Contacts of the helix formed by residues 189 - 200 (chain A) in PDB entry 4BN4
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 PRO 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A PHE* 3.3 45.3 - - + +
186A PHE 4.5 3.8 - - - +
187A HIS 4.2 2.7 - - - +
188A ASN* 1.3 88.2 - - - +
190A LYS* 1.3 76.5 + - + +
191A PRO* 3.5 1.1 - - - -
192A PHE* 3.3 5.5 + - - +
193A PHE* 3.0 33.5 + - + -
277A VAL* 4.2 19.3 - - + -
279A ARG* 6.0 1.3 - - - +
286A VAL* 4.9 8.1 - - + -
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Residues in contact with LYS 190 (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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188A ASN* 3.0 24.7 - - - +
189A PRO* 1.3 91.6 - - + +
191A PRO* 1.4 63.7 - - + +
193A PHE* 3.2 6.6 + - - +
194A THR* 2.9 34.5 + - - +
277A VAL* 4.5 14.6 - - + -
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Residues in contact with PRO 191 (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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172A ASP 5.6 0.4 - - - +
173A LEU* 4.6 9.6 - - + -
179A ILE* 3.8 18.7 - - + +
184A PHE* 4.1 18.6 - - + -
188A ASN* 3.4 35.2 - - - +
189A PRO 3.7 0.2 - - - -
190A LYS* 1.4 88.7 - - + +
192A PHE* 1.3 62.3 + - - +
194A THR* 3.2 6.5 + - - +
195A LEU* 3.1 17.3 + - - +
1396A OP2 3.5 31.9 - - - +
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Residues in contact with PHE 192 (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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179A ILE* 3.6 26.8 - - + +
180A PHE* 4.2 17.5 - + - -
184A PHE* 6.0 0.2 - - - -
185A PHE* 3.8 26.5 - + + -
188A ASN 5.2 0.6 + - - +
189A PRO* 3.3 7.6 + - + +
190A LYS 3.3 0.4 - - - -
191A PRO* 1.3 79.5 - - - +
193A PHE* 1.3 65.9 + + - +
195A LEU* 3.0 16.0 + - + +
196A ALA* 2.9 27.6 + - + -
251A PHE* 4.0 8.7 - + - -
288A LYS* 5.0 0.7 - - + -
289A PRO* 3.8 30.1 - - + -
291A ILE* 3.8 28.0 - - + -
293A PHE* 3.6 33.9 - + - -
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Residues in contact with PHE 193 (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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185A PHE* 3.7 25.4 - + - -
189A PRO* 3.0 32.3 + - + +
190A LYS* 3.2 6.0 + - - +
192A PHE* 1.3 79.4 - + - +
194A THR* 1.3 56.0 + - - +
196A ALA* 3.7 9.5 - - + +
197A LYS* 2.9 29.5 + - - +
272A VAL* 4.1 20.8 - - + +
276A ARG 5.3 2.5 - - - +
277A VAL* 4.0 30.1 - - + -
278A PRO* 3.5 26.0 - - + -
286A VAL* 4.0 1.1 - - + -
287A VAL 3.2 23.1 - - - -
289A PRO* 3.6 28.3 - - + -
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Residues in contact with THR 194 (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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190A LYS* 2.9 17.4 + - - +
191A PRO* 3.2 11.0 + - - +
193A PHE* 1.3 74.5 - - - +
195A LEU* 1.3 62.9 + - - +
197A LYS* 3.5 7.4 + - + +
198A GLU* 3.3 21.3 + - - +
1396A OP2 3.8 29.4 - - - +
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Residues in contact with LEU 195 (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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164A LEU* 4.2 9.6 - - + -
179A ILE* 4.2 16.6 - - + -
180A PHE* 4.1 23.1 - - + -
191A PRO 3.1 10.5 + - - +
192A PHE* 3.0 20.5 + - + +
194A THR* 1.3 74.4 - - - +
196A ALA* 1.3 67.1 + - - +
198A GLU* 3.2 5.0 + - - +
199A LEU* 3.1 36.0 + - + +
230A ILE* 4.1 8.3 - - + -
251A PHE* 4.0 14.4 - - + -
1396A OP2 3.8 45.2 - - - +
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Residues in contact with ALA 196 (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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192A PHE* 2.9 21.4 + - + +
193A PHE* 3.3 20.8 + - + +
195A LEU* 1.3 75.8 - - - +
197A LYS* 1.3 58.3 + - - +
200A TYR* 2.9 37.0 + - + -
251A PHE* 3.5 33.2 - - + -
272A VAL* 4.1 7.9 - - + -
289A PRO* 4.7 3.4 - - + -
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Residues in contact with LYS 197 (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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193A PHE 2.9 18.4 + - - +
194A THR* 3.7 7.9 - - + +
195A LEU 3.3 0.2 - - - -
196A ALA* 1.3 77.0 - - - +
198A GLU* 1.3 64.3 + - - +
200A TYR* 3.8 10.5 + - - +
203A ASN* 3.9 8.3 + - - -
272A VAL* 3.4 31.4 - - + +
273A MET* 3.1 37.6 + - - +
275A ASP* 3.1 35.4 + - - +
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Residues in contact with GLU 198 (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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194A THR 3.3 9.9 + - - +
195A LEU 3.2 9.3 + - - +
197A LYS* 1.3 82.5 - - - +
199A LEU* 1.3 60.0 + - + +
200A TYR 3.6 0.9 - - - +
203A ASN* 3.1 34.0 + - - +
204A TYR* 2.6 44.3 + - + +
1396A OP2 4.0 31.9 - - - +
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Residues in contact with LEU 199 (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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154A ILE* 4.2 34.8 - - + -
195A LEU* 3.1 34.3 + - + +
198A GLU* 1.3 81.1 - - + +
200A TYR* 1.3 67.2 + - - +
201A PRO* 3.4 2.9 - - - +
204A TYR* 4.6 7.9 - - + -
230A ILE* 4.0 22.4 - - + +
231A ASP* 3.9 24.0 - - + +
251A PHE* 3.7 20.0 - - + -
1396A OP2 3.9 34.3 - - - +
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Residues in contact with TYR 200 (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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196A ALA* 2.9 26.9 + - + +
197A LYS 4.1 3.4 - - - +
198A GLU 3.6 6.0 - - - +
199A LEU* 1.3 79.2 - - - +
201A PRO* 1.3 82.3 - - + +
202A GLY* 3.2 3.3 + - - -
203A ASN* 4.2 4.5 + - - -
204A TYR* 6.0 0.3 - - - -
251A PHE* 3.5 42.5 + + + -
265A GLY* 2.7 36.1 + - - -
266A GLU* 5.0 0.4 - - - -
268A ILE* 3.2 22.3 - - + +
269A ARG* 3.9 34.5 - - + -
272A VAL* 4.2 16.6 - - + -
273A MET* 3.5 23.5 - - + +
289A PRO* 5.0 1.8 - - + +
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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