Contacts of the helix formed by residues 200 - 211 (chain A) in PDB entry 3FPL
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 ARG 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 4.4 2.5 - - - +
176A GLY* 3.7 23.6 - - - +
177A PRO* 5.4 1.0 - - - +
199A SER* 1.3 79.8 - - - +
201A PRO* 1.4 73.3 - - + +
202A VAL 3.3 0.2 - - - -
203A CYS* 3.0 49.9 + - + +
204A VAL* 3.0 12.2 + - - +
340A LYS 5.8 2.9 - - - -
341A PRO 5.4 1.8 + - - -
342A LYS* 4.4 28.2 + - + +
344A LEU 4.9 7.3 + - - -
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Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A SER 3.2 9.2 - - - +
200A ARG* 1.4 81.4 - - + +
202A VAL* 1.3 62.5 + - - +
204A VAL* 3.3 8.8 + - + +
205A ASP* 3.0 30.2 + - - +
342A LYS* 5.6 8.1 - - + +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ARG* 4.8 1.3 - - + -
201A PRO* 1.3 78.6 - - - +
203A CYS* 1.3 79.3 + - - +
205A ASP* 3.6 8.0 + - + +
206A ALA* 3.2 20.4 + - - +
321A THR* 4.5 6.3 - - + -
342A LYS 3.2 26.4 + - - +
343A ASP* 4.1 23.6 - - + +
344A LEU 4.2 5.6 - - - +
345A ILE* 3.7 18.6 - - + +
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Residues in contact with CYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.3 38.6 - - + +
176A GLY* 4.6 2.7 - - - -
177A PRO* 5.9 0.2 - - - -
180A LEU* 3.5 6.0 - - - +
200A ARG* 3.0 44.3 + - + +
202A VAL* 1.3 92.9 - - - +
204A VAL* 1.3 54.0 + - - +
206A ALA* 3.2 5.4 + - - -
207A ALA* 2.8 35.3 + - - +
344A LEU 4.7 2.0 - - - -
345A ILE* 4.4 14.1 - - - -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 4.0 11.9 - - + -
198A GLY 3.8 22.0 - - - +
199A SER* 4.2 6.1 - - - +
200A ARG 3.0 21.9 + - - +
201A PRO* 3.7 9.9 - - + +
203A CYS* 1.3 75.7 - - - +
205A ASP* 1.3 65.2 + - - +
207A ALA* 3.1 4.1 + - - +
208A LYS* 3.0 34.2 + - + +
215A ILE* 3.9 31.2 - - + -
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Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PRO* 3.0 22.2 + - - +
202A VAL* 3.9 7.0 - - - +
203A CYS 3.3 0.2 - - - -
204A VAL* 1.3 77.4 - - - +
206A ALA* 1.3 58.7 + - - +
208A LYS* 3.4 18.4 + - - +
209A TYR* 3.1 25.7 + - - +
318A LYS* 4.6 9.5 - - - -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.7 25.8 - - + -
202A VAL 3.2 11.2 + - - +
203A CYS 3.2 8.8 + - - +
205A ASP* 1.3 75.4 - - - +
207A ALA* 1.3 65.8 + - - +
209A TYR* 3.2 8.5 + - - +
210A TYR* 2.9 34.3 + - + -
318A LYS* 4.3 20.6 - - + +
345A ILE* 4.2 8.7 - - + -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 4.3 7.4 - - + -
180A LEU* 3.4 15.7 - - + +
183A VAL* 3.7 7.7 - - + +
196A ALA* 4.1 10.5 - - + -
203A CYS 2.8 19.9 + - - +
204A VAL* 3.1 6.3 + - - +
206A ALA* 1.3 73.5 - - - +
208A LYS* 1.3 61.1 + - - +
210A TYR* 3.2 3.6 + - - +
211A GLY 3.1 7.1 + - - -
212A ALA* 2.9 36.9 + - + +
215A ILE* 4.1 10.8 - - + -
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 3.0 28.8 + - + +
205A ASP* 3.6 18.5 + - - +
207A ALA* 1.3 73.2 - - - +
209A TYR* 1.3 65.4 + - - +
211A GLY* 3.3 12.3 + - - -
212A ALA 3.9 16.7 + - - +
215A ILE* 4.1 19.1 - - + -
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Residues in contact with TYR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LYS* 5.3 4.9 + - - -
205A ASP 3.1 14.4 + - - +
206A ALA 3.2 7.6 + - - +
208A LYS* 1.3 76.9 - - - +
210A TYR* 1.3 86.8 + + - +
211A GLY* 3.4 1.0 + - - -
315A ASP* 3.3 34.8 + - + +
318A LYS* 3.5 36.1 - - + -
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 4.0 24.7 - - + +
181A MET* 3.4 21.6 - - + +
183A VAL* 3.7 19.2 - - + +
184A ALA* 3.6 31.8 - - + +
187A LYS* 3.7 14.7 - - - +
206A ALA* 2.9 31.5 + - + +
207A ALA 3.2 0.8 + - - -
209A TYR* 1.3 91.5 - + - +
211A GLY* 1.3 56.5 + - - +
314A VAL* 3.8 9.0 - - + -
315A ASP 2.7 29.4 + - - -
316A LEU* 3.9 0.2 - - - -
318A LYS* 3.3 26.3 + - + +
319A LEU* 3.7 27.4 + - + +
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 4.0 4.0 - - - -
187A LYS* 4.3 15.9 - - - -
192A GLY 5.2 0.3 - - - +
194A ILE* 3.9 15.5 - - - +
207A ALA 3.1 0.4 + - - -
208A LYS 3.3 8.7 + - - -
209A TYR 3.3 1.5 - - - -
210A TYR* 1.3 80.3 - - - +
212A ALA* 1.3 67.5 + - - +
213A THR* 3.3 13.9 + - - +
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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