Contacts of the helix formed by residues 181 - 196 (chain E) in PDB entry 1F9E
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 GLY 181 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179E ARG 3.0 0.2 + - - -
180E ASN* 1.3 74.9 - - - +
182E THR* 1.3 55.9 + - - +
183E HIS* 2.9 18.0 + - - -
184E LEU* 2.6 41.3 + - - +
185E ASP 3.5 1.7 + - - -
341F ARG* 4.8 3.6 - - - -
342F ASN 4.6 4.0 - - - -
343F PRO* 3.9 18.1 + - - -
346F GLY* 4.2 7.5 - - - -
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Residues in contact with THR 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ASN* 3.3 33.7 - - - +
170E ASN 3.5 5.0 + - - +
171E HIS* 4.1 4.7 - - - +
179E ARG* 2.5 58.7 + - - +
181E GLY* 1.3 73.0 - - - +
183E HIS* 1.3 57.7 + - - +
185E ASP* 2.5 36.0 + - - +
186E ALA 2.9 11.3 + - - -
235E LEU* 3.4 20.6 - - + -
341F ARG* 4.6 2.6 - - - +
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Residues in contact with HIS 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E ASN* 4.2 11.4 - - - +
171E HIS* 3.3 45.4 + + + -
180E ASN* 4.1 1.8 - - + -
181E GLY* 3.2 29.5 + - - -
182E THR* 1.3 74.9 - - - +
184E LEU* 1.3 65.0 + - + +
186E ALA* 3.3 3.1 + - - +
187E GLY* 2.7 28.6 + - - -
204E HIS* 6.4 0.4 - + - -
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Residues in contact with LEU 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E GLY* 2.6 22.4 + - - +
183E HIS* 1.3 84.6 - - + +
185E ASP* 1.3 55.0 + - - +
187E GLY* 3.5 1.4 + - - -
188E ALA* 2.9 30.3 + - - +
343F PRO 3.8 12.3 - - - +
344F ALA 3.6 32.8 - - - +
345F GLU* 3.8 11.0 - - - +
346F GLY 4.0 9.9 - - - +
351F GLN* 3.6 4.6 + - - +
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Residues in contact with ASP 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ARG* 4.6 1.9 + - - -
181E GLY 3.5 0.2 + - - -
182E THR* 2.5 24.0 + - - +
184E LEU* 1.3 70.7 - - - +
186E ALA* 1.3 55.8 + - - +
188E ALA* 3.0 3.3 + - - +
189E LEU* 2.6 40.8 + - - +
235E LEU* 3.7 15.8 - - + +
283E GLN* 4.3 2.6 - - - +
346F GLY* 3.6 2.4 - - - -
347F THR* 3.0 55.0 + - - +
350F ILE* 3.3 20.7 - - + +
351F GLN* 3.2 17.7 + - - +
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ILE* 4.2 12.1 - - + +
169E ASN* 3.0 31.0 - - + +
182E THR 2.9 4.6 + - - -
183E HIS* 3.5 8.1 - - - +
185E ASP* 1.3 75.4 - - - +
187E GLY* 1.3 58.2 + - - +
189E LEU* 3.3 6.0 + - - +
190E THR* 2.5 37.3 + - - +
202E PRO* 6.4 0.9 - - + -
204E HIS* 5.1 8.1 - - + -
235E LEU* 3.8 7.5 - - + +
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Residues in contact with GLY 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E HIS 2.7 19.8 + - - -
184E LEU* 3.8 2.0 - - - -
185E ASP 3.1 0.2 - - - -
186E ALA* 1.3 74.3 - - - +
188E ALA* 1.3 57.3 + - - +
190E THR* 3.0 6.9 + - - -
191E THR* 2.8 35.0 + - - -
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Residues in contact with ALA 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E LEU 2.9 18.4 + - - +
185E ASP* 3.4 3.1 - - - +
187E GLY* 1.3 72.8 - - - +
189E LEU* 1.3 60.6 + - - +
191E THR* 3.7 6.5 - - - -
192E THR* 2.5 34.3 + - - -
351F GLN* 3.9 21.3 - - - +
354F CYS* 3.6 17.9 - - + -
358F ARG* 4.8 9.0 - - - +
