3.3 0.5 + - - -
86A PHE* 3.9 13.0 - - - -
92A GLN* 5.7 3.5 - - - +
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Residues in contact with ALA 41 (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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37A ARG 3.0 5.0 + - - +
38A MET 2.6 17.1 + - - +
40A GLU* 1.3 72.1 - - - +
42A GLY* 1.3 55.4 + - - -
43A PHE* 3.5 20.2 - - + -
73A PRO* 3.7 25.1 - - + +
74A ILE* 3.9 17.7 - - + +
77A HIS* 2.9 26.8 + - - +
86A PHE* 3.2 12.3 - - - -
87A LEU* 4.2 1.4 - - - +
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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