Contacts of the helix formed by residues 201 - 212 (chain C) in PDB entry 4SBV
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 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C MET* 4.4 0.9 - - - -
94C PHE* 3.8 15.5 - - + -
105C GLN* 4.7 9.4 - - - +
199C PHE* 4.8 4.3 - - + -
200C LYS* 1.3 77.9 - - - +
202C ALA* 1.3 64.6 + - - +
203C THR* 3.9 8.5 + - - -
204C ASP* 2.8 28.4 + - - +
205C TYR* 3.0 16.6 + - - +
259C ASN 3.8 8.3 - - - +
260C LEU* 2.9 40.2 + - + +
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Residues in contact with ALA 202 (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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92C MET* 4.3 8.3 - - + -
94C PHE* 3.9 32.7 - - + -
95C THR* 5.5 2.2 - - - +
201C THR* 1.3 72.0 - - - +
203C THR* 1.3 60.0 + - + +
205C TYR* 2.9 10.7 + - - +
206C ALA* 2.8 36.8 + - - +
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Residues in contact with THR 203 (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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94C PHE* 5.8 3.4 - - + -
201C THR* 4.0 7.5 + - - +
202C ALA* 1.3 80.9 - - + +
204C ASP* 1.4 71.3 + - - +
206C ALA* 3.2 7.5 - - - +
207C THR* 2.9 28.7 + - - -
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Residues in contact with ASP 204 (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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140B ALA* 4.3 5.8 - - - +
212B ASN* 4.5 4.6 + - - +
214B ASN* 3.2 10.9 + - - +
200C LYS* 2.6 25.3 + - - +
201C THR* 2.8 23.4 + - - +
203C THR* 1.4 81.7 + - - +
205C TYR* 1.3 68.6 - - - +
207C THR* 3.2 7.6 + - - +
208C ALA* 3.0 13.3 + - - +
260C LEU* 3.3 33.3 - - + +
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Residues in contact with TYR 205 (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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90C LEU* 3.2 32.9 - - + +
92C MET* 4.2 12.6 - - + -
139C MET* 3.9 19.4 - - - +
200C LYS* 4.7 4.6 - - + +
201C THR 3.0 12.7 + - - +
202C ALA* 2.9 11.8 + - - +
204C ASP* 1.3 75.9 - - - +
206C ALA* 1.3 59.5 + - + +
208C ALA* 2.5 33.1 + - - +
209C VAL* 2.9 45.0 + - + +
216C GLY* 4.0 11.5 - - - -
219C LEU* 3.6 37.0 - - + -
220C VAL* 3.9 26.9 - - + +
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Residues in contact with ALA 206 (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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202C ALA 2.8 18.2 + - - +
203C THR* 3.2 11.0 - - - +
205C TYR* 1.3 76.5 - - + +
207C THR* 1.3 66.3 + - - +
209C VAL* 3.0 10.8 + - - +
210C GLY* 2.6 24.1 + - - -
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Residues in contact with THR 207 (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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212B ASN* 3.6 13.2 - - - +
203C THR* 2.9 14.7 + - - -
204C ASP* 3.5 14.2 - - - +
206C ALA* 1.3 81.2 - - - +
208C ALA* 1.3 65.8 + - - +
210C GLY* 3.1 8.2 + - - -
211C VAL* 3.2 16.6 + - + +
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Residues in contact with ALA 208 (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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212B ASN* 3.1 34.3 - - - +
214B ASN* 3.8 2.5 - - - +
204C ASP 3.0 6.6 + - - +
205C TYR 2.5 19.2 + - - +
207C THR* 1.3 76.8 - - - +
209C VAL* 1.3 59.4 + - - +
211C VAL* 2.9 14.6 + - - +
212C ASN 3.2 13.1 + - - +
215C ILE* 4.0 10.9 - - + +
219C LEU* 3.8 24.2 - - + -
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Residues in contact with VAL 209 (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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139C MET* 6.0 1.3 - - + +
205C TYR* 2.9 67.1 - - + +
206C ALA* 3.3 6.5 - - - +
208C ALA* 1.3 75.8 - - + +
210C GLY* 1.3 64.2 + - - +
212C ASN 3.8 6.1 - - - -
213C ALA* 3.0 43.0 + - + +
216C GLY* 4.9 5.1 - - - +
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Residues in contact with GLY 210 (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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206C ALA 2.6 17.8 + - - -
207C THR 3.5 5.8 - - - -
208C ALA 3.1 0.4 - - - -
209C VAL* 1.3 74.6 - - - +
211C VAL* 1.3 67.2 + - - +
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Residues in contact with VAL 211 (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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211A VAL* 3.6 34.8 - - + +
211B VAL* 3.7 22.4 - - + +
212B ASN* 3.9 20.0 - - + +
207C THR* 3.2 17.1 + - + +
208C ALA 2.9 8.7 + - - +
210C GLY* 1.3 82.5 - - - +
212C ASN* 1.3 62.2 + - - +
215C ILE* 4.2 10.1 - - + -
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Residues in contact with ASN 212 (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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204A ASP* 4.7 3.5 + - - +
207A THR* 4.0 12.5 - - - +
208A ALA* 3.4 25.6 - - - +
211A VAL* 4.3 8.4 - - + +
215A ILE* 4.0 22.4 - - + -
208C ALA 3.2 4.8 + - - +
209C VAL* 3.1 4.9 - - - +
211C VAL* 1.3 83.5 - - + +
213C ALA* 1.3 65.4 - - - +
214C ASN* 2.2 72.8 + - - +
215C ILE* 2.9 19.5 + - + +
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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