Contacts of the helix formed by residues 200 - 214 (chain A) in PDB entry 3K4H
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 ASP 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASN* 3.2 12.6 + - - +
26A PRO* 5.8 0.2 - - - +
174A PHE* 3.4 27.1 - - + -
198A ALA* 3.2 3.9 + - - +
199A THR* 1.3 81.7 + - - +
201A ASP* 1.3 59.3 + - - +
202A LEU* 2.6 39.7 + - - +
203A ILE* 2.8 29.3 + - + +
204A GLY 3.0 8.0 + - - -
226A SER* 3.8 5.2 - - - -
227A PHE 3.9 4.9 - - - -
228A ASN* 3.6 7.5 - - - +
1C GLC 2.7 32.3 + - - +
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Residues in contact with ASP 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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26A PRO* 6.2 0.7 - - + -
200A ASP* 1.3 73.5 + - - +
202A LEU* 1.3 56.5 + - + +
204A GLY* 3.5 1.7 - - - +
205A LEU* 2.7 39.6 + - + +
226A SER* 2.1 36.5 + - - -
227A PHE 2.8 19.1 + - - +
228A ASN* 4.2 2.9 - - + +
229A ASN 3.0 6.1 + - - -
230A ALA* 2.7 43.9 + - + -
233A SER* 3.2 20.8 - - - -
240A LEU* 4.0 2.9 - - + +
242A THR* 2.7 11.7 + - - -
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Residues in contact with LEU 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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24A GLN* 4.0 21.5 - - + +
25A ASN* 4.1 19.5 - - + +
26A PRO* 4.4 16.6 - - + -
174A PHE 3.8 16.8 - - - +
175A SER* 4.0 20.9 - - - +
176A ARG* 3.5 35.1 - - + +
200A ASP* 2.6 20.0 + - - +
201A ASP* 1.3 74.0 - - + +
203A ILE* 1.3 55.9 + - - +
205A LEU* 3.4 7.6 + - + +
206A GLY 3.2 20.4 + - - -
232A LEU* 4.9 14.6 - - + -
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Residues in contact with ILE 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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137A ILE* 3.6 31.9 - - + +
138A GLY 4.1 22.0 - - - +
173A ASP 4.2 4.7 - - - +
174A PHE* 3.8 43.5 - - + -
175A SER 3.9 9.4 - - - +
178A SER* 4.7 1.3 - - - -
179A GLY* 3.7 17.2 - - - +
198A ALA* 4.3 6.1 - - + -
199A THR* 4.2 6.7 - - - +
200A ASP* 2.8 15.7 + - + +
202A LEU* 1.3 73.4 - - - +
204A GLY* 1.3 61.6 + - - +
206A GLY 3.3 0.3 + - - -
207A VAL* 2.8 39.3 + - + +
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Residues in contact with GLY 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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198A ALA* 4.0 14.0 - - - +
200A ASP 3.0 11.5 + - - -
201A ASP 3.0 4.7 + - - -
203A ILE* 1.3 76.5 - - - +
205A LEU* 1.3 61.5 + - - +
207A VAL* 3.1 6.6 + - - +
208A LEU* 3.0 25.3 + - - +
224A ILE* 4.6 8.3 - - - +
226A SER* 4.4 10.5 - - - -
240A LEU* 4.5 9.6 - - - +
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Residues in contact with LEU 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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176A ARG* 5.2 10.5 - - - -
201A ASP* 2.7 29.5 + - + +
202A LEU* 3.9 10.5 - - + +
203A ILE 3.2 0.2 - - - -
204A GLY* 1.3 72.7 - - - +
206A GLY* 1.3 54.2 + - - +
208A LEU* 3.3 11.4 - - + +
209A SER* 2.8 31.9 + - - -
230A ALA* 5.5 0.7 - - + -
232A LEU* 3.5 44.2 - - + +
233A SER* 4.4 2.9 - - - +
236A ALA* 3.5 31.9 - - + -
240A LEU* 4.2 14.8 - - + -
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Residues in contact with GLY 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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176A ARG* 3.7 29.3 - - - +
179A GLY 3.9 7.2 - - - -
180A GLN* 3.9 6.7 - - - +
