Contacts of the helix formed by residues 193 - 205 (chain A) in PDB entry 1EBF
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A PHE* 3.9 1.8 - - - -
191A ASP 3.6 6.7 + - - +
192A VAL* 1.3 77.6 - - - +
194A PHE* 1.3 66.4 + - - +
195A SER* 4.0 2.0 - - - +
196A ASP* 3.0 28.7 + - - +
197A VAL* 3.2 23.9 + - - +
265A SER* 5.6 1.4 + - - -
268A ASP* 3.2 38.6 + - + +
269A LYS 5.6 0.2 - - - +
272A THR* 4.9 9.1 + - - +
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Residues in contact with PHE 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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180A ILE* 3.6 27.4 - - + -
181A PHE* 4.0 17.7 - + - -
184A PHE* 3.4 36.5 - + + -
193A LYS* 1.3 72.8 - - - +
195A SER* 1.3 63.6 + - - +
197A VAL* 3.3 4.2 + - - +
198A VAL* 3.0 43.9 + - + +
215A LEU* 4.2 15.0 - - + -
246A LEU* 4.1 31.2 - - + -
264A LEU* 4.8 12.3 - - + -
268A ASP* 3.9 13.0 + - + +
271A LEU* 3.2 36.6 - - + -
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Residues in contact with SER 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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193A LYS* 4.0 3.1 - - - +
194A PHE* 1.3 76.2 - - - +
196A ASP* 1.3 68.3 + - - +
198A VAL* 3.5 1.6 + - - +
199A LYS* 3.1 36.7 + - - +
264A LEU* 4.2 17.4 - - - +
265A SER* 3.5 33.1 - - - -
268A ASP* 2.5 37.0 + - - -
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Residues in contact with ASP 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 VAL* 4.9 5.8 - - + +
193A LYS* 3.0 41.5 + - - +
195A SER* 1.3 81.0 + - - +
197A VAL* 1.3 65.7 + - - +
199A LYS* 3.4 14.1 + - - +
200A VAL* 2.9 33.8 + - + +
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Residues in contact with VAL 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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179A TYR* 4.7 3.8 - - + -
180A ILE* 3.4 43.1 - - + +
183A GLU* 3.8 16.4 - - + -
184A PHE* 4.0 20.2 - - + +
192A VAL* 3.5 22.7 - - + -
193A LYS 3.2 14.3 + - - +
194A PHE 3.7 6.5 - - - +
196A ASP* 1.3 76.9 - - - +
198A VAL* 1.3 52.6 + - - +
200A VAL* 3.1 8.7 + - + +
201A ALA* 2.7 34.0 + - - +
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Residues in contact with VAL 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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180A ILE* 4.1 20.4 - - + -
194A PHE* 3.0 49.2 + - + +
195A SER 3.7 5.2 - - - +
197A VAL* 1.3 75.8 - - - +
199A LYS* 1.3 59.2 + - - +
201A ALA* 2.9 9.8 + - - +
202A LYS* 2.8 25.3 + - - +
207A THR* 4.4 1.8 + - - +
211A PRO* 4.1 24.7 - - + -
215A LEU* 4.4 8.5 - - + -
260A PHE* 5.6 0.2 - - + -
261A LEU* 4.3 9.2 - - + -
264A LEU* 4.1 19.3 - - + -
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Residues in contact with LYS 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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195A SER* 3.1 24.8 + - - +
196A ASP* 3.4 20.0 + - - +
198A VAL* 1.3 79.1 - - - +
200A VAL* 1.3 59.3 + - + +
202A LYS* 3.4 9.8 + - + +
203A LYS* 2.9 28.4 + - - +
261A LEU* 4.1 41.1 + - + +
262A GLU* 4.6 8.1 - - - +
264A LEU* 6.1 0.2 - - - -
265A SER* 4.6 14.8 + - - -
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Residues in contact with VAL 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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179A TYR* 4.0 8.3 - - + +
196A ASP* 2.9 31.8 + - + +
197A VAL* 3.3 8.5 - - + +
199A LYS* 1.3 76.5 - - + +
201A ALA* 1.3 67.2 + - - +
203A LYS* 3.2 6.0 + - - +
204A LEU* 3.0 43.5 + - + +
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Residues in contact with ALA 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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176A THR* 5.2 0.4 - - + -
179A TYR* 3.5 33.0 - - + -
180A ILE* 4.1 12.6 - - + -
197A VAL 2.7 16.3 + - - +
198A VAL* 3.3 9.2 - - - +
200A VAL* 1.3 75.3 - - - +
202A LYS* 1.3 61.0 + - - +
204A LEU* 3.3 3.1 + - - +
205A GLY 3.0 5.4 + - - -
206A TYR* 2.9 31.0 + - + +
207A THR* 3.6 13.0 - - - +
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Residues in contact with LYS 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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198A VAL 2.8 12.0 + - - +
199A LYS* 3.5 10.8 - - + +
200A VAL 3.2 0.2 - - - -
201A ALA* 1.3 77.6 - - - +
203A LYS* 1.3 62.7 + - - +
205A GLY* 3.0 14.0 + - - -
207A THR* 3.5 14.6 + - - +
208A GLU 5.0 0.7 - - - +
209A PRO* 3.5 25.5 + - - +
211A PRO* 3.8 23.8 - - + -
258A ASP* 5.2 7.0 - - - -
261A LEU* 3.4 33.4 - - + -
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Residues in contact with LYS 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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199A LYS 2.9 17.0 + - - +
200A VAL* 3.2 7.6 + - - +
202A LYS* 1.3 77.1 - - - +
204A LEU* 1.3 65.4 + - + +
205A GLY* 3.0 1.6 + - - -
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Residues in contact with LEU 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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179A TYR* 3.3 27.6 - - + +
200A VAL* 3.0 30.6 + - + +
201A ALA 3.9 3.6 - - - +
203A LYS* 1.3 80.2 - - + +
205A GLY* 1.3 59.9 + - - +
206A TYR* 3.6 36.3 - - + +
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Residues in contact with GLY 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 ALA 3.0 3.0 + - - -
202A LYS 3.0 10.9 + - - -
203A LYS 3.0 5.3 - - - -
204A LEU* 1.3 78.6 - - - +
206A TYR* 1.3 63.8 + - - +
207A THR 3.1 14.0 + - - +
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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