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Residues in contact with LEU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ILE* 3.7 15.5 - - + -
185E ASP 2.6 22.8 + - - +
186E ALA 3.6 3.8 - - - +
188E ALA* 1.3 73.4 - - - +
190E THR* 1.3 57.1 + - - +
193E PHE* 2.8 66.9 + - + +
200E ILE* 5.4 0.2 - - - -
233E CYS* 4.0 30.7 - - + -
235E LEU* 4.0 24.0 - - + -
350F ILE* 3.8 25.8 - - + -
353F LEU* 4.9 7.0 - - + -
354F CYS* 3.8 15.5 - - - -
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Residues in contact with THR 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ILE* 4.0 8.2 - - - +
186E ALA* 2.5 24.7 + - - +
187E GLY* 3.3 8.3 - - - -
189E LEU* 1.3 75.6 - - - +
191E THR* 1.3 53.5 + - - +
194E GLU* 2.7 55.2 + - - +
200E ILE* 3.6 36.1 - - + +
202E PRO* 6.0 1.6 - - + +
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Residues in contact with THR 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E GLY 2.8 20.7 + - - -
188E ALA* 3.7 6.5 - - - -
190E THR* 1.3 74.0 - - - +
192E THR* 1.3 59.6 + - - +
194E GLU* 3.4 8.8 - - - +
195E GLU* 2.8 59.3 + - + +
358F ARG* 4.3 13.2 - - - +
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Residues in contact with THR 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E ALA 2.5 25.8 + - - -
189E LEU* 3.6 2.7 - - - -
191E THR* 1.3 74.9 - - - +
193E PHE* 1.3 64.3 + - + +
195E GLU* 3.2 12.4 + - - +
196E LEU* 3.2 28.0 + - + +
354F CYS* 3.4 23.3 - - - +
357F LEU* 3.8 37.7 - - + -
358F ARG* 3.8 25.2 + - + -
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Residues in contact with PHE 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E CYS* 4.0 16.4 - - - -
189E LEU* 2.8 52.0 + - + +
192E THR* 1.3 72.9 - - - +
194E GLU* 1.3 65.6 + - - +
196E LEU* 3.1 25.0 + - + +
197E HIS 3.2 0.2 + - - -
198E PHE* 2.9 37.0 + + + +
200E ILE* 3.8 15.3 - - + -
231E ILE* 3.4 27.1 - - + -
233E CYS* 4.6 5.4 - - - -
281E PHE* 3.7 25.1 - + - -
353F LEU* 5.4 0.2 - - + -
357F LEU* 3.7 24.0 - - + -
400F PHE* 4.0 15.9 - + - -
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Residues in contact with GLU 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E THR* 2.7 37.9 + - - +
191E THR* 3.4 8.9 - - - +
193E PHE* 1.3 74.7 - - - +
195E GLU* 1.3 56.7 + - + +
197E HIS* 2.7 29.8 + - - -
198E PHE 3.8 11.8 + - - +
200E ILE* 3.8 11.2 - - + +
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Residues in contact with GLU 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E THR* 2.8 48.8 + - + +
192E THR* 3.4 6.7 - - - +
193E PHE 3.2 0.2 - - - -
194E GLU* 1.3 77.4 - - + +
196E LEU* 1.3 58.2 + - + +
197E HIS* 3.1 19.2 + - - -
358F ARG* 3.8 30.8 + - + +
402F SER* 4.2 13.8 + - - +
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Residues in contact with LEU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ARG* 3.6 15.1 + - - -
192E THR* 3.2 19.0 + - + +
193E PHE* 3.1 28.2 + - + +
194E GLU 3.0 1.4 - - - -
195E GLU* 1.3 78.7 - - + +
197E HIS* 1.3 75.1 + - - +
198E PHE* 3.6 15.2 - - + -
357F LEU* 4.6 4.7 - - + -
361F CYS* 4.0 20.4 - - + -
362F PRO* 5.8 0.4 - - + -
400F PHE* 3.5 52.8 - - + +
401F PRO 4.1 8.4 - - - +
402F SER* 4.5 9.2 - - - +
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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