Contacts of the helix formed by residues 209 - 216 (chain F) in PDB entry 6S1M
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 LEU 209 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148F CYS* 4.1 24.5 - - + +
151F LEU* 3.6 34.1 - - + +
152F SER* 3.6 12.6 - - - +
155F GLY 3.4 23.1 - - - +
156F ASP* 2.9 12.8 + - - +
157F ALA 3.7 16.4 - - - +
158F VAL* 3.5 31.0 - - + -
171F ALA* 4.6 0.4 - - + -
207F PHE 3.6 0.4 + - - -
208F ALA* 1.3 69.2 - - - +
210F ARG* 1.3 62.2 + - + +
212F LEU* 3.7 10.0 - - + +
213F ASN* 2.7 34.9 + - - -
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Residues in contact with ARG 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931A LYS* 4.5 27.8 - - - +
156F ASP* 4.9 21.4 - - + +
208F ALA* 4.7 4.9 - - + -
209F LEU* 1.3 81.1 - - - +
211F TYR* 1.3 79.9 + - + +
213F ASN* 3.5 9.6 + - - +
214F PHE* 3.5 29.0 + - + -
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Residues in contact with TYR 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930A ALA* 4.8 5.7 + - + +
22F LEU* 4.5 3.1 - - + -
41F ASP* 3.3 24.9 - - - -
43F SER* 2.6 30.3 + - - -
45F VAL* 4.1 16.9 - - + +
46F SER* 4.4 10.8 - - - -
208F ALA* 3.1 25.8 + - + +
210F ARG* 1.3 87.3 - - + +
212F LEU* 1.3 62.8 + - - +
213F ASN 3.0 1.6 - - - -
214F PHE* 2.8 39.4 + + - +
215F PHE* 3.0 23.2 + - + -
251F LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F PHE* 4.6 10.8 - - + -
148F CYS* 3.7 21.1 - - - -
158F VAL* 3.4 33.2 - - + -
160F ILE* 5.0 6.1 - - + -
169F PHE* 6.4 0.4 - - + -
207F PHE* 4.0 7.9 - - + -
208F ALA 3.3 12.3 + - - +
209F LEU* 3.3 11.6 + - + +
211F TYR* 1.3 75.7 - - - +
213F ASN* 1.3 62.9 + - - +
215F PHE* 3.1 19.1 + - + +
216F THR* 3.0 28.5 + - - +
235F LEU* 3.8 20.2 - - + -
237F VAL* 4.5 4.3 - - + -
251F LEU* 3.8 18.8 - - + -
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Residues in contact with ASN 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F ALA 4.9 0.7 - - - +
148F CYS* 3.3 27.6 + - - +
149F ARG* 3.9 6.5 + - - +
152F SER* 2.7 28.2 + - - -
209F LEU 2.7 25.8 + - - +
210F ARG* 3.6 9.4 - - - +
211F TYR 3.0 0.4 - - - -
212F LEU* 1.3 78.3 - - - +
214F PHE* 1.3 59.7 + - + +
216F THR* 2.6 24.0 + - - +
217F LYS* 3.2 21.0 + - - +
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Residues in contact with PHE 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930A ALA* 4.8 22.0 - - + -
18F ALA 4.5 8.0 - - - +
21F ASP* 4.0 36.6 - - + -
22F LEU* 3.8 37.6 - - + +
210F ARG* 3.5 23.1 + - + -
211F TYR* 2.8 25.3 + + - +
213F ASN* 1.3 75.8 - - + +
215F PHE* 1.3 70.9 + - + +
216F THR 3.1 0.2 - - - -
217F LYS* 3.1 31.1 + - + +
249F TYR* 4.5 0.8 + - - -
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Residues in contact with PHE 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 3.8 22.7 - - + -
46F SER* 3.8 19.3 - - - -
144F PHE* 5.5 1.1 - - + -
211F TYR* 3.0 22.8 + - + -
212F LEU* 3.1 16.1 + - + +
214F PHE* 1.3 80.5 - - + +
216F THR* 1.3 57.2 + - + +
217F LYS 3.1 5.6 + - - -
218F ALA* 3.2 21.3 + - - +
237F VAL* 3.8 27.8 - - + -
239F TYR* 3.5 5.9 - - - +
249F TYR* 3.4 52.1 - + + -
250F TYR 4.4 0.7 - - - -
251F LEU* 3.6 39.7 - - + -
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Residues in contact with THR 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F PHE* 4.1 14.1 - - + -
145F ALA* 3.9 30.2 + - + +
148F CYS* 4.5 7.6 - - + -
212F LEU 3.2 14.6 - - - +
213F ASN* 2.6 29.5 + - - +
215F PHE* 1.3 72.7 - - - +
217F LYS* 1.3 58.0 + - - +
218F ALA 2.8 9.3 + - - -
219F THR* 2.5 29.8 + - - -
220F PRO* 4.5 0.3 - - - +
239F TYR* 3.5 15.9 - - - +
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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