Contacts of the helix formed by residues 201 - 210 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.8 25.4 - - - -
199A PHE* 4.5 2.2 - - - -
200A LYS* 1.3 72.3 - - - +
202A ALA* 1.3 54.0 + - - +
203A THR* 4.1 12.6 + - - +
204A ASP* 2.5 37.8 + - + +
205A TYR* 3.2 6.8 + - - -
259A ASN 4.0 7.0 - - - +
260A LEU* 2.5 56.2 + - + +
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Residues in contact with ALA 202 (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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90A LEU* 5.8 4.0 - - + -
92A MET* 5.3 3.7 - - - -
94A PHE* 3.3 35.4 - - + -
95A THR* 5.5 6.3 - - + -
200A LYS 3.9 2.2 + - - -
201A THR* 1.3 69.0 + - - +
203A THR* 1.3 72.9 + - + +
204A ASP 2.8 0.9 + - - -
205A TYR* 2.9 9.6 + - - +
206A ALA* 2.7 27.9 + - - +
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Residues in contact with THR 203 (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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94A PHE* 6.0 1.8 - - + -
201A THR* 3.0 15.0 + - - +
202A ALA* 1.3 85.0 - - + +
204A ASP* 1.3 65.1 + - - +
206A ALA* 3.1 19.6 - - - +
207A THR* 3.1 13.7 + - - -
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Residues in contact with ASP 204 (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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200A LYS* 3.5 24.4 + - - +
201A THR* 2.5 22.4 + - + +
203A THR* 1.3 72.3 + - - +
205A TYR* 1.3 70.0 + - - +
207A THR* 2.7 25.1 + - - +
208A ALA* 2.9 16.1 + - - +
260A LEU* 3.4 33.8 - - + +
140C ALA* 4.0 6.9 - - - +
212C ASN* 4.7 2.8 + - - +
213C ALA* 6.1 0.3 - - - +
214C ASN* 3.8 8.5 - - - +
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Residues in contact with TYR 205 (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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90A LEU* 3.3 37.2 - - + +
92A MET* 4.6 3.8 - - + -
139A MET* 3.0 29.1 - - - +
200A LYS* 4.8 12.5 - - + +
201A THR 3.2 4.6 + - - +
202A ALA* 3.2 16.6 - - - +
204A ASP* 1.3 82.8 + - - +
206A ALA* 1.3 57.5 + - - +
208A ALA* 3.0 6.2 + - - +
209A VAL* 2.7 70.1 + - + +
216A GLY* 3.7 11.7 - - - -
219A LEU* 4.2 15.9 - - + -
220A VAL* 3.6 30.7 - - + -
223A ARG* 5.6 0.5 + - - -
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Residues in contact with ALA 206 (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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202A ALA 2.7 19.5 + - - +
203A THR* 3.1 12.3 - - - +
205A TYR* 1.3 82.1 - - - +
207A THR* 1.3 64.2 + - - +
209A VAL* 3.4 5.6 + - - +
210A GLY* 3.1 20.1 + - - -
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Residues in contact with THR 207 (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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203A THR 3.5 9.7 + - - -
204A ASP* 2.7 21.7 + - - +
206A ALA* 1.3 79.0 - - - +
208A ALA* 1.3 64.2 - - + +
210A GLY* 3.3 9.9 + - - -
211A VAL* 3.5 15.0 + - + +
212C ASN* 4.0 11.4 - - - +
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Residues in contact with ALA 208 (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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204A ASP* 2.9 13.0 + - - +
205A TYR* 3.3 11.2 - - - +
207A THR* 1.3 73.1 - - - +
209A VAL* 1.3 56.8 + - + +
210A GLY 2.8 4.9 - - - -
211A VAL* 2.7 30.0 + - - +
212A ASN 3.3 7.6 - - - +
215A ILE* 3.9 11.8 - - + +
219A LEU* 5.0 3.6 - - + -
212C ASN* 3.4 29.8 - - - +
214C ASN* 4.0 15.5 - - - +
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Residues in contact with VAL 209 (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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139A MET* 5.5 3.4 - - + +
205A TYR* 2.7 70.7 + - + +
206A ALA* 3.6 5.8 - - - +
208A ALA* 1.3 73.6 - - + +
210A GLY* 1.4 58.3 + - - +
211A VAL 3.1 1.6 - - - -
212A ASN 3.5 8.1 - - - -
213A ALA* 3.3 33.3 + - + +
216A GLY* 3.8 15.3 - - - +
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Residues in contact with GLY 210 (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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206A ALA 3.1 12.0 + - - -
207A THR 3.3 7.4 + - - -
208A ALA 2.8 2.0 - - - -
209A VAL* 1.4 79.5 - - - +
211A VAL* 1.3 66.3 + - - +
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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