Contacts of the helix formed by residues 203 - 211 (chain A) in PDB entry 6VSU
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 SER 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ASP 3.4 2.9 - - - -
191A TYR* 2.7 26.6 + - - +
192A ASP 4.4 0.2 - - - -
193A CYS 3.9 0.3 + - - -
194A PHE* 3.3 24.8 + - - +
197A ASN 4.6 0.7 - - - -
198A LYS 4.0 5.2 - - - -
200A SER* 3.0 12.8 + - - -
202A ALA* 1.3 78.9 + - - +
204A SER* 1.3 65.6 + - - +
205A PHE 3.0 4.2 + - - -
206A ALA* 3.1 11.2 + - - +
207A ARG* 3.1 33.1 + - - +
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Residues in contact with SER 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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161A HIS* 2.7 36.2 + - - +
162A SER* 3.3 10.7 - - - +
164A SER* 4.5 1.8 - - - -
165A TYR* 3.9 19.2 - - - +
189A ASP 3.4 2.2 + - - -
200A SER 3.6 3.4 + - - -
201A HIS 3.4 10.3 + - - -
202A ALA 3.8 0.2 - - - -
203A SER* 1.3 74.9 - - - +
205A PHE* 1.3 71.8 + - - +
207A ARG* 3.5 5.9 - - - +
208A ILE* 3.0 31.9 + - - +
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Residues in contact with PHE 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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161A HIS* 3.3 34.5 - + - -
164A SER* 4.4 3.6 - - - -
168A VAL* 5.9 1.3 - - + -
181A ILE* 4.4 9.6 - - + -
183A HIS* 3.3 44.6 - + + -
188A PRO 3.7 8.1 - - - +
189A ASP* 2.9 23.1 + - + +
190A ILE* 3.9 7.6 - - + -
204A SER* 1.3 76.9 - - - +
206A ALA* 1.3 60.0 + - - +
208A ILE* 3.7 25.6 - - + +
209A MET* 3.0 35.3 + - - +
217A LEU* 3.9 28.3 - - + -
219A GLN* 4.3 4.9 - - - +
268A SER* 3.8 10.3 - - - -
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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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189A ASP 3.7 1.2 + - - -
190A ILE* 3.6 23.9 - - - +
191A TYR 3.5 21.5 - - - +
203A SER 3.1 9.1 + - - +
205A PHE* 1.3 73.6 - - - +
207A ARG* 1.3 64.4 + - - +
209A MET* 3.4 1.2 + - - +
210A GLU* 2.9 49.6 + - - +
232A GLN* 4.0 8.3 - - - +
236A PHE* 4.2 6.4 - - + -
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Residues in contact with ARG 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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165A TYR* 3.5 47.2 - - + -
192A ASP* 2.8 36.8 + - - -
198A LYS* 2.9 53.8 + - - +
199A TYR* 5.6 0.7 - - - -
203A SER* 3.1 19.2 + - - +
204A SER* 3.5 9.2 - - - +
206A ALA* 1.3 81.3 - - - +
208A ILE* 1.3 62.0 + - - +
210A GLU* 2.8 44.6 + - - +
211A GLY* 3.3 17.5 + - - -
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Residues in contact with ILE 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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164A SER* 3.9 22.9 - - - +
165A TYR* 3.8 16.4 - - + +
168A VAL* 3.8 32.8 - - + -
181A ILE* 4.0 13.9 - - + -
204A SER 3.0 18.9 + - - +
205A PHE* 3.7 36.1 - - + +
206A ALA 3.4 0.2 - - - -
207A ARG* 1.3 74.9 - - - +
209A MET* 1.3 64.9 + - - +
211A GLY 3.0 10.6 + - - -
212A GLY 3.5 7.3 + - - -
213A TYR* 3.5 22.3 + - + -
214A ALA* 4.4 7.1 + - + -
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Residues in contact with MET 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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190A ILE* 4.6 0.9 - - + -
205A PHE 3.0 21.4 + - - +
206A ALA 4.0 0.2 - - - +
208A ILE* 1.3 73.8 - - - +
210A GLU* 1.3 64.0 + - - +
211A GLY 3.0 5.9 + - - -
212A GLY* 3.2 12.7 + - - +
213A TYR 5.5 0.4 - - - +
214A ALA* 3.9 37.0 - - + +
215A ARG 4.3 9.4 - - - +
217A LEU* 3.9 34.3 - - + -
236A PHE* 3.5 60.2 - - + +
237A GLY 5.8 0.7 - - - -
238A VAL* 4.4 2.9 - - + -
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Residues in contact with GLU 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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192A ASP* 4.1 6.6 - - - +
206A ALA* 2.9 28.7 + - - +
207A ARG* 2.8 48.6 + - - +
208A ILE 3.4 0.2 - - - -
209A MET* 1.3 74.4 - - - +
211A GLY* 1.3 58.4 + - - +
212A GLY 3.5 0.2 - - - -
235A ARG* 4.4 12.4 + - - +
236A PHE* 3.9 22.4 - - + -
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Residues in contact with GLY 211 (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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207A ARG 3.3 5.6 + - - -
208A ILE 3.0 8.2 + - - -
209A MET 3.0 1.6 + - - -
210A GLU* 1.3 77.8 - - - +
212A GLY* 1.3 63.2 + - - +
213A TYR* 3.4 32.6 + - - -
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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