Contacts of the helix formed by residues 42 - 52 (chain B) in PDB entry 1ML3
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ASN* 3.7 8.2 - - + +
41B THR* 1.3 75.1 + - - +
43B ALA* 1.3 61.3 + - - +
44B GLU* 3.3 23.0 + - - +
45B TYR* 3.1 39.3 + - + +
46B PHE* 2.9 20.1 + - + -
74B LYS* 3.5 20.6 + - - +
208C VAL* 5.3 11.8 - - + +
211C TRP* 4.5 10.4 + - - -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR 2.6 11.1 + - - +
42B ASP* 1.3 67.9 - - - +
44B GLU* 1.3 66.2 + - - +
46B PHE* 2.8 8.9 + - - +
47B ALA* 2.8 28.4 + - - +
65B THR* 3.7 12.9 - - + +
75B ASP* 3.2 27.0 + - + +
76B ASP* 4.4 2.0 - - - -
77B THR 4.3 5.6 - - - +
78B LEU* 3.5 26.3 - - + +
87B CYS* 4.5 1.8 - - - -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP* 3.4 16.3 - - - +
43B ALA* 1.3 90.1 + - - +
45B TYR* 1.3 61.8 + - - +
47B ALA* 3.2 6.4 + - - +
48B TYR* 3.0 21.0 + - - +
51B ARG* 5.7 0.2 + - - -
65B THR* 4.1 19.5 - - - +
74B LYS* 5.1 8.0 - - - +
75B ASP* 3.6 23.4 + - + +
211C TRP* 4.1 13.5 - - + -
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASN* 5.3 3.8 - - + -
42B ASP* 3.1 26.6 + - + +
44B GLU* 1.3 73.3 - - - +
46B PHE* 1.3 73.2 + + - +
48B TYR* 3.0 18.6 + + - +
49B GLN* 3.0 64.6 + - + +
205C GLY 3.6 5.2 + - - -
206C VAL* 3.5 20.8 - - + -
207C SER* 2.9 31.4 + - - -
208C VAL* 4.6 14.8 - - + -
211C TRP* 3.2 62.0 + + + +
214C GLY* 5.1 0.2 - - - -
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 3.4 46.9 - + + -
15B ARG* 5.0 1.6 - - - -
36B VAL* 4.5 6.1 - - + -
38B ASP* 3.8 19.5 - - + -
40B ASN* 3.3 41.1 - - + -
41B THR 4.5 0.9 - - - -
42B ASP 2.9 25.8 - - - -
43B ALA* 2.8 14.5 + - - +
45B TYR* 1.3 84.1 - + + +
47B ALA* 1.3 60.6 + - - +
49B GLN* 3.4 13.4 + - - +
50B MET* 3.1 28.9 + - + +
78B LEU* 3.9 15.3 - - + -
87B CYS* 4.2 20.2 - - + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA 2.8 11.6 + - - +
44B GLU* 3.2 9.8 + - - +
46B PHE* 1.3 76.2 - - - +
48B TYR* 1.3 56.6 + - - +
50B MET* 3.9 2.1 - - - +
51B ARG* 3.0 54.1 + - - +
63B VAL* 3.8 20.0 - - + +
64B THR 5.0 0.2 - - - -
65B THR* 3.9 11.9 - - + -
78B LEU* 3.7 10.9 - - + +
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU 3.0 6.4 + - - +
45B TYR* 3.0 23.1 + + - +
47B ALA* 1.3 75.0 - - - +
49B GLN* 1.3 73.2 + - + +
51B ARG* 3.2 12.5 + - - +
52B TYR* 3.2 46.5 + + + +
211C TRP* 3.6 59.0 + + + -
212C ARG 4.5 0.2 + - - -
215C ARG* 3.0 38.0 + - - +
294D GLU* 5.1 4.7 - - + -
295D GLU* 2.6 40.1 + - + -
296D LEU* 4.4 1.8 - - + -
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 5.2 5.3 + - - -
15B ARG* 3.6 49.0 + - - +
19B GLN* 4.5 2.4 - - - +
45B TYR* 3.0 61.5 + - + +
46B PHE* 4.0 15.0 - - - +
48B TYR* 1.3 82.5 - - + +
50B MET* 1.3 59.7 + - - +
52B TYR 2.8 22.3 - - - +
53B ASP* 5.3 1.7 - - - +
205C GLY* 4.1 4.2 - - - +
206C VAL* 4.0 19.5 + - - +
215C ARG* 6.6 0.2 - - - +
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Residues in contact with MET 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 3.8 28.7 - - + -
15B ARG* 4.2 7.8 - - + +
18B PHE* 3.8 30.5 - - + -
19B GLN* 3.6 26.1 - - + +
46B PHE* 3.1 19.1 + - + +
47B ALA* 3.9 4.5 - - - +
49B GLN* 1.3 78.0 - - - +
51B ARG* 1.3 62.4 + - - +
52B TYR 3.6 1.9 + - - +
53B ASP* 5.9 0.5 - - - +
59B PHE* 3.2 32.0 + - + +
63B VAL* 3.9 20.4 - - + -
78B LEU* 4.0 25.1 - - + -
80B VAL* 4.0 6.1 - - + -
85B ILE* 6.4 0.4 - - + -
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU 5.7 0.4 + - - -
47B ALA* 3.0 42.2 + - - +
48B TYR* 3.2 11.9 + - - +
50B MET* 1.3 79.7 - - - +
52B TYR* 1.3 92.7 - - + +
58B LYS* 3.6 4.2 - - - +
59B PHE* 3.2 30.7 + - + +
63B VAL* 2.7 37.4 + - + +
64B THR* 4.7 1.8 - - - +
294D GLU* 3.1 20.2 + - - -
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 5.6 0.5 + - - -
48B TYR* 3.2 29.2 + + + +
49B GLN* 2.8 22.3 - - - +
50B MET 3.4 1.3 - - - -
51B ARG* 1.3 105.3 - - + +
53B ASP* 1.3 63.1 + - - +
57B GLY 4.4 1.3 - - - -
58B LYS* 4.1 33.7 - - + +
204C ASP* 4.5 1.6 - - - +
215C ARG* 3.8 14.6 + - - +
294D GLU* 2.5 36.8 + - - -
296D LEU* 3.5 31.2 - - + +
300D ASP* 3.3 28.9 - - + +
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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