Contacts of the helix formed by residues 197 - 211 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C GLN* 4.4 2.2 - - - -
147C SER* 4.8 1.1 - - - -
148C ALA* 3.3 17.1 - - - +
195C PHE* 3.3 7.9 - - - +
196C SER* 1.3 81.4 - - - +
198C LYS* 1.3 65.6 + - - +
199C PRO* 3.5 8.7 - - - -
200C ALA* 3.4 13.3 + - - +
201C ALA 3.7 0.5 + - - -
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Residues in contact with LYS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C SER* 3.3 45.1 + - - +
148C ALA* 3.8 4.5 - - - +
197C GLY* 1.3 68.4 - - - -
199C PRO* 1.4 73.2 - - + +
201C ALA* 3.2 4.8 + - + +
202C ARG* 3.1 25.4 + - + +
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Residues in contact with PRO 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C GLY* 3.5 7.6 - - - -
198C LYS* 1.4 91.9 - - + +
200C ALA* 1.4 54.3 + - - +
202C ARG* 3.5 7.7 + - + +
203C LYS* 2.9 35.1 + - - +
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Residues in contact with ALA 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PHE* 3.2 26.6 - - - +
172C GLY* 3.8 9.0 - - - -
173C GLN 4.8 0.9 - - - +
195C PHE* 3.5 28.4 - - + -
197C GLY 3.4 7.6 + - - +
198C LYS 3.3 1.0 - - - -
199C PRO* 1.4 73.1 - - - +
201C ALA* 1.4 56.3 + - - +
203C LYS* 3.3 7.0 + - - +
204C ALA* 2.8 34.1 + - - +
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Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C SER 4.8 1.3 - - - +
148C ALA* 3.6 34.5 - - + -
150C LEU* 3.7 13.7 - - + +
195C PHE* 3.7 18.4 - - + -
197C GLY 3.7 2.6 + - - -
198C LYS* 3.2 9.9 + - + +
200C ALA* 1.4 75.3 - - - +
202C ARG* 1.4 51.4 + - - +
204C ALA* 3.3 3.5 + - - +
205C LEU* 2.8 41.0 + - + +
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Residues in contact with ARG 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LYS* 3.1 15.5 + - + +
199C PRO* 3.5 12.3 - - + +
201C ALA* 1.4 71.3 - - - +
203C LYS* 1.3 64.4 + - - +
205C LEU* 3.2 27.1 + - - +
206C ASP* 2.9 65.1 + - - +
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C VAL 5.0 2.7 - - - +
171C PHE* 2.8 37.3 + - + +
172C GLY* 4.7 2.8 - - - -
199C PRO* 2.9 20.7 + - - +
200C ALA* 3.4 15.3 - - - +
202C ARG* 1.3 70.4 - - - +
204C ALA* 1.4 57.1 + - - +
206C ASP* 3.8 4.2 - - - +
207C ARG* 2.9 64.1 + - + +
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 3.9 11.4 - - + -
168C PHE* 4.3 5.4 - - + -
171C PHE* 3.6 33.4 - - + -
195C PHE* 3.9 12.3 - - + -
200C ALA 2.8 18.7 + - - +
201C ALA 3.5 4.9 - - - +
203C LYS* 1.4 76.6 - - - +
205C LEU* 1.3 58.5 + - - +
208C CYS* 3.3 30.8 + - - +
224C VAL* 4.3 3.2 - - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 3.6 23.3 - - + -
201C ALA* 2.8 22.0 + - + +
202C ARG* 3.2 30.0 + - - +
204C ALA* 1.3 73.0 - - - +
206C ASP* 1.3 64.2 + - - +
208C CYS* 4.3 1.2 - - - +
209C SER* 3.3 22.7 + - - -
224C VAL* 3.6 31.4 - - + +
225C GLU* 3.9 20.6 - - - -
226C PRO* 4.0 17.9 - - + -
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Residues in contact with ASP 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ARG* 2.9 59.2 + - - +
203C LYS* 3.8 2.3 - - - +
205C LEU* 1.3 74.1 - - - +
207C ARG* 1.3 89.7 + - - +
209C SER* 2.8 22.2 + - - -
210C GLU* 3.0 20.4 + - - +
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PHE* 3.5 29.2 - - + -
203C LYS* 2.9 44.5 + - + +
206C ASP* 1.3 98.1 + - - +
208C CYS* 1.3 57.0 + - - +
210C GLU* 2.9 41.2 + - - -
211C GLY 3.0 21.1 + - - -
257D PHE* 3.1 24.3 - - + -
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Residues in contact with CYS 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PHE* 4.3 0.7 - - - -
171C PHE* 3.7 22.7 - - - -
204C ALA 3.3 21.5 + - - +
205C LEU 4.6 0.7 - - - +
206C ASP 3.2 1.0 + - - -
207C ARG* 1.3 74.1 - - - +
209C SER* 1.4 53.3 + - - +
211C GLY 3.0 7.2 - - - +
213C PHE* 3.6 34.1 + - + -
222C VAL* 4.3 11.6 - - - +
223C THR* 5.8 0.3 - - - -
224C VAL* 3.7 32.0 + - + +
257D PHE* 4.3 1.8 - - - -
272D LYS* 2.8 24.8 + - - -
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Residues in contact with SER 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LEU 3.3 13.5 + - - -
206C ASP* 2.8 22.6 + - - -
208C CYS* 1.4 78.1 - - - +
210C GLU* 1.4 64.7 + - - +
224C VAL 6.1 0.9 - - - -
272D LYS* 3.2 18.0 + - - +
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Residues in contact with GLU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ASP* 3.0 20.1 + - - +
207C ARG* 2.9 39.0 + - - +
209C SER* 1.4 86.0 + - - +
211C GLY* 1.3 58.4 + - - +
269D MET* 5.7 5.2 - - - +
272D LYS* 4.3 4.2 - - - -
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Residues in contact with GLY 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ARG 3.0 15.3 + - - -
208C CYS 3.0 11.4 - - - +
210C GLU* 1.3 80.6 - - - +
212C SER* 1.3 59.7 + - - -
213C PHE 3.8 0.7 - - - -
257D PHE* 4.0 8.5 - - - -
258D ALA 6.1 0.2 - - - -
269D MET* 6.6 0.2 - - - -
272D LYS* 2.8 24.9 + - - -
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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