Contacts of the helix formed by residues 192 - 203 (chain A) in PDB entry 4FE1
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 ASN 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ARG 4.2 15.2 + - - +
188A GLU* 3.3 27.3 + - - +
189A TRP* 2.8 31.8 + - + +
190A PHE 2.9 6.7 + - - -
191A GLN* 1.3 74.0 - - - +
193A VAL* 1.3 59.3 + - - +
194A GLU* 3.4 3.8 - - - +
195A SER* 3.4 19.1 + - - +
196A MET* 3.0 29.5 + - + +
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Residues in contact with VAL 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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190A PHE 4.8 4.7 - - - +
191A GLN* 3.1 8.0 + - - +
192A ASN* 1.3 75.3 - - - +
194A GLU* 1.3 61.3 + - - +
196A MET* 3.3 9.7 + - + +
197A LEU* 2.9 36.4 + - + +
325A LEU* 3.6 21.5 - - + -
345A TYR* 3.3 34.1 - - + +
348A LEU 4.7 10.5 - - - +
349A THR* 3.7 19.5 - - - +
355A GLN* 5.0 6.7 - - - +
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 3.4 1.0 - - - -
193A VAL* 1.3 78.7 - - - +
195A SER* 1.3 57.0 + - - +
197A LEU* 3.8 1.0 - - - +
198A ASN* 2.9 36.8 + - - +
315A TYR* 3.5 28.9 - - + -
316A ARG* 3.3 23.7 - - - +
317A THR* 4.6 2.8 - - + -
323A HIS 4.1 2.5 - - - +
324A SER* 3.5 27.0 + - - -
325A LEU* 3.5 20.6 + - + -
345A TYR* 3.8 18.1 + - - -
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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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192A ASN* 3.4 23.8 + - - +
193A VAL 3.3 0.6 - - - -
194A GLU* 1.3 79.2 - - - +
196A MET* 1.3 58.2 + - - +
198A ASN* 3.4 0.6 + - - -
199A HIS* 2.6 59.3 + - - -
317A THR* 4.3 18.5 - - - +
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Residues in contact with MET 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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189A TRP* 5.2 9.6 - - + +
190A PHE* 3.5 34.8 - - + +
192A ASN* 3.0 17.5 + - + +
193A VAL* 3.6 9.9 - - + +
195A SER* 1.3 77.4 - - - +
197A LEU* 1.3 57.7 + - + +
199A HIS* 4.6 3.1 - - - -
200A HIS* 2.9 68.1 + - + +
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Residues in contact with LEU 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 VAL* 2.9 18.2 + - + +
194A GLU 3.8 0.2 - - - +
196A MET* 1.3 75.0 - - + +
198A ASN* 1.3 67.0 + - - +
200A HIS* 4.7 3.1 - - + -
201A LEU* 2.9 53.1 + - + +
315A TYR* 3.5 36.3 - - + +
325A LEU* 3.8 27.8 - - + -
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Residues in contact with ASN 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 GLU 2.9 15.5 + - - +
195A SER* 3.8 3.8 - - - +
197A LEU* 1.3 75.2 - - - +
199A HIS* 1.3 64.3 + - + +
202A ALA* 3.0 36.6 + - - +
312A GLY* 3.0 28.0 + - - +
313A HIS* 5.0 1.8 - - - +
314A MET 4.9 0.6 - - - +
315A TYR* 2.8 57.8 + - - +
317A THR* 3.4 17.9 - - + +
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Residues in contact with HIS 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* 2.6 48.9 + - - +
196A MET* 3.9 4.3 - - - +
198A ASN* 1.3 83.0 - - + +
200A HIS* 1.3 63.4 + - + +
203A GLY* 2.7 34.6 + - - +
204A LEU 3.1 2.3 + - - -
317A THR* 5.9 3.1 - - + -
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Residues in contact with HIS 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 MET* 2.9 53.6 + - + +
197A LEU* 4.2 4.5 - - + +
199A HIS* 1.3 78.3 - - + +
201A LEU* 1.3 64.1 + - + +
204A LEU* 3.4 21.5 - - + +
205A LEU* 3.1 32.3 + - - +
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Residues in contact with LEU 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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197A LEU* 2.9 48.8 + - + +
198A ASN 4.1 1.3 - - - +
200A HIS* 1.3 82.9 - - + +
202A ALA* 1.3 59.0 + - - +
205A LEU* 3.2 24.6 - - + +
206A GLY 2.9 22.0 + - - -
308A PHE* 3.6 21.7 - - + +
311A ALA* 4.9 14.8 - - + +
312A GLY* 4.3 10.1 - - - +
315A TYR* 4.5 12.6 - - + +
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Residues in contact with ALA 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 ASN 3.0 15.6 + - - +
201A LEU* 1.3 80.3 - - - +
203A GLY* 1.3 58.0 + - - +
206A GLY* 3.0 4.9 - - - -
207A LEU* 3.0 23.8 + - - +
308A PHE 3.6 13.2 - - - +
309A ILE* 3.1 26.1 - - + +
312A GLY* 3.5 19.5 - - - -
313A HIS* 5.0 3.8 - - + -
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Residues in contact with GLY 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 HIS* 2.7 22.9 + - - +
202A ALA* 1.3 72.3 - - - +
204A LEU* 1.3 65.5 + - - +
207A LEU* 2.9 42.4 + - - +
208A GLY 3.5 0.2 + - - -
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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