Contacts of the helix formed by residues 47 - 55 (chain C) in PDB entry 1SOZ
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A TYR* 4.4 11.4 + - - -
152A GLY* 2.8 25.2 + - - +
154A VAL* 3.5 23.1 - - + +
172A ILE* 4.0 10.1 - - + -
45B ALA* 4.6 9.5 - - + +
47B TYR* 4.7 6.6 + - - -
46C SER* 1.3 78.2 - - - +
48C ASN* 1.3 66.1 + - - +
49C LEU* 3.1 3.8 - - - -
50C ALA* 2.9 17.0 + - + +
51C VAL* 3.1 10.4 + - - +
154C VAL* 3.7 34.1 - - + +
156C LEU* 3.7 27.4 - - + -
170C GLN* 4.0 17.2 + - + -
208C SER* 3.9 27.4 - - - -
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Residues in contact with ASN 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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150A HIS* 3.7 26.9 + - + +
151A ILE* 2.9 31.3 + - - +
152A GLY* 3.9 1.6 - - - -
46C SER* 2.9 18.3 + - - +
47C TYR* 1.3 78.1 - - - +
49C LEU* 1.3 51.8 + - - +
51C VAL* 2.8 7.9 + - - +
52C ARG* 2.7 78.4 + - - +
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Residues in contact with LEU 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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42B MET* 3.9 35.9 - - + -
46C SER 5.1 2.1 + - - +
47C TYR* 3.1 2.4 + - - -
48C ASN* 1.3 78.7 + - - +
50C ALA* 1.3 63.1 + - - +
52C ARG* 3.0 35.2 + - + +
53C ARG* 3.0 45.9 + - + +
208C SER 4.8 8.3 - - - +
209C LEU* 5.1 3.8 - - + +
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Residues in contact with ALA 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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47C TYR* 2.9 11.6 + - + +
49C LEU* 1.3 79.1 - - - +
51C VAL* 1.3 60.9 + - - +
54C ALA* 3.1 28.8 + - - +
156C LEU* 3.6 17.3 - - + -
158C ILE* 4.8 0.7 - - - +
206C VAL* 4.6 3.5 - - + +
207C ASN 3.3 26.2 - - - +
208C SER* 3.4 18.3 + - - +
209C LEU 4.3 0.7 - - - -
210C GLY* 3.8 12.1 - - - +
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Residues in contact with VAL 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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151A ILE* 3.7 42.8 - - + +
152A GLY* 4.2 2.9 - - - -
47C TYR 3.1 13.0 + - - +
48C ASN* 2.8 13.3 + - - +
50C ALA* 1.3 77.3 - - - +
52C ARG* 1.3 66.5 + - + +
55C ALA* 2.9 46.2 + - + +
56C PRO* 3.6 0.7 - - - +
156C LEU* 4.5 4.0 - - + -
158C ILE* 5.3 2.7 - - + -
166C GLN* 5.6 0.9 - - - +
168C ILE* 4.1 30.7 - - + -
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Residues in contact with ARG 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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48C ASN* 2.7 56.9 + - - +
49C LEU* 3.0 40.0 - - + +
51C VAL* 1.3 74.5 - - + +
53C ARG* 1.3 62.1 + - + +
56C PRO* 3.4 20.7 - - - +
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Residues in contact with ARG 53 (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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49C LEU* 3.0 37.0 + - + +
50C ALA 4.2 2.2 - - - +
52C ARG* 1.3 80.5 - - + +
54C ALA* 1.3 59.7 + - - +
56C PRO* 4.3 2.8 - - - +
57C ALA* 5.7 0.2 - - - +
140C THR 4.1 6.4 - - - +
142C PRO* 3.4 50.4 - - + +
143C ILE 5.9 0.6 + - - -
209C LEU* 2.7 29.9 + - - +
210C GLY* 4.5 1.1 - - - -
211C GLU* 4.6 10.5 + - - +
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Residues in contact with ALA 54 (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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50C ALA 3.1 16.7 + - - +
53C ARG* 1.3 77.4 - - - +
55C ALA* 1.3 65.3 + - - +
56C PRO* 3.2 4.3 - - - -
57C ALA* 3.1 22.5 + - - +
58C VAL* 3.8 1.4 + - - +
141C ILE* 3.7 18.9 - - + +
142C PRO* 3.9 5.2 - - - -
158C ILE* 4.0 6.3 - - + -
206C VAL* 3.9 12.3 - - + -
210C GLY* 3.5 23.8 - - - +
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Residues in contact with ALA 55 (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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51C VAL* 2.9 39.0 + - + +
54C ALA* 1.3 72.3 - - - +
56C PRO* 1.3 57.2 - - + +
58C VAL* 2.8 19.7 + - - +
109C GLN* 3.9 0.9 - - - +
158C ILE* 3.7 19.2 - - + +
166C GLN* 3.0 42.7 - - - +
168C ILE* 4.4 2.0 - - + -
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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