Contacts of the helix formed by residues 176 - 191 (chain F) in PDB entry 6E07
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 ASP 176 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174F GLY 5.1 0.2 - - - -
175F ARG* 1.3 89.8 - - + +
177F LEU* 1.3 66.8 + - - +
178F GLN* 3.1 13.3 + - - +
179F SER* 3.2 39.2 + - - -
180F SER* 3.1 25.7 + - - -
257F ARG* 5.5 3.1 - - - +
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Residues in contact with LEU 177 (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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176F ASP* 1.3 73.0 - - - +
178F GLN* 1.4 57.3 + - - +
180F SER* 3.9 5.1 - - - -
181F ASP* 2.9 48.0 + - + +
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Residues in contact with GLN 178 (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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176F ASP* 3.1 12.2 + - - +
177F LEU* 1.4 81.3 - - + +
179F SER* 1.3 59.6 + - - +
181F ASP* 3.7 4.0 - - - +
182F ARG* 3.0 54.8 + - + +
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Residues in contact with SER 179 (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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175F ARG* 3.8 24.0 + - - +
176F ASP* 3.2 26.3 + - - -
178F GLN* 1.3 78.6 - - - +
180F SER* 1.3 61.1 + - - +
182F ARG* 3.5 6.5 + - - +
183F LEU* 3.1 23.7 + - - +
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Residues in contact with SER 180 (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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172F PRO 4.5 10.7 - - - +
173F PHE* 4.1 4.7 - - - +
174F GLY* 2.6 39.3 + - - +
175F ARG* 4.3 1.7 - - - +
176F ASP 3.1 16.2 + - - -
177F LEU* 3.9 5.4 - - - -
179F SER* 1.3 75.0 - - - +
181F ASP* 1.3 54.1 + - - +
183F LEU* 3.3 8.7 + - - +
184F SER* 2.8 34.9 + - - -
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Residues in contact with ASP 181 (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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177F LEU* 2.9 36.4 + - + +
178F GLN* 3.7 4.9 - - - +
180F SER* 1.3 77.1 - - - +
182F ARG* 1.3 59.7 + - + +
184F SER* 3.5 6.8 + - - -
185F ASN* 3.0 50.0 + - - +
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Residues in contact with ARG 182 (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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178F GLN* 3.0 47.5 + - + +
179F SER* 4.1 5.8 - - - +
181F ASP* 1.3 74.0 - - + +
183F LEU* 1.3 60.9 + - - +
185F ASN* 3.3 8.4 + - - +
186F HIS* 2.9 29.3 + - - +
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Residues in contact with LEU 183 (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 PRO* 4.0 15.0 - - + +
147F TYR* 3.9 29.6 - - + -
148F GLU* 3.7 41.1 - - + +
171F LYS 5.5 2.7 - - - +
174F GLY* 6.3 1.3 - - - -
175F ARG* 4.6 14.6 - - - +
179F SER 3.1 17.5 + - - +
180F SER* 3.5 7.2 - - - +
182F ARG* 1.3 76.5 - - - +
184F SER* 1.3 60.3 + - - +
186F HIS* 3.2 6.7 + - + +
187F ILE* 3.0 40.6 + - + +
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Residues in contact with SER 184 (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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172F PRO 5.2 5.4 + - - -
180F SER 2.8 21.0 + - - -
181F ASP* 3.6 10.5 - - - -
183F LEU* 1.3 73.9 - - - +
185F ASN* 1.3 62.1 + - - +
187F ILE* 3.4 7.5 + - - +
188F SER* 3.0 34.5 + - - -
198F ARG* 4.3 20.8 + - - +
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Residues in contact with ASN 185 (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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181F ASP* 3.0 38.9 + - - +
182F ARG* 3.8 8.7 - - - +
183F LEU 3.3 0.2 - - - -
184F SER* 1.3 77.4 - - - +
186F HIS* 1.3 61.1 + - - +
188F SER* 3.8 6.1 - - - -
189F SER* 3.0 29.6 + - - -
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Residues in contact with HIS 186 (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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148F GLU* 3.0 58.6 + - + +
151F THR* 3.2 19.1 + - - -
152F LYS* 4.0 15.9 + - + -
182F ARG 2.9 17.9 + - - +
183F LEU* 3.5 8.1 - - + +
184F SER 3.2 0.2 - - - -
185F ASN* 1.3 74.9 - - - +
187F ILE* 1.3 69.3 - - + +
189F SER* 2.6 23.9 + - - -
190F LEU* 3.5 27.5 + - + +
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Residues in contact with ILE 187 (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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147F TYR* 4.8 5.8 - - + -
151F THR* 4.0 26.2 - - + +
167F ILE* 4.1 16.6 - - + -
169F VAL* 4.3 24.7 - - + -
183F LEU* 3.0 38.2 + - + +
184F SER* 3.9 6.1 - - - +
186F HIS* 1.3 78.2 - - + +
188F SER* 1.3 57.6 + - - +
190F LEU* 3.1 5.7 + - - -
191F PHE* 2.9 32.5 + - + +
196F ILE* 3.7 30.7 - - + -
198F ARG* 5.6 3.1 - - - +
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Residues in contact with SER 188 (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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184F SER* 3.0 21.1 + - - -
185F ASN* 3.9 7.0 - - - -
187F ILE* 1.3 72.5 - - - +
189F SER* 1.3 64.2 + - - +
190F LEU 3.1 2.0 - - - -
191F PHE 3.1 20.5 - - - +
193F GLU* 4.6 4.0 + - - -
196F ILE* 4.4 4.0 - - - +
198F ARG* 4.1 16.3 + - - -
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Residues in contact with SER 189 (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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185F ASN 3.0 15.7 + - - -
186F HIS* 2.6 25.8 + - - -
188F SER* 1.3 75.3 - - - +
190F LEU* 1.3 66.5 + - - +
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Residues in contact with LEU 190 (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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151F THR* 3.9 8.7 - - - +
152F LYS* 3.7 28.3 - - + +
155F HIS* 3.0 50.6 + - + -
156F GLU* 5.8 3.8 - - + +
186F HIS* 3.7 40.8 - - + +
187F ILE 3.1 5.9 + - - +
189F SER* 1.3 87.2 - - - +
191F PHE* 1.3 70.5 + - + +
192F ARG 4.4 0.2 + - - -
195F GLN* 4.7 0.7 - - - +
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Residues in contact with PHE 191 (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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151F THR* 3.7 29.8 - - - -
154F ILE* 4.1 11.7 - - + -
155F HIS* 3.9 15.7 - - + -
159F MET* 3.7 26.7 - - + -
165F ASN* 5.2 3.4 - - + -
167F ILE* 3.6 43.5 - - + -
187F ILE* 2.9 18.7 + - + +
188F SER* 3.1 25.3 - - - +
190F LEU* 1.3 86.0 - - + +
192F ARG* 1.3 65.4 + - - +
193F GLU 3.9 0.3 + - - -
195F GLN* 3.5 23.6 - - + +
196F ILE* 3.8 18.9 - - + +
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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