Contacts of the helix formed by residues 42 - 52 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B VAL* 6.1 2.4 - - + +
211B TRP* 4.6 7.4 - - - -
40C ASN* 3.3 16.9 + - + +
41C THR* 1.3 73.0 + - - +
43C ALA* 1.3 63.7 + - - +
44C GLU* 2.9 27.7 + - - +
45C TYR* 2.9 28.8 + - + +
46C PHE* 3.0 14.9 + - - -
74C LYS* 3.4 29.6 - - + +
75C ASP 4.6 2.5 - - - -
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR 2.8 8.0 + - - -
42C ASP* 1.3 71.8 + - - +
44C GLU* 1.3 61.9 + - - +
46C PHE* 3.3 11.5 + - - +
47C ALA 3.2 17.7 + - - -
65C THR* 3.4 25.1 - - + +
75C ASP* 3.7 8.1 + - + -
76C ASP* 3.5 14.4 - - - +
77C THR 3.4 30.1 - - - +
78C LEU* 3.6 1.7 - - + +
87C CYS* 4.2 7.9 - - - -
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TRP* 3.9 16.2 - - + -
42C ASP* 2.9 13.2 + - - +
43C ALA* 1.3 78.9 - - - +
45C TYR* 1.3 59.7 + - - +
47C ALA* 3.5 4.5 + - - +
48C TYR* 3.2 20.6 + - - +
51C ARG* 4.8 1.7 + - - -
65C THR* 4.4 17.3 - - - +
74C LYS* 3.1 34.6 + - + +
75C ASP* 4.7 16.8 + - + +
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Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLY 3.8 5.0 + - - -
206B VAL* 3.5 24.9 - - + -
207B SER* 2.6 34.7 + - - -
208B VAL* 4.0 13.2 - - + -
211B TRP* 3.3 54.4 + + + +
214B GLY* 5.1 0.7 - - - -
40C ASN* 3.6 20.4 - - - -
42C ASP* 2.9 24.8 + - + +
44C GLU* 1.3 75.3 - - - +
46C PHE* 1.3 64.7 + - - +
48C TYR* 3.4 9.2 + + - +
49C GLN* 3.0 58.0 + - + +
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Residues in contact with PHE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.6 30.5 - + + -
15C ARG* 4.9 0.5 - - - -
36C VAL* 4.5 9.0 - - + -
38C ASP* 3.7 33.7 - - + -
40C ASN* 2.9 46.9 - - - -
41C THR 4.2 2.2 - - - -
42C ASP 3.0 27.1 + - - -
43C ALA* 3.6 8.7 - - - +
44C GLU 3.3 0.2 - - - -
45C TYR* 1.3 77.4 - - - +
47C ALA* 1.3 63.7 + - - +
49C GLN* 3.0 27.7 + - - +
50C MET* 3.0 28.5 + - + +
78C LEU* 4.0 5.2 - - + -
87C CYS* 4.4 19.7 - - + -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA 3.2 10.0 + - - +
44C GLU* 3.7 7.9 - - - +
45C TYR 3.3 0.2 - - - -
46C PHE* 1.3 80.0 - - - +
48C TYR* 1.3 51.3 + - - +
50C MET* 2.9 13.5 + - - +
51C ARG* 2.7 60.2 + - - +
63C VAL* 3.9 22.6 - - + +
65C THR* 4.4 8.1 - - + -
78C LEU* 4.1 3.6 - - + -
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Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU* 4.7 7.0 - - + +
295A GLU* 2.7 44.7 + - + -
296A LEU* 4.4 1.3 - - + -
211B TRP* 3.6 55.1 + + + -
215B ARG* 3.0 38.7 + - - +
44C GLU 3.2 5.1 + - - +
45C TYR* 3.6 20.6 - + - +
46C PHE 3.2 0.2 - - - -
47C ALA* 1.3 78.4 - - - +
49C GLN* 1.3 69.7 - - + +
50C MET 3.2 0.9 + - - -
51C ARG* 3.3 21.6 + - - +
52C TYR* 3.3 37.8 + + + +
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Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLY 3.7 14.5 - - - +
206B VAL* 4.0 10.5 - - - +
215B ARG* 6.5 0.2 - - - +
10C PHE 4.8 2.4 - - - +
15C ARG* 3.3 49.7 + - - +
38C ASP* 5.7 1.6 + - - +
40C ASN* 5.3 0.8 + - - +
45C TYR* 3.0 66.1 + - + +
46C PHE* 3.0 18.9 + - - +
48C TYR* 1.3 83.3 - - + +
50C MET* 1.3 56.1 + - - +
52C TYR 3.2 18.0 - - - +
53C ASP* 5.4 2.3 - - - +
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Residues in contact with MET 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.7 25.1 - - + -
15C ARG* 4.0 20.6 - - + +
18C PHE* 4.7 10.3 - - + -
19C GLN* 4.7 5.6 - - - +
46C PHE* 3.0 35.8 + - + +
47C ALA* 2.9 11.3 + - - +
49C GLN* 1.3 78.3 - - - +
51C ARG* 1.3 64.7 + - - +
52C TYR* 3.3 1.8 - - - -
53C ASP* 5.8 0.7 - - - +
59C PHE* 3.1 28.5 + - + +
63C VAL* 4.8 12.3 - - + -
78C LEU* 3.5 31.6 - - + -
80C VAL* 4.6 19.1 - - - -
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Residues in contact with ARG 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU* 4.0 21.8 + - - -
44C GLU 4.8 1.8 + - - -
47C ALA* 2.7 47.8 + - - +
48C TYR* 3.6 14.2 - - - +
50C MET* 1.3 74.3 - - - +
52C TYR* 1.3 81.4 + - + +
58C LYS* 3.3 11.3 - - - +
59C PHE* 3.0 31.8 + - - -
63C VAL* 3.0 40.9 + - + +
64C THR* 4.2 5.1 - - - +
65C THR* 6.0 0.2 - - - +
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Residues in contact with TYR 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU* 2.8 39.8 + - - -
296A LEU* 3.6 28.1 - - + +
300A ASP* 2.9 35.4 - - + +
204B ASP* 4.4 2.4 - - - +
215B ARG* 3.8 14.2 + - - +
12C ARG* 5.8 0.2 + - - -
48C TYR* 3.3 22.5 + + - +
49C GLN* 3.2 20.8 - - - +
50C MET 4.7 1.3 - - - -
51C ARG* 1.3 102.9 - - + +
53C ASP* 1.3 60.2 + - - +
57C GLY 4.5 1.1 - - - -
58C LYS* 3.8 36.6 - - + +
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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