Contacts of the helix formed by residues 209 - 216 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148G CYS* 4.0 25.1 - - + +
151G LEU* 3.6 35.0 - - + +
152G SER* 3.7 11.2 - - - +
155G GLY 3.4 24.7 - - - +
156G ASP* 2.9 16.8 + - - +
157G ALA 3.9 13.2 - - - +
158G VAL* 3.6 31.2 - - + +
171G ALA* 4.6 0.7 - - + -
207G PHE 3.6 0.6 + - - -
208G ALA* 1.3 69.4 - - - +
210G ARG* 1.3 62.5 + - - +
212G LEU* 3.7 10.0 - - + +
213G ASN* 2.7 34.7 + - - -
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Residues in contact with ARG 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G ASP 4.2 2.9 + - - +
208G ALA* 3.0 4.5 - - + -
209G LEU* 1.3 80.1 - - - +
211G TYR* 1.3 93.9 + - + +
213G ASN* 3.5 9.7 + - - +
214G PHE* 3.5 48.2 + - + -
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Residues in contact with TYR 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G LEU* 4.4 7.2 - - + -
41G ASP* 3.3 24.9 - - - -
43G SER* 2.5 29.2 + - - -
45G VAL* 4.3 14.9 - - + +
46G SER* 4.5 7.6 - - - -
208G ALA* 3.1 24.3 + - + +
210G ARG* 1.3 102.1 + - + +
212G LEU* 1.3 66.3 + - - +
213G ASN 3.0 1.8 - - - -
214G PHE* 2.9 32.2 + + - +
215G PHE* 3.0 24.9 + - + -
251G LEU* 3.8 27.8 - - + -
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Residues in contact with LEU 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G PHE* 4.4 15.6 - - + -
148G CYS* 3.7 20.9 - - - -
158G VAL* 3.4 33.4 - - + -
160G ILE* 5.0 5.4 - - + -
169G PHE* 6.4 0.4 - - + -
207G PHE* 4.0 9.4 - - + -
208G ALA 3.3 13.3 + - - +
209G LEU* 3.8 12.3 - - + +
211G TYR* 1.3 75.9 - - - +
213G ASN* 1.3 61.9 + - - +
215G PHE* 3.1 18.2 + - + +
216G THR* 3.1 28.1 + - - +
235G LEU* 3.8 19.5 - - + -
237G VAL* 4.5 0.9 - - + -
251G LEU* 3.7 18.8 - - + -
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Residues in contact with ASN 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G ALA 4.9 0.5 - - - +
148G CYS* 3.3 27.7 + - - +
149G ARG* 3.9 6.5 + - - +
152G SER* 2.7 27.0 + - - -
209G LEU 2.7 27.2 + - - +
210G ARG* 3.6 10.4 - - - +
211G TYR 3.0 0.2 - - - -
212G LEU* 1.3 78.9 - - - +
214G PHE* 1.3 59.1 + - + +
216G THR* 2.6 23.0 + - - +
217G LYS* 3.2 20.4 + - - +
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Residues in contact with PHE 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ALA 4.5 3.3 - - - +
21G ASP* 4.0 35.9 - - + -
22G LEU* 3.8 36.1 - - + +
210G ARG* 3.5 56.3 + - + -
211G TYR* 2.9 20.9 + + - +
213G ASN* 1.3 77.7 - - + +
215G PHE* 1.3 70.5 + - + +
216G THR 3.1 0.2 - - - -
217G LYS* 3.0 32.7 + - + +
249G TYR* 4.5 4.5 + - - -
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Residues in contact with PHE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G LEU* 3.7 22.7 - - + -
46G SER* 3.8 26.2 - - - -
144G PHE* 5.4 0.9 - - + -
211G TYR* 3.2 21.3 - - + -
212G LEU* 3.1 22.2 + - + +
214G PHE* 1.3 80.9 - - + +
216G THR* 1.3 58.1 + - + +
217G LYS 3.0 5.9 + - - -
218G ALA* 3.1 20.4 + - - +
237G VAL* 3.9 21.1 - - + -
239G TYR* 3.5 5.4 - - - +
249G TYR* 3.4 53.1 - + + -
250G TYR 4.3 0.7 - - - -
251G LEU* 3.6 34.3 - - + -
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Residues in contact with THR 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G PHE* 4.0 14.8 - - + -
145G ALA* 3.8 28.7 - - + -
148G CYS* 4.5 7.6 - - + -
212G LEU 3.2 14.4 - - - +
213G ASN* 2.6 29.4 + - - +
215G PHE* 1.3 72.3 - - - +
217G LYS* 1.3 57.5 + - - +
218G ALA 2.8 9.6 + - - -
219G THR* 2.5 30.7 + - - -
220G PRO* 4.5 0.3 - - - +
239G TYR* 3.5 15.7 - - - +
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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