Contacts of the helix formed by residues 44 - 54 (chain A) in PDB entry 3MOS
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 ALA 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A SER 4.1 7.4 - - - +
41A CYS* 3.0 11.7 + - - +
43A SER* 1.3 78.0 + - - +
45A ALA* 1.3 60.1 + - - +
46A GLU 3.4 2.2 - - - -
47A ILE* 3.3 13.0 + - + +
48A MET* 2.9 35.3 + - + +
75A LYS* 4.3 2.5 - - - +
81A ILE* 5.0 3.6 - - + -
152A LEU* 3.8 25.8 - - + -
183A ASP* 3.6 16.4 - - - +
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Residues in contact with ALA 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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19A ALA* 3.5 26.2 - - - +
22A LEU* 3.8 3.2 - - + +
23A ARG* 3.6 31.2 - - + +
41A CYS 3.3 2.5 + - - +
42A CYS 3.4 5.6 + - - +
43A SER 3.4 2.6 - - - -
44A ALA* 1.3 79.2 - - - +
46A GLU* 1.3 57.1 + - - +
48A MET* 3.4 2.1 + - - +
49A ALA* 2.9 30.5 + - - +
81A ILE* 3.6 19.7 - - + -
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Residues in contact with GLU 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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16A LYS* 5.4 4.2 - - + +
19A ALA* 3.8 11.6 - - + +
20A ASN* 5.5 0.7 + - - -
23A ARG* 2.9 36.6 + - - -
44A ALA 3.4 0.2 - - - -
45A ALA* 1.3 71.2 - - - +
47A ILE* 1.3 66.8 + - - +
49A ALA* 3.2 1.3 + - - -
50A VAL* 2.9 28.9 + - - +
218A GLY 3.6 13.4 + - - +
219A HIS* 2.8 46.1 + - - +
221A VAL* 3.5 25.6 - - + -
224A LEU* 3.7 11.7 - - + -
246A ARG* 5.3 0.7 + - - +
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Residues in contact with ILE 47 (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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43A SER 4.5 0.4 - - - +
44A ALA* 3.3 20.8 + - - +
46A GLU* 1.3 76.1 - - - +
48A MET* 1.3 60.2 + - - +
50A VAL* 4.0 1.2 - - - +
51A LEU* 2.8 52.4 + - + +
152A LEU* 3.9 25.6 - - + -
181A ILE* 3.8 32.8 - - + -
183A ASP* 4.7 6.5 - - - -
218A GLY 4.3 3.3 + - - +
224A LEU* 3.6 29.1 - - + +
228A PHE* 4.7 2.7 - - + -
240A ALA* 4.0 18.2 - - + -
242A THR* 4.5 11.9 - - + -
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Residues in contact with MET 48 (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 LEU* 4.0 6.7 - - + -
44A ALA* 2.9 25.7 + - + +
45A ALA 3.8 3.6 - - - +
47A ILE* 1.3 76.8 - - - +
49A ALA* 1.3 64.6 + - - +
51A LEU* 4.8 1.1 - - - -
52A PHE* 3.0 45.6 + - + +
71A PHE* 3.5 42.2 - - + -
73A LEU* 4.9 1.8 - - + -
81A ILE* 4.0 24.5 - - + +
82A LEU* 3.9 32.3 - - + +
85A VAL* 4.0 13.2 - - + +
152A LEU* 4.1 11.7 - - + -
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Residues in contact with ALA 49 (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 LEU* 3.4 33.8 - - + +
18A THR* 3.8 13.0 - - + -
19A ALA* 3.6 14.4 - - + +
22A LEU* 3.9 6.7 - - + +
45A ALA 2.9 18.1 + - - +
46A GLU* 3.2 3.6 + - - +
48A MET* 1.3 76.3 - - - +
50A VAL* 1.3 58.6 + - + +
53A PHE* 2.9 36.4 + - - +
221A VAL* 5.4 0.2 - - + -
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Residues in contact with VAL 50 (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 LEU* 4.1 10.1 - - + -
46A GLU 2.9 20.1 + - - +
47A ILE 4.0 1.3 - - - +
49A ALA* 1.3 74.6 - - - +
51A LEU* 1.3 67.3 + - - +
54A HIS* 3.0 19.0 + - + +
55A THR* 3.0 24.1 + - - +
221A VAL* 3.7 41.7 - - + +
224A LEU* 4.0 8.1 - - + -
225A CYS* 3.7 28.9 - - - +
228A PHE* 3.7 15.5 - - + -
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Residues in contact with LEU 51 (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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47A ILE* 2.8 40.1 + - + +
48A MET* 4.1 3.6 - - - +
50A VAL* 1.3 73.5 - - - +
52A PHE* 1.3 61.9 + - + +
55A THR* 4.0 7.0 - - - -
56A MET* 2.8 45.5 + - + +
71A PHE* 3.6 33.2 - - + -
150A TYR* 3.6 34.1 - - + -
181A ILE* 4.1 11.4 - - + -
228A PHE* 3.6 29.2 - - + -
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Residues in contact with PHE 52 (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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48A MET* 3.0 37.0 + - + +
51A LEU* 1.3 79.2 - - + +
53A PHE* 1.3 81.5 + - + +
54A HIS 3.7 0.4 - - - -
56A MET* 3.4 28.4 - - + +
58A TYR* 2.7 44.6 + + - +
71A PHE* 3.7 39.3 - + + -
82A LEU* 4.6 0.9 - - + -
85A VAL* 3.8 25.1 - - + -
86A TRP* 3.7 37.7 - + - -
89A ALA* 5.7 0.2 - - + -
286A ALA* 4.5 4.2 - - - -
625A EDO 5.1 1.8 - - - -
627A EDO 5.5 0.2 - - - -
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Residues in contact with PHE 53 (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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11A LYS* 3.2 24.4 + - - -
15A LEU* 3.9 4.5 - - + -
18A THR* 3.7 19.1 - - + -
49A ALA* 2.9 19.8 + - - +
52A PHE* 1.3 92.8 - - + +
54A HIS* 1.3 60.0 + - - +
58A TYR* 3.8 13.9 - - - -
85A VAL* 3.7 16.2 - - + -
88A GLU* 3.6 28.9 - - + -
89A ALA* 3.6 28.3 - - + -
284A ILE* 3.5 55.7 - - + +
285A LEU 4.9 2.4 - - - +
286A ALA* 4.4 8.5 - - - +
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Residues in contact with HIS 54 (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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4A TYR* 3.9 12.8 - + - -
5A HIS* 2.8 40.4 + - + +
7A PRO* 3.8 23.2 - - + +
11A LYS* 2.9 29.2 + - + +
15A LEU* 4.2 7.6 - - + -
50A VAL* 3.0 10.6 + - + +
52A PHE 3.7 0.2 - - - -
53A PHE* 1.3 79.2 - - - +
55A THR* 1.3 68.2 + - - +
56A MET 3.8 1.3 - - - -
57A ARG* 3.0 27.9 + - - -
225A CYS* 3.8 30.5 - - + -
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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