Contacts of the helix formed by residues 47 - 59 (chain A) in PDB entry 3FIW
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A THR* 5.3 3.1 - - - -
45A PHE* 3.1 9.4 - - - +
46A ARG* 1.3 91.4 - - + +
48A LYS* 1.3 63.1 + - - +
49A ARG* 3.8 24.9 + - - +
50A ASP* 3.0 40.5 + - - +
51A LEU* 3.2 10.0 + - - +
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Residues in contact with LYS 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* 4.4 10.3 + - - +
23A ASP 5.5 1.2 + - - -
25A VAL* 2.8 33.1 + - - +
26A SER* 4.8 7.9 - - - +
27A THR* 4.8 12.1 + - - +
47A THR* 1.3 69.0 - - - +
49A ARG* 1.3 67.9 + - - +
51A LEU* 3.2 16.0 + - + +
52A LEU* 3.0 46.1 + - + +
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Residues in contact with ARG 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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47A THR* 3.8 21.9 + - - +
48A LYS* 1.3 79.1 - - - +
50A ASP* 1.3 84.3 + - - +
52A LEU* 3.5 9.7 + - - +
53A THR* 3.1 32.1 + - - +
103A SER* 5.0 0.3 + - - -
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Residues in contact with ASP 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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6A ARG* 5.1 1.0 + - - -
45A PHE* 3.7 14.5 - - + -
46A ARG* 3.9 22.9 + - - +
47A THR* 3.0 29.4 + - - +
49A ARG* 1.3 98.9 + - - +
51A LEU* 1.3 65.1 + - - +
53A THR* 3.8 7.5 + - - -
54A ALA* 3.2 23.2 + - - +
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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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10A ILE* 5.6 0.7 - - + -
13A ALA* 4.2 6.7 - - + -
25A VAL* 4.2 22.2 - - + -
26A SER 4.7 0.7 - - - -
27A THR* 4.5 22.9 - - - +
30A LEU* 3.9 27.1 - - + -
45A PHE* 3.5 41.5 - - + -
47A THR 3.2 10.0 + - - +
48A LYS* 3.2 16.1 + - + +
50A ASP* 1.3 77.0 - - - +
52A LEU* 1.3 58.3 + - + +
54A ALA* 3.3 5.2 + - + +
55A MSE 2.9 44.9 + - + +
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Residues in contact with LEU 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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22A LEU* 3.8 30.3 - - + -
25A VAL* 4.5 9.9 - - + -
48A LYS* 3.0 43.1 + - + +
49A ARG* 3.7 10.8 - - - +
51A LEU* 1.3 72.9 - - + +
53A THR* 1.3 54.2 + - - +
55A MSE 3.1 22.9 + - + +
56A ALA* 2.8 36.2 + - - +
99A LEU* 4.0 6.6 - - + +
103A SER* 3.5 16.3 + - - +
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Residues in contact with THR 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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49A ARG* 3.1 24.3 + - - +
50A ASP* 3.8 9.0 + - - -
52A LEU* 1.3 73.9 - - - +
54A ALA* 1.3 57.1 + - - +
56A ALA* 3.3 3.3 + - - +
57A GLN* 3.1 29.8 + - + +
103A SER* 3.7 23.9 + - - +
104A ARG 5.9 2.0 - - - +
105A PRO* 5.7 2.5 - - + +
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Residues in contact with ALA 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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6A ARG* 4.1 10.8 - - - +
10A ILE* 3.8 16.8 - - + +
45A PHE* 3.5 27.6 - - + -
50A ASP 3.2 12.0 + - - +
51A LEU 3.4 8.3 - - - +
53A THR* 1.3 77.2 - - - +
55A MSE 1.3 64.4 + - - +
57A GLN* 3.9 5.2 - - - +
58A ALA* 3.1 24.6 + - - +
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Residues in contact with MSE 55 (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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10A ILE* 4.3 8.7 - - + +
13A ALA* 3.7 48.0 - - + +
14A LEU* 3.6 16.9 - - + +
17A LEU* 3.9 22.9 - - + -
22A LEU* 5.0 0.2 - - + -
25A VAL* 3.9 17.9 - - + -
51A LEU* 2.9 36.9 + - + +
52A LEU* 3.1 21.3 + - + +
54A ALA* 1.3 72.3 - - - +
56A ALA* 1.3 57.7 + - - +
58A ALA* 3.4 1.0 + - - +
59A ALA* 2.9 29.6 + - - +
99A LEU* 4.0 20.6 - - + -
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Residues in contact with ALA 56 (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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52A LEU 2.8 19.7 + - - +
53A THR 3.6 2.7 - - - +
54A ALA 3.3 0.4 - - - -
55A MSE 1.3 71.9 - - - +
57A GLN* 1.3 62.8 + - - +
59A ALA* 3.4 13.8 + - - +
60A MSE 3.6 6.2 - - - +
99A LEU* 3.8 31.8 - - + +
100A HIS* 4.6 2.0 - - - +
103A SER* 3.4 26.7 - - - +
105A PRO* 3.5 19.4 - - + +
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Residues in contact with GLN 57 (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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53A THR* 3.1 18.4 + - + +
54A ALA* 3.9 6.5 - - - +
56A ALA* 1.3 76.1 - - - +
58A ALA* 1.3 62.6 + - - +
60A MSE 3.2 23.0 + - - +
61A ALA* 4.1 2.1 + - - -
105A PRO* 3.3 13.6 - - + +
106A THR* 2.8 53.2 + - - +
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Residues in contact with ALA 58 (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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10A ILE* 3.5 32.8 - - + -
14A LEU* 4.0 10.7 - - + +
54A ALA 3.1 10.2 + - - +
55A MSE 3.8 2.7 - - - +
57A GLN* 1.3 75.8 - - - +
59A ALA* 1.3 61.4 + - - +
60A MSE 3.1 1.4 + - - -
61A ALA* 3.2 22.1 + - - +
62A PRO* 4.2 1.7 - - - +
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Residues in contact with ALA 59 (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* 4.1 12.3 - - + +
55A MSE 2.9 18.8 + - - +
56A ALA* 3.5 10.1 - - - +
57A GLN 3.2 0.4 - - - -
58A ALA* 1.3 75.9 - - - +
60A MSE 1.3 64.4 + - + +
61A ALA 3.3 0.4 - - - -
62A PRO* 3.5 8.9 - - - +
89A THR* 3.0 24.9 - - - +
93A ARG* 4.9 12.3 - - + +
96A GLY* 6.0 1.3 - - - +
99A LEU* 4.2 16.4 - - + -
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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