Contacts of the helix formed by residues 197 - 211 (chain E) in PDB entry 5IFM
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 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E GLN* 4.4 2.0 - - - -
147E SER* 4.8 0.7 - - - -
148E ALA* 3.2 17.7 - - - +
195E PHE* 3.3 4.6 - - - +
196E SER* 1.3 80.3 - - - +
198E LYS* 1.4 64.4 + - - -
199E PRO* 3.5 9.5 - - - -
200E ALA* 3.6 13.3 + - - +
201E ALA 3.7 4.7 + - - -
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Residues in contact with LYS 198 (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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305B HIS* 3.4 43.5 - - - +
306B GLU* 5.9 0.2 - - + -
308B GLN 5.7 0.2 - - - -
309B VAL* 3.5 40.9 + - + +
147E SER* 3.0 50.1 + - - +
148E ALA* 3.9 3.8 - - - +
150E LEU* 5.9 1.6 - - - +
197E GLY* 1.4 68.9 - - - -
199E PRO* 1.4 70.6 - - + +
201E ALA* 3.4 14.3 + - - +
202E ARG* 3.1 38.2 + - + +
205E LEU* 5.2 4.8 - - - +
226E PRO* 6.4 0.2 - - - +
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Residues in contact with PRO 199 (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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309B VAL* 3.5 33.1 - - + +
310B MET* 3.8 27.6 - - + -
197E GLY* 3.5 7.9 - - - -
198E LYS* 1.4 87.5 - - + +
200E ALA* 1.4 55.0 + - - +
202E ARG* 3.3 6.5 + - + +
203E LYS* 2.9 39.2 + - - +
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Residues in contact with ALA 200 (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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171E PHE* 3.4 29.2 - - - +
172E GLY* 3.7 11.2 - - - -
173E GLN 4.4 2.5 - - - +
195E PHE* 3.6 24.5 - - + -
197E GLY* 3.6 10.5 + - - +
198E LYS 3.4 0.4 - - - -
199E PRO* 1.4 76.2 - - - +
201E ALA* 1.3 56.6 - - - +
203E LYS* 3.2 6.7 - - - +
204E ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 201 (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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148E ALA* 3.7 28.9 - - + -
150E LEU* 3.8 14.0 - - + +
195E PHE* 3.6 26.6 - - + -
197E GLY 3.7 1.4 + - - -
198E LYS* 3.4 16.5 + - - +
199E PRO 3.4 0.2 - - - -
200E ALA* 1.3 76.2 - - - +
202E ARG* 1.4 53.1 + - - +
204E ALA* 3.2 4.3 + - - +
205E LEU* 2.9 36.1 + - - +
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Residues in contact with ARG 202 (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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302B ALA 5.9 0.4 - - - -
305B HIS* 2.8 36.3 + - - -
306B GLU* 3.7 31.0 + - + +
309B VAL* 5.9 2.2 - - + -
198E LYS* 3.1 26.8 + - + +
199E PRO* 3.5 11.9 - - + +
201E ALA* 1.4 70.6 - - - +
203E LYS* 1.3 64.8 + - - +
205E LEU* 3.3 37.6 + - - +
206E ASP* 3.1 62.4 + - - +
226E PRO* 5.4 2.4 - - - +
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Residues in contact with LYS 203 (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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170E VAL 5.5 1.3 - - - +
171E PHE* 3.4 32.6 + - + +
199E PRO* 2.9 19.5 + - - +
200E ALA* 3.2 10.8 - - - +
202E ARG* 1.3 74.4 - - - +
204E ALA* 1.4 55.2 + - - +
206E ASP* 3.6 3.6 + - - +
207E ARG* 3.2 43.2 + - + +
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Residues in contact with ALA 204 (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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150E LEU* 3.8 11.7 - - + -
168E PHE* 4.4 5.2 - - + -
171E PHE* 3.6 32.7 - - + +
195E PHE* 3.8 14.1 - - + -
200E ALA 3.0 13.4 + - - +
201E ALA 3.2 9.4 + - - +
203E LYS* 1.4 72.2 - - - +
205E LEU* 1.4 63.6 + - - +
208E CYS* 3.1 32.1 + - - +
224E VAL* 4.3 2.2 - - + -
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Residues in contact with LEU 205 (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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305B HIS* 5.8 0.2 - - + -
150E LEU* 3.9 21.3 - - + -
198E LYS* 5.2 5.2 - - - +
201E ALA 2.9 17.2 + - - +
202E ARG* 3.5 47.8 - - - +
204E ALA* 1.4 73.0 - - - +
206E ASP* 1.4 61.0 + - - +
208E CYS* 4.0 1.9 - - - +
209E SER* 3.3 23.9 + - - -
224E VAL* 3.4 32.4 - - + +
225E GLU* 3.9 15.5 - - - -
226E PRO* 3.9 17.7 - - + -
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Residues in contact with ASP 206 (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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202E ARG* 3.1 49.7 + - - +
203E LYS* 4.1 4.6 - - - +
205E LEU* 1.4 73.4 - - - +
207E ARG* 1.3 61.7 + - + +
209E SER* 2.9 19.2 + - - -
210E GLU* 3.1 36.6 + - - +
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Residues in contact with ARG 207 (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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170E VAL* 5.0 13.3 + - - +
171E PHE* 3.7 32.3 - - + -
203E LYS* 3.2 27.1 + - + +
206E ASP* 1.3 76.9 - - + +
208E CYS* 1.3 57.5 + - - +
210E GLU* 4.1 10.9 - - - +
211E GLY* 2.9 29.3 + - - -
213E PHE* 5.8 0.6 - - - +
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Residues in contact with CYS 208 (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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168E PHE* 4.3 0.4 - - - -
171E PHE* 3.6 27.6 - - - -
204E ALA 3.1 23.9 + - - +
205E LEU 4.0 0.9 - - - +
207E ARG* 1.3 75.2 - - - +
209E SER* 1.4 58.2 + - - +
211E GLY 3.1 15.2 - - - +
213E PHE* 3.8 32.3 + - + -
221E PRO* 6.1 0.3 - - - +
222E VAL 4.4 12.0 - - - +
223E THR* 5.7 0.5 - - - -
224E VAL* 3.9 33.7 + - + -
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Residues in contact with SER 209 (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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205E LEU 3.3 14.2 + - - -
206E ASP* 2.9 20.4 + - - -
208E CYS* 1.4 77.9 - - - +
210E GLU* 1.4 65.0 + - - +
211E GLY 3.5 2.7 - - - +
224E VAL 5.9 1.8 - - - -
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Residues in contact with GLU 210 (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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206E ASP* 3.1 35.6 + - - +
207E ARG* 4.1 10.9 - - - +
209E SER* 1.4 86.7 + - - +
211E GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 211 (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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207E ARG 2.9 16.2 + - - -
208E CYS 3.1 22.2 - - - +
209E SER 4.0 2.4 - - - +
210E GLU* 1.3 79.1 - - - +
212E SER* 1.3 62.8 + - - -
213E PHE 3.9 0.7 - - - -
221E PRO* 5.4 0.3 - - - +
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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