202A LEU 3.2 11.3 + - - -
203A ILE 3.3 2.4 + - - -
204A GLY 3.2 0.2 - - - -
205A LEU* 1.3 76.8 - - - +
207A VAL* 1.3 64.0 + - - +
209A SER* 3.3 5.7 + - - -
210A ALA* 3.0 25.6 + - - +
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Residues in contact with VAL 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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137A ILE* 3.5 29.8 - - + -
179A GLY* 3.6 20.2 - - - +
183A VAL* 3.5 13.7 - - + +
196A ILE* 4.3 15.5 - - + -
198A ALA* 5.3 1.6 - - + -
203A ILE* 2.8 27.5 + - + +
204A GLY* 3.5 7.2 - - - +
206A GLY* 1.3 75.0 - - - +
208A LEU* 1.3 53.8 + - - +
210A ALA* 3.0 4.5 + - - +
211A LEU* 2.8 43.6 + - + +
224A ILE* 3.9 24.2 - - + -
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Residues in contact with LEU 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 GLY 3.0 10.7 + - - +
205A LEU* 3.3 17.9 - - + +
207A VAL* 1.3 76.5 - - - +
209A SER* 1.3 63.5 + - - +
211A LEU* 3.4 4.3 + - - +
212A SER* 3.1 31.3 + - - +
218A VAL* 3.7 34.1 - - + -
224A ILE* 3.8 15.3 - - + -
236A ALA* 4.1 16.8 - - + -
237A SER 4.0 24.2 - - - +
238A PRO* 4.1 18.8 - - + +
240A LEU* 4.6 9.0 - - + -
283A THR* 4.9 2.7 - - + -
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Residues in contact with SER 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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180A GLN* 5.0 9.2 + - - -
205A LEU 2.8 17.2 + - - -
206A GLY* 3.3 7.2 + - - -
208A LEU* 1.3 77.7 - - - +
210A ALA* 1.3 59.6 + - - +
212A SER* 3.1 6.6 + - - -
213A LYS* 2.8 29.2 + - - +
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Residues in contact with ALA 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 GLN* 3.7 25.8 - - + +
183A VAL* 3.6 25.1 - - + -
206A GLY 3.0 16.5 + - - +
207A VAL 3.0 4.6 + - - +
209A SER* 1.3 77.9 - - - +
211A LEU* 1.3 62.9 + - - +
213A LYS* 3.2 7.5 + - - +
214A LYS* 3.2 29.0 + - - +
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Residues in contact with LEU 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* 3.6 26.7 - - + -
187A MSE 3.8 28.3 - - + -
196A ILE* 4.6 1.6 - - + -
207A VAL* 2.8 32.2 + - + +
208A LEU* 3.8 4.9 - - - +
210A ALA* 1.3 77.5 - - - +
212A SER* 1.3 58.9 + - - +
214A LYS 3.4 0.3 + - - -
215A GLY 3.4 2.1 + - - -
216A PHE* 2.9 53.2 + - + +
218A VAL* 4.0 19.1 - - + -
222A VAL* 3.9 31.9 - - + -
224A ILE* 4.3 1.8 - - + -
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Residues in contact with SER 212 (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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208A LEU* 3.1 25.9 + - - +
209A SER* 3.6 6.3 - - - -
211A LEU* 1.3 76.5 - - - +
213A LYS* 1.3 65.1 + - - +
214A LYS 3.1 1.3 - - - -
215A GLY* 3.1 12.5 + - - -
216A PHE 3.9 13.4 + - - -
217A VAL* 5.5 0.2 - - - -
218A VAL* 5.4 4.2 + - - +
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A SER 2.8 16.4 + - - +
210A ALA* 3.2 9.4 + - - +
212A SER* 1.3 77.8 - - - +
214A LYS* 1.3 63.4 + - + +
215A GLY* 3.2 1.3 + - - -
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A VAL* 4.2 16.2 + - + -
184A GLU* 3.3 53.8 + - - +
187A MSE 4.7 9.3 - - + +
188A GLY* 5.3 1.0 - - - +
210A ALA* 3.2 14.8 + - - +
211A LEU 3.4 0.4 + - - -
212A SER 3.1 0.8 - - - -
213A LYS* 1.3 80.5 - - + +
215A GLY* 1.3 60.3 + - - +
216A PHE* 3.4 30.8 + - + -
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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