Contacts of the helix formed by residues 47 - 55 (chain A) in PDB entry 1SOT
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 TYR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A SER* 1.3 77.3 - - - +
48A ASN* 1.3 64.7 + - - +
49A LEU* 3.1 4.9 + - - +
50A ALA* 3.1 17.1 + - + +
51A VAL* 3.3 12.0 + - - +
154A VAL* 3.8 35.8 - - + +
156A LEU* 3.9 26.9 - - + -
170A GLN* 4.6 9.8 + - - -
208A SER* 4.1 18.6 - - - -
47B TYR* 4.7 6.9 + - - -
152B GLY* 2.8 23.8 + - - +
154B VAL* 3.6 22.4 - - + -
172B ILE* 3.9 15.3 - - + -
45C ALA* 4.3 18.2 - - + +
47C TYR* 4.6 8.5 + - - -
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Residues in contact with ASN 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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46A SER* 2.9 17.7 + - - +
47A TYR* 1.3 79.5 - - - +
49A LEU* 1.3 55.8 + - - +
51A VAL* 3.2 7.2 + - - +
52A ARG* 2.5 72.4 + - - +
150B HIS* 3.9 26.6 + - + +
151B ILE* 2.9 34.6 + - - +
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Residues in contact with LEU 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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46A SER 5.2 1.1 + - - +
47A TYR* 3.1 1.7 + - - -
48A ASN* 1.3 78.9 - - - +
50A ALA* 1.3 63.5 + - - +
52A ARG* 3.6 32.4 - - + +
53A ARG* 3.1 79.1 + - + +
208A SER 4.7 9.9 - - - +
209A LEU* 5.4 0.4 - - + -
42C MSE 4.1 25.8 - - + -
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Residues in contact with ALA 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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47A TYR* 3.1 11.9 + - + +
49A LEU* 1.3 79.8 - - - +
51A VAL* 1.3 63.1 + - - +
53A ARG* 3.8 0.9 - - - +
54A ALA* 3.0 28.5 + - - +
156A LEU* 3.7 16.4 - - + -
206A VAL* 4.5 3.1 - - + -
207A ASN 3.6 18.2 - - - +
208A SER* 3.6 20.9 + - - +
209A LEU 4.3 0.4 - - - -
210A GLY* 3.8 14.6 - - - +
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Residues in contact with VAL 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 TYR 3.6 12.6 - - - +
48A ASN* 3.2 11.6 + - - +
49A LEU 3.2 0.4 - - - -
50A ALA* 1.3 76.9 - - - +
52A ARG* 1.3 62.1 + - + +
55A ALA* 2.7 51.4 + - + +
156A LEU* 3.8 16.8 - - + -
158A ILE* 5.2 4.3 - - + -
166A GLN* 5.4 1.1 - - - +
168A ILE* 4.1 20.4 - - + -
151B ILE* 4.0 39.9 - - + +
152B GLY* 4.3 3.4 - - - -
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Residues in contact with ARG 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 ASN* 2.5 67.2 + - - +
49A LEU* 3.6 38.9 - - - +
51A VAL* 1.3 74.5 - - + +
53A ARG* 1.3 62.4 + - + +
56A PRO* 3.5 18.7 - - - +
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Residues in contact with ARG 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 LEU* 3.1 59.2 + - + +
50A ALA 3.8 2.9 - - - +
52A ARG* 1.3 82.1 - - + +
54A ALA* 1.3 60.0 + - - +
56A PRO* 4.3 3.7 - - - +
57A ALA* 6.0 0.3 - - - +
140A THR 5.0 2.3 - - - +
142A PRO* 3.6 22.8 - - + +
209A LEU* 3.1 43.8 + - - +
210A GLY* 4.6 0.4 - - - -
42C MSE 4.3 11.3 - - - -
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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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50A ALA 3.0 13.2 + - - +
53A ARG* 1.3 77.4 - - - +
55A ALA* 1.3 65.3 + - - +
56A PRO* 3.3 4.5 - - - -
57A ALA* 3.1 21.1 + - - +
58A VAL* 4.1 2.3 + - - +
141A ILE* 3.8 20.1 - - + +
142A PRO* 3.8 6.3 - - + -
158A ILE* 4.1 7.6 - - + -
206A VAL* 3.8 13.2 - - + -
210A GLY* 3.5 24.0 - - - +
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Residues in contact with ALA 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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51A VAL* 2.7 40.8 + - + +
54A ALA* 1.3 72.0 - - - +
56A PRO* 1.4 62.1 - - + +
57A ALA 3.1 1.2 + - - -
58A VAL* 3.1 9.5 + - - +
109A GLN* 4.3 1.1 - - - +
158A ILE* 4.2 17.7 - - + +
166A GLN* 2.8 46.9 - - - +
168A ILE* 4.7 0.7 - - + -
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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