Contacts of the helix formed by residues 200 - 213 (chain A) in PDB entry 4BLV
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 LEU 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A TYR* 5.7 0.4 + - - -
198A VAL* 4.8 0.4 - - - -
199A VAL* 1.3 95.6 - - + +
201A ARG* 1.3 67.6 + - - +
202A GLN* 2.9 23.8 + - + +
203A GLN* 3.0 20.4 + - + +
204A ILE* 3.7 8.8 + - - +
231A ASP* 4.0 31.4 - - + +
1283A PEG 3.1 5.2 - - - +
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Residues in contact with ARG 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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198A VAL* 3.7 25.5 - - - +
199A VAL 4.1 0.2 - - - -
200A LEU* 1.3 70.5 - - - +
202A GLN* 1.3 62.4 + - - +
204A ILE* 3.0 19.4 + - - +
205A LYS* 3.0 49.0 + - - +
221A GLN* 4.9 1.8 - - - +
223A GLU* 2.8 42.0 + - - -
229A ASP* 2.9 38.4 + - - +
237A ALA* 4.8 2.0 - - - +
271A HIS* 4.3 4.8 - - - -
1283A PEG 2.7 42.3 + - - +
1288A EDO 3.0 19.4 + - - -
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Residues in contact with GLN 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 LEU* 4.4 19.4 - - + +
201A ARG* 1.3 78.2 - - - +
203A GLN* 1.3 61.6 + - + +
205A LYS* 3.3 11.3 + - - +
206A ARG* 3.0 49.3 + - - +
1283A PEG 5.1 2.4 + - - -
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Residues in contact with GLN 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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170A LYS* 5.0 9.7 + - - +
173A TYR* 3.2 60.8 - - + +
174A GLN* 4.2 9.2 + - - +
200A LEU* 3.0 17.2 + - + +
202A GLN* 1.3 81.9 - - + +
204A ILE* 1.3 58.0 - - - +
206A ARG* 2.9 41.0 + - - +
207A MET* 3.0 28.1 + - - +
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Residues in contact with ILE 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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173A TYR* 3.9 22.0 - - + -
196A TYR* 3.6 34.8 - - + -
197A PRO 3.1 28.5 - - - +
198A VAL* 4.2 11.0 - - + -
200A LEU 4.1 10.8 - - - +
201A ARG* 3.0 24.7 + - - +
203A GLN* 1.3 77.1 + - + +
205A LYS* 1.3 64.9 + - - +
207A MET* 3.2 9.9 + - + +
208A ILE* 2.9 50.2 + - + +
221A GLN* 4.9 0.2 - - - +
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Residues in contact with LYS 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 ARG* 3.0 42.0 + - + +
202A GLN* 3.3 10.5 + - - +
204A ILE* 1.3 77.0 - - + +
206A ARG* 1.3 56.2 + - - +
208A ILE* 3.3 8.3 + - - +
209A HIS* 2.9 27.5 + - - +
1283A PEG 5.1 8.1 - - - -
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Residues in contact with ARG 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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174A GLN* 5.1 8.1 - - - +
202A GLN* 3.0 55.6 + - - +
203A GLN* 2.9 43.2 + - - +
205A LYS* 1.3 76.6 - - - +
207A MET* 1.3 64.7 + - - +
209A HIS* 3.1 11.6 - - + +
210A ASP* 2.9 36.9 + - - +
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Residues in contact with MET 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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167A TYR* 4.4 6.3 - - - -
173A TYR* 3.7 38.6 - - + +
176A VAL* 3.7 19.7 - - - -
177A VAL* 3.7 14.7 - - + +
194A LEU* 4.2 8.3 - - + -
196A TYR* 3.9 23.6 - - + -
203A GLN* 3.0 20.6 + - - +
204A ILE* 3.2 10.5 + - + +
206A ARG* 1.3 77.0 - - - +
208A ILE* 1.3 66.2 + - + +
210A ASP* 3.3 7.3 + - - +
211A LEU* 3.0 27.8 + - + +
241A ILE* 3.9 27.6 - - + -
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Residues in contact with ILE 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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201A ARG* 5.9 0.2 - - - +
204A ILE* 2.9 35.0 + - + +
205A LYS* 3.7 6.5 - - - +
207A MET* 1.3 75.4 - - + +
209A HIS* 1.3 65.2 + - - +
211A LEU* 3.3 7.4 + - + +
212A GLU* 3.0 40.5 + - - +
221A GLN* 3.6 34.1 - - - +
241A ILE* 4.2 19.7 - - + -
277A ILE* 3.9 22.9 - - + -
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Residues in contact with HIS 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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205A LYS 2.9 14.1 + - - +
206A ARG* 3.1 16.4 - - + +
208A ILE* 1.3 75.6 - - - +
210A ASP* 1.3 76.4 + - - +
212A GLU* 3.2 18.3 + - - +
213A ALA* 3.0 27.2 + - + +
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Residues in contact with ASP 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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173A TYR 5.4 1.2 - - - +
174A GLN* 4.8 14.6 + - - +
177A VAL* 3.5 21.1 - - + +
206A ARG* 2.9 25.2 + - - +
207A MET* 3.7 9.8 - - - +
209A HIS* 1.3 94.4 - - - +
211A LEU* 1.3 60.8 + - - +
213A ALA* 3.4 13.5 + - - +
214A THR* 3.3 18.5 + - - +
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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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177A VAL* 3.8 20.4 - - + +
180A ILE* 4.3 31.0 - - + -
194A LEU* 5.1 6.7 - - + -
207A MET* 3.0 14.4 + - + +
208A ILE* 3.5 10.8 - - + +
209A HIS 3.1 0.2 - - - -
210A ASP* 1.3 75.5 - - - +
212A GLU* 1.3 62.9 + - + +
214A THR* 2.7 32.7 + - + +
215A GLY 4.2 0.2 + - - -
216A ILE* 4.7 1.4 + - + -
219A ILE* 4.0 25.7 - - + +
241A ILE* 3.7 39.7 - - + -
243A ILE* 4.7 6.5 - - + -
277A ILE* 4.9 5.2 - - + -
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Residues in contact with GLU 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 ILE* 3.0 27.1 + - - +
209A HIS* 3.2 18.5 + - - +
211A LEU* 1.3 75.1 - - - +
213A ALA* 1.3 56.8 + - - +
215A GLY* 3.1 21.3 + - - -
216A ILE 4.6 1.4 + - - +
219A ILE* 5.4 0.4 - - - +
277A ILE* 3.7 32.1 - - + +
278A VAL* 4.3 17.4 - - + +
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Residues in contact with ALA 213 (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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209A HIS* 3.0 20.1 + - + +
210A ASP* 3.6 14.6 - - - +
211A LEU 3.2 0.4 - - - -
212A GLU* 1.3 72.6 - - - +
214A THR* 1.3 60.0 + - - +
215A GLY* 3.0 7.1 + - - -
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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