Contacts of the helix formed by residues 212 - 222 (chain A) in PDB entry 1S0R
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A HIS* 3.5 39.0 - + - -
83A ASN* 2.6 37.2 + - - -
85A ILE* 3.8 32.3 - - + -
159A ASN* 3.1 27.7 + - + +
207A THR* 3.7 16.2 - - + -
208A LYS 3.2 29.2 - - - -
209A VAL* 2.8 11.7 + - - +
211A ASN* 1.3 87.8 - - + +
213A VAL* 1.3 57.8 + - - +
214A SER 3.3 3.1 - - - -
215A TRP* 3.2 12.6 + + + +
216A ILE* 2.8 31.0 + - + +
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Residues in contact with VAL 213 (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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105A LEU* 4.2 11.2 - - + -
106A PRO* 3.6 44.6 - - + +
209A VAL* 3.7 15.9 - - + +
210A CYS* 3.8 11.2 + - - +
211A ASN 3.6 1.6 - - - -
212A TYR* 1.3 77.6 - - - +
214A SER* 1.3 58.8 + - - +
216A ILE* 3.3 7.5 + - + +
217A LYS* 2.9 58.7 + - + +
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Residues in contact with SER 214 (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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211A ASN 5.2 2.0 + - - -
212A TYR 3.3 0.8 - - - -
213A VAL* 1.3 78.9 - - - +
215A TRP* 1.3 58.7 + - - +
217A LYS* 3.9 5.7 - - - +
218A GLN* 3.0 33.0 + - - +
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Residues in contact with TRP 215 (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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71A ILE* 3.9 32.3 - - + +
73A HIS* 3.7 51.6 - + + +
74A PRO* 3.5 22.2 - - + +
85A ILE* 4.0 20.2 - - + -
87A LEU* 3.8 27.6 - - + -
211A ASN 5.6 0.2 + - - -
212A TYR* 3.2 16.8 + - + +
214A SER* 1.3 75.2 - - - +
216A ILE* 1.3 87.5 + - + +
218A GLN* 3.6 18.2 - - - +
219A THR* 2.8 48.5 + - - -
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Residues in contact with ILE 216 (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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30A ILE* 3.6 27.4 - - + -
36A VAL* 4.3 9.0 - - + -
85A ILE* 4.1 17.7 - - + -
87A LEU* 4.1 15.9 - - + -
105A LEU* 3.8 30.7 - - + -
209A VAL* 4.5 7.2 - - + -
212A TYR* 2.8 27.9 + - + +
213A VAL* 3.7 6.7 - - - +
215A TRP* 1.3 95.5 - - + +
217A LYS* 1.3 64.6 + - - +
219A THR* 3.8 1.0 - - - -
220A ILE* 2.9 32.6 + - + +
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Residues in contact with LYS 217 (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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105A LEU* 4.5 18.5 - - + +
213A VAL* 2.9 43.0 + - + +
214A SER* 3.9 5.2 - - - +
216A ILE* 1.3 77.4 - - - +
218A GLN* 1.3 63.1 + - - +
220A ILE* 3.4 6.7 + - + +
221A ALA* 3.0 23.2 + - - +
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Residues in contact with GLN 218 (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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214A SER 3.0 22.7 + - - +
215A TRP* 3.6 19.2 - - - +
217A LYS* 1.3 77.6 - - - +
219A THR* 1.3 77.0 + - - +
221A ALA* 3.3 15.4 + - - +
222A SER* 3.3 17.8 + - - -
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Residues in contact with THR 219 (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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34A TRP* 4.6 3.6 - - + -
71A ILE* 3.5 36.8 - - + -
87A LEU* 3.7 20.0 - - + -
215A TRP* 2.8 45.6 + - - -
216A ILE 3.8 2.9 - - - -
218A GLN* 1.3 84.5 + - - +
220A ILE* 1.3 63.0 + - - +
222A SER* 3.2 1.3 + - - -
223A ASN* 2.9 36.6 + - - +
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Residues in contact with ILE 220 (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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30A ILE* 3.8 17.7 - - + -
31A ASN* 4.0 22.0 - - - +
34A TRP* 3.8 45.3 + - + +
87A LEU* 4.9 3.8 - - + -
105A LEU* 5.9 1.1 - - + -
216A ILE* 2.9 40.0 + - + +
217A LYS* 3.9 6.5 - - + +
219A THR* 1.3 75.9 - - - +
221A ALA* 1.3 63.7 + - - +
222A SER 3.1 1.2 + - - -
223A ASN* 3.4 16.5 + - - +
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Residues in contact with ALA 221 (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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217A LYS 3.0 18.2 + - - +
218A GLN* 3.6 10.1 - - - +
219A THR 3.2 0.4 - - - -
220A ILE* 1.3 78.1 - - - +
222A SER* 1.3 61.6 + - - +
223A ASN* 3.6 0.7 - - - -
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Residues in contact with SER 222 (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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218A GLN* 3.3 16.2 + - - -
219A THR* 3.2 2.4 + - - -
220A ILE 3.1 0.4 - - - -
221A ALA* 1.3 79.9 + - - +
223A ASN* 1.3 74.0 + - - +
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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