Contacts of the helix formed by residues 34 - 46 (chain A) in PDB entry 1MUW
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ALA 4.1 1.6 + - - -
33A LEU* 1.3 75.4 - - - +
35A PRO* 1.3 68.5 - - - +
36A VAL* 2.9 17.2 + - - +
37A GLU* 2.9 25.4 + - + +
38A THR* 3.1 10.0 + - - -
73A ARG* 2.7 48.5 + - - -
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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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14A LEU* 4.0 31.1 - - + +
33A LEU 3.4 7.8 - - - +
34A ASP* 1.3 89.4 - - - +
36A VAL* 1.3 56.5 + - + +
38A THR* 3.3 4.8 + - - +
39A VAL* 2.9 34.3 + - - +
56A ASP 4.0 17.9 - - - +
57A LEU* 4.6 3.1 - - + -
73A ARG* 4.5 2.0 - - - +
74A PHE* 4.2 14.6 - - + -
454A MG 3.4 26.2 - - - -
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Residues in contact with VAL 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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34A ASP* 2.9 13.0 + - - +
35A PRO* 1.3 76.9 - - + +
37A GLU* 1.3 62.6 + - - +
39A VAL* 3.3 2.6 + - - +
40A GLN* 3.0 45.9 + - - +
73A ARG* 3.6 58.6 - - + +
74A PHE* 4.4 3.4 - - - +
76A GLN* 6.2 0.4 - - - +
77A ALA* 4.0 17.3 - - + -
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Residues in contact with GLU 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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33A LEU* 4.1 19.1 - - + -
34A ASP* 2.9 23.6 + - + +
36A VAL* 1.3 75.4 - - - +
38A THR* 1.3 68.1 + - - +
40A GLN* 3.3 13.1 + - - +
41A ARG* 2.9 71.5 + - + +
299A TRP* 5.0 2.7 + - + -
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Residues in contact with THR 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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14A LEU* 3.8 29.2 + - + -
17A VAL* 3.6 24.8 - - + +
33A LEU* 3.3 28.8 - - - +
34A ASP 3.1 9.8 + - - -
35A PRO* 3.5 9.4 - - - +
37A GLU* 1.3 76.4 - - - +
39A VAL* 1.3 62.1 + - - +
41A ARG* 4.1 0.2 - - - +
42A LEU* 2.9 39.6 + - + +
50A VAL* 4.6 1.3 - - + -
299A TRP* 4.1 8.1 - - - -
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Residues in contact with VAL 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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14A LEU* 4.9 1.1 - - + -
35A PRO 2.9 21.4 + - - +
36A VAL 3.7 4.7 - - - +
38A THR* 1.3 75.7 - - - +
40A GLN* 1.4 58.3 + - - +
43A ALA* 3.0 29.1 + - - +
50A VAL* 4.3 11.2 - - + -
74A PHE* 3.6 30.3 - - + -
77A ALA* 3.7 23.6 - - + +
78A LEU* 4.1 8.7 - - + +
81A THR* 3.5 24.7 - - + +
83A MET* 3.9 21.0 - - + +
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Residues in contact with GLN 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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36A VAL* 3.0 36.5 + - + +
37A GLU* 3.3 21.8 + - - +
39A VAL* 1.4 76.0 - - - +
41A ARG* 1.3 76.4 + - - +
43A ALA* 3.4 2.1 + - - +
44A GLU* 3.1 30.8 + - - +
77A ALA* 5.0 7.6 - - + +
81A THR* 4.3 19.7 - - + -
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Residues in contact with ARG 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 GLU* 2.9 57.9 + - - +
40A GLN* 1.3 87.8 + - - +
42A LEU* 1.3 63.7 + - - +
44A GLU* 2.4 46.4 + - - +
45A LEU* 3.1 26.9 + - + +
299A TRP* 3.6 48.9 - - + +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.8 44.9 - - + +
13A GLY 5.5 0.2 - - - +
17A VAL* 4.5 8.5 - - + -
38A THR* 2.9 31.3 + - + +
41A ARG* 1.3 72.6 - - - +
43A ALA* 1.3 67.5 + - - +
45A LEU* 3.1 19.0 + - + +
46A GLY 3.2 0.3 + - - -
47A ALA* 3.0 26.6 + - + +
50A VAL* 3.5 29.6 - - + -
83A MET* 3.8 11.9 - - + -
299A TRP* 3.8 25.6 - - + -
302A ALA* 4.5 1.8 - - + -
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Residues in contact with ALA 43 (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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6A PRO* 5.9 1.2 - - - +
39A VAL 3.0 18.5 + - - +
40A GLN 3.7 4.7 - - - +
41A ARG 3.3 0.2 - - - -
42A LEU* 1.3 76.8 - - - +
44A GLU* 1.3 63.5 + - + +
46A GLY* 3.0 14.9 + - - -
47A ALA 4.2 4.2 + - - +
81A THR* 3.8 22.4 - - + +
83A MET* 3.7 25.9 - - + -
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLN* 5.4 2.1 + - - -
40A GLN* 3.1 16.1 + - - +
41A ARG* 2.4 44.4 + - - +
42A LEU 3.2 0.4 - - - -
43A ALA* 1.3 77.7 - - + +
45A LEU* 1.3 63.4 + - + +
46A GLY 3.5 0.5 + - - -
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Residues in contact with LEU 45 (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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3A GLN* 3.8 8.8 + - - -
4A PRO* 3.3 21.8 - - - +
41A ARG* 3.1 16.6 + - + +
42A LEU* 3.1 14.7 + - + +
44A GLU* 1.3 77.4 - - + +
46A GLY* 1.3 57.5 + - - +
47A ALA 3.6 0.2 - - - -
299A TRP* 3.8 50.5 - - + +
302A ALA* 4.1 11.9 - - + -
303A ALA* 4.2 18.4 - - + +
306A MET* 3.6 12.8 - - + +
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Residues in contact with GLY 46 (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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3A GLN* 4.7 0.7 - - - -
4A PRO* 3.6 18.8 - - - +
5A THR* 3.2 30.2 + - - +
6A PRO* 4.4 4.7 - - - -
10A PHE* 5.0 1.6 - - - +
43A ALA 3.0 13.2 + - - -
44A GLU 3.2 1.2 + - - -
45A LEU* 1.3 77.8 - - - +
47A ALA* 1.3 65.9 + - - +
306A MET* 4.3 5.2 - - - +
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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