Contacts of the helix formed by residues 201 - 212 (chain C) in PDB entry 5FI0
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 LYS 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C GLN* 3.2 24.7 - - - +
198C ARG* 2.9 21.3 + - - +
200C CYS* 1.3 79.1 - - - +
202C TYR* 1.3 65.2 + - - +
203C PRO 3.4 0.2 - - - -
204C LEU* 3.0 21.6 + - + +
205C LEU* 3.1 19.4 + - + +
35D THR* 4.0 19.8 + - + +
36D VAL* 4.3 30.3 - - + -
37D PHE 4.2 10.3 + - - +
57D ASP* 3.4 31.7 + - - +
59D ALA* 3.4 28.7 + - - +
61D GLN* 5.9 1.1 - - - +
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Residues in contact with TYR 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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57C ILE* 5.7 1.1 - - + -
61C GLU* 2.2 29.9 + - + -
110C HIS* 3.0 23.1 - + - -
113C PHE* 4.1 15.5 - + - -
135C PHE* 3.6 22.4 - + + -
142C PHE* 5.0 2.5 - + - -
145C TYR* 4.9 0.2 - - - -
198C ARG* 2.9 54.6 + - + +
199C ILE* 3.6 24.9 - - + -
201C LYS* 1.3 77.9 - - - +
203C PRO* 1.4 69.0 - - + +
205C LEU* 3.3 13.2 + - + +
206C LEU* 2.9 29.5 + - - +
230C MET* 3.6 28.9 - - + -
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Residues in contact with PRO 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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199C ILE 3.4 9.2 - - - +
200C CYS* 3.4 15.7 - - - +
202C TYR* 1.4 93.7 - - + +
204C LEU* 1.3 58.0 + - + +
206C LEU* 4.5 1.6 - - + -
207C LYS* 2.9 24.8 + - - +
227C LEU* 3.2 18.9 - - + +
230C MET* 4.1 20.4 - - + -
231C LYS* 3.9 23.6 - - + +
234C CYS* 4.1 17.7 - - - -
64D TYR* 4.8 5.8 - - + +
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Residues in contact with LEU 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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200C CYS 4.3 4.9 - - - +
201C LYS* 3.0 13.3 + - + +
203C PRO* 1.3 80.2 - - + +
205C LEU* 1.3 60.8 + - - +
207C LYS* 3.0 18.0 + - + +
208C GLU* 2.9 29.1 + - - +
35D THR* 3.5 25.1 - - + +
59D ALA* 3.9 15.5 - - + +
60D GLY* 3.7 36.1 - - - +
62D GLU* 5.5 2.2 - - - +
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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
----------------------------------------------------------
53C VAL* 3.6 9.3 - - + +
56C GLU* 3.8 25.1 - - + +
57C ILE* 4.0 28.0 - - + -
60C THR* 4.5 4.3 - - - +
135C PHE* 5.7 1.6 - - + -
198C ARG* 4.3 19.1 - - - +
201C LYS 3.1 17.8 + - - +
202C TYR* 3.3 25.8 + - + +
204C LEU* 1.3 78.0 - - - +
206C LEU* 1.3 59.2 + - + +
208C GLU* 3.4 2.7 + - - +
209C LEU* 2.9 29.2 + - - +
32D TYR* 5.2 1.3 - - - +
35D THR* 3.6 30.7 - - + +
36D VAL* 4.2 7.0 - - + -
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Residues in contact with LEU 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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57C ILE* 5.3 0.7 - - + -
132C GLY* 5.5 1.6 - - - -
135C PHE* 3.6 39.5 - - + -
202C TYR 2.9 17.3 + - - +
203C PRO 3.9 3.6 - - - +
205C LEU* 1.3 75.3 - - - +
207C LYS* 1.3 60.1 + - - +
209C LEU* 4.0 20.9 - - + -
210C ALA* 2.9 30.1 + - - +
223C VAL* 3.6 11.0 - - + +
226C ALA* 3.6 29.4 - - + +
227C LEU* 3.9 15.7 - - + +
230C MET* 3.5 31.6 - - + -
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Residues in contact with LYS 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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203C PRO 2.9 16.3 + - - +
204C LEU* 3.0 21.3 + - + +
206C LEU* 1.3 77.9 - - - +
208C GLU* 1.3 60.1 + - - +
210C ALA* 3.4 3.6 + - + +
211C LYS* 2.9 36.5 + - - +
227C LEU* 3.9 22.2 - - + +
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Residues in contact with GLU 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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49C LEU* 5.8 0.2 - - - +
53C VAL* 3.7 22.9 - - + -
204C LEU 2.9 15.0 + - - +
205C LEU* 3.8 6.5 - - - +
207C LYS* 1.3 75.9 - - - +
209C LEU* 1.3 67.1 + - - +
211C LYS* 3.1 20.6 + - - +
212C ARG* 3.1 57.4 + - + +
32D TYR* 4.5 15.5 - - + +
33D ILE 5.7 3.4 - - - +
35D THR* 4.7 9.4 - - - +
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Residues in contact with LEU 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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50C ARG* 3.6 26.5 - - + +
53C VAL* 3.6 20.6 - - + +
54C LEU* 3.5 28.9 - - + -
57C ILE* 4.3 8.3 - - + -
131C LEU* 4.1 21.3 - - + -
132C GLY 5.2 0.2 - - - +
205C LEU 2.9 18.3 + - - +
206C LEU* 3.7 19.1 - - + +
208C GLU* 1.3 77.2 - - - +
210C ALA* 1.3 57.4 + - - +
212C ARG* 3.1 3.9 + - - -
213C THR* 2.7 31.4 + - - -
219C ASP* 4.3 1.3 - - - +
223C VAL* 3.9 25.1 - - + -
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Residues in contact with ALA 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 LEU 2.9 18.3 + - - +
207C LYS* 3.6 7.4 - - - +
209C LEU* 1.3 76.2 - - - +
211C LYS* 1.3 62.6 + - - +
213C THR* 3.0 25.7 + - - +
220C HIS* 5.2 3.4 - - - -
223C VAL* 3.6 19.2 - - + +
224C GLN* 4.6 23.8 + - + +
227C LEU* 4.7 9.2 - - + -
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Residues in contact with LYS 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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46C GLN* 3.5 12.6 + - - -
207C LYS* 2.9 25.1 + - + +
208C GLU* 3.1 26.7 + - - +
210C ALA* 1.3 77.0 - - - +
212C ARG* 1.3 92.3 + - - +
213C THR 3.3 2.2 + - - +
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Residues in contact with ARG 212 (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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45C ARG* 4.0 16.6 - - - +
46C GLN* 3.1 43.1 + - - +
47C LEU* 5.4 0.3 - - - +
49C LEU* 3.6 30.7 - - + +
50C ARG* 3.4 46.1 - - + +
53C VAL* 4.0 10.1 - - + -
208C GLU* 3.1 39.4 + - - +
209C LEU 3.1 5.1 + - - +
210C ALA 3.1 0.4 - - - -
211C LYS* 1.3 105.0 + - - +
213C THR* 1.3 58.6 + - - +
214C PRO* 3.3 10.7 - - - +
32D TYR* 6.1 0.2 - - - -
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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