Contacts of the helix formed by residues 51 - 63 (chain A) in PDB entry 1SNG
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 ARG 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ALA 3.1 22.8 + - - -
49A GLY 3.7 7.9 - - - -
50A ALA* 1.3 87.6 + - - +
52A ALA* 1.3 72.9 + - + +
54A THR* 3.3 9.9 + - - -
55A ARG* 3.2 24.7 + - - +
98A ARG* 4.1 1.6 - - - +
285A ASP* 3.0 34.7 + - - +
287A SER* 4.1 13.0 - - - +
288A GLY* 3.7 18.3 - - - -
502A SO4 3.2 38.4 + - - -
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Residues in contact with ALA 52 (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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51A ARG* 1.3 78.6 - - + +
53A THR* 1.3 61.3 + - - +
55A ARG* 3.2 4.2 + - - +
56A THR* 3.0 32.4 + - - -
285A ASP* 4.2 16.2 - - + +
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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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52A ALA* 1.3 77.3 - - - +
54A THR* 1.3 64.7 + - - +
56A THR* 4.2 7.4 - - - -
57A GLU* 3.0 48.1 + - + +
278A THR* 4.0 11.0 - - + +
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Residues in contact with THR 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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50A ALA* 4.0 13.5 - - + -
51A ARG 3.3 8.3 + - - -
52A ALA 3.2 0.6 - - - -
53A THR* 1.3 79.1 - - - +
55A ARG* 1.3 60.6 + - - +
57A GLU* 3.7 4.5 + - - +
58A LEU* 3.5 23.0 + - + +
276A VAL* 5.8 0.2 - - - +
278A THR* 3.4 21.3 - - - +
279A LEU* 3.8 41.3 - - + +
283A SER 4.3 0.5 + - - -
285A ASP* 2.9 32.7 + - - +
286A LEU* 4.1 3.8 - - + -
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Residues in contact with ARG 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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47A ALA 2.9 30.1 + - - +
48A ALA* 3.8 13.1 + - - +
50A ALA* 3.6 29.5 + - - +
51A ARG* 3.2 16.8 + - - +
52A ALA 3.2 9.7 + - - +
54A THR* 1.3 77.8 - - - +
56A THR* 1.3 60.7 - - - +
58A LEU* 3.1 7.5 + - - +
59A THR* 2.9 40.8 + - + +
65A ASP* 4.7 10.9 + - - +
66A PRO* 3.5 28.5 - - - +
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Residues in contact with THR 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 ALA 3.0 19.4 + - - -
53A THR* 3.8 8.7 - - - -
55A ARG* 1.3 77.1 - - - +
57A GLU* 1.3 58.6 + - + +
59A THR* 3.1 8.8 + - - +
60A THR* 2.9 43.7 + - - +
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Residues in contact with GLU 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* 3.0 32.7 + - + +
54A THR* 3.9 4.6 - - - +
56A THR* 1.3 77.1 - - + +
58A LEU* 1.3 62.4 + - - +
60A THR* 3.6 6.1 + - - -
61A LEU* 3.1 23.0 + - - +
275A GLY 3.4 22.3 - - - +
276A VAL* 3.7 11.2 - - + +
277A ARG* 2.8 29.7 + - - +
278A THR* 2.8 32.0 + - - -
279A LEU 4.5 1.6 + - - -
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Residues in contact with LEU 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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43A LEU* 3.9 35.9 - - + +
46A LEU* 4.2 5.6 - - + -
47A ALA* 3.8 38.4 - - + +
50A ALA* 4.3 7.9 - - + -
54A THR* 3.5 16.5 + - + +
55A ARG 3.1 7.7 + - - +
57A GLU* 1.3 78.3 - - - +
59A THR* 1.3 56.9 + - - +
61A LEU* 3.2 3.7 + - + +
62A LEU* 2.9 35.7 + - + +
276A VAL* 3.7 31.2 - - + -
279A LEU* 4.2 18.4 - - + -
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Residues in contact with THR 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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47A ALA* 4.7 5.6 - - + -
55A ARG* 2.9 29.2 + - + +
56A THR* 3.1 18.4 + - - +
58A LEU* 1.3 73.0 - - - +
60A THR* 1.3 60.4 + - - +
62A LEU* 4.5 1.6 - - + +
63A GLY* 2.8 24.3 + - - -
64A THR 3.2 31.7 + - - +
65A ASP* 4.1 10.8 - - - +
66A PRO* 3.9 22.4 - - + -
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Residues in contact with THR 60 (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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56A THR* 2.9 33.2 + - - +
57A GLU* 3.7 6.7 - - - -
58A LEU 3.2 0.2 - - - -
59A THR* 1.3 75.7 + - - +
61A LEU* 1.3 66.5 + - - +
63A GLY* 3.3 11.6 + - - -
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Residues in contact with LEU 61 (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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15A PHE* 3.7 34.6 - - + +
18A HIS* 6.0 6.1 - - + -
19A LEU* 5.1 4.3 - - + -
43A LEU* 4.1 13.2 - - + -
57A GLU 3.1 14.5 + - - +
58A LEU* 3.2 7.8 + - + +
60A THR* 1.3 79.9 - - - +
62A LEU* 1.3 61.6 + - + +
271A LEU* 3.6 25.8 - - + -
274A ALA* 3.7 34.1 - - + +
276A VAL* 3.4 24.9 - - + -
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Residues in contact with LEU 62 (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 ASP* 3.6 25.3 - - - +
15A PHE* 4.1 24.4 - - + +
40A ALA* 4.1 26.7 - - + +
43A LEU* 4.1 15.5 - - + +
44A GLY* 3.9 29.8 - - - +
47A ALA* 4.9 4.9 - - + -
58A LEU 2.9 23.5 + - - +
59A THR* 5.0 0.4 - - + -
61A LEU* 1.3 78.1 - - + +
63A GLY* 1.3 61.6 + - - +
64A THR* 3.5 19.5 + - - +
66A PRO* 5.5 2.7 - - + -
69A LEU* 3.9 23.5 - - + +
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Residues in contact with GLY 63 (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 ASP* 3.9 14.9 - - - +
59A THR 2.8 11.4 + - - -
60A THR* 3.3 7.4 + - - -
61A LEU 3.3 3.6 - - - -
62A LEU* 1.3 76.9 - - - +
64A THR* 1.3 62.9 + - - +
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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