Contacts of the helix formed by residues 195 - 212 (chain A) in PDB entry 4EJJ
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 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A PHE* 3.6 20.7 - - + +
192A ASP* 3.3 26.3 + - + +
193A TYR 4.0 4.5 - - - +
194A LYS* 1.3 79.0 - - - +
196A LYS* 1.3 62.4 + - - +
197A GLU* 3.3 24.7 + - - +
198A PHE* 3.6 24.9 - - + +
199A LEU* 3.9 5.5 + - - +
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Residues in contact with LYS 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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194A LYS 3.1 5.8 + - - +
195A ASP* 1.3 71.4 + - - +
197A GLU* 1.3 64.6 + - - +
198A PHE 3.3 0.7 - - - -
199A LEU* 3.7 22.2 + - + +
200A SER* 3.2 21.7 + - - -
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Residues in contact with GLU 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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191A PHE* 5.5 1.5 - - + -
195A ASP* 3.3 13.9 + - - +
196A LYS* 1.3 76.2 - - - +
198A PHE* 1.3 63.4 + - - +
200A SER* 3.0 11.7 + - - -
201A LEU* 2.9 33.6 + - + +
247A PHE* 3.4 35.3 - - + +
250A LYS* 2.9 29.7 + - - -
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Residues in contact with PHE 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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176A ARG* 3.7 44.0 - - + -
179A SER* 3.7 22.2 - - - -
180A ASN* 3.5 22.0 - - - -
191A PHE* 3.3 50.8 - + + -
192A ASP 4.1 8.5 - - - -
193A TYR* 4.8 2.0 - + - -
195A ASP* 3.6 24.9 + - + +
197A GLU* 1.3 76.6 - - - +
199A LEU* 1.3 63.6 + - - +
201A LEU* 3.1 11.6 + - + +
202A LEU* 3.0 37.7 + - + +
299A PHE* 5.0 2.2 - + - -
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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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172A PHE* 3.9 28.3 - - + -
176A ARG* 4.0 24.0 - - - +
195A ASP 3.9 6.9 + - - +
196A LYS* 3.7 23.4 + - + +
197A GLU 3.5 0.2 - - - -
198A PHE* 1.3 78.3 - - - +
200A SER* 1.3 63.2 + - - +
202A LEU* 3.3 9.2 + - - -
203A ARG* 2.9 65.9 + - + +
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Residues in contact with SER 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 LYS 3.2 14.7 + - - -
197A GLU* 3.0 19.3 + - - -
199A LEU* 1.3 77.9 - - - +
201A LEU* 1.3 61.1 + - - +
203A ARG* 3.3 10.7 + - - +
204A MET* 3.1 45.8 + - - +
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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
----------------------------------------------------------
191A PHE* 4.0 14.6 - - + -
197A GLU* 2.9 27.0 + - + +
198A PHE* 3.5 7.6 - - + +
200A SER* 1.3 75.5 - - - +
202A LEU* 1.3 57.9 + - - +
204A MET* 3.1 24.0 - - + +
205A MET* 2.9 33.4 + - - +
243A GLY 4.7 0.9 - - - +
244A LEU* 3.8 19.9 - - + +
247A PHE* 3.7 60.6 - - + -
299A PHE* 4.3 15.0 - - + -
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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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172A PHE* 4.1 20.1 - - + +
175A SER* 4.0 13.5 - - - +
176A ARG* 3.5 41.5 - - + +
179A SER* 3.7 31.4 - - - +
198A PHE* 3.0 36.9 + - + +
199A LEU* 3.7 7.4 - - - +
201A LEU* 1.3 75.6 - - + +
203A ARG* 1.3 56.2 + - - +
205A MET* 3.4 10.7 + - + +
206A LEU* 3.0 30.1 + - - +
303A THR* 4.0 13.2 - - + -
304A GLU* 4.4 1.8 - - - +
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Residues in contact with ARG 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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172A PHE* 3.9 35.4 - - + -
199A LEU* 2.9 56.5 + - + +
200A SER* 3.3 9.6 + - - +
202A LEU* 1.3 68.9 - - - +
204A MET* 1.3 55.9 - - + +
206A LEU* 3.5 5.2 + - + +
207A GLY* 2.8 31.0 + - - -
240A LEU* 4.7 3.9 - - + +
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Residues in contact with MET 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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200A SER* 3.1 41.5 + - - +
201A LEU* 3.1 20.0 - - + +
203A ARG* 1.3 74.2 - - + +
205A MET* 1.3 65.0 + - - +
207A GLY 3.3 1.2 + - - -
208A ILE* 3.1 31.3 + - - +
240A LEU* 3.8 34.2 - - + +
243A GLY* 3.7 40.4 - - - +
244A LEU* 3.7 21.1 - - + -
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Residues in contact with MET 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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179A SER* 4.7 1.3 - - - +
201A LEU 2.9 22.1 + - - +
202A LEU* 3.8 7.0 - - + +
204A MET* 1.3 71.1 - - - +
206A LEU* 1.3 62.6 + - - +
208A ILE* 3.2 6.5 + - - +
209A PHE* 3.2 26.0 + - - +
244A LEU* 3.6 27.1 - - + -
299A PHE* 3.1 54.7 - - + -
300A ILE* 4.0 23.6 - - + +
303A THR* 3.8 29.2 - - + +
304A GLU* 3.3 18.1 - - + +
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Residues in contact with LEU 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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171A THR* 4.1 12.1 - - + -
172A PHE* 3.4 34.1 - - + -
202A LEU 3.0 17.2 + - - +
203A ARG* 3.7 5.2 - - - +
205A MET* 1.3 78.2 - - - +
207A GLY* 1.3 62.2 + - - +
208A ILE 3.2 0.2 + - - -
209A PHE* 3.4 4.4 + - + +
210A GLN* 3.1 51.1 + - + +
304A GLU* 3.6 23.3 + - - +
311A ARG* 4.0 25.8 - - - +
483A ILE* 6.4 0.9 - - + -
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Residues in contact with GLY 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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203A ARG 2.8 20.0 + - - -
204A MET 3.3 2.4 + - - -
206A LEU* 1.3 74.0 - - - +
208A ILE* 1.3 56.2 + - - +
210A GLN* 3.8 9.7 - - - +
211A PHE* 3.0 28.1 + - - +
240A LEU* 4.0 17.4 - - - +
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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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106A THR* 4.8 7.2 - - + -
107A PHE* 3.5 34.5 - - + -
204A MET 3.1 18.7 + - - +
205A MET* 3.7 5.8 - - - +
206A LEU 3.1 1.0 - - - -
207A GLY* 1.3 75.8 - - - +
209A PHE* 1.3 66.7 + - + +
210A GLN 3.2 0.2 - - - -
211A PHE* 3.4 4.4 + - - +
212A THR* 3.1 30.8 + - + +
237A ALA* 4.3 11.9 - - + +
240A LEU* 3.6 25.4 - - + -
241A LEU* 3.8 20.4 - - + -
244A LEU* 3.6 26.9 - - + -
300A ILE* 5.8 1.1 - - + -
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Residues in contact with PHE 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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107A PHE* 4.4 12.1 - + - -
205A MET 3.2 10.6 + - - +
206A LEU* 3.4 7.6 + - + +
208A ILE* 1.3 79.3 - - + +
210A GLN* 1.3 61.6 + - - +
212A THR* 3.1 10.8 + - - -
213A SER* 2.9 23.7 + - - -
300A ILE* 4.3 17.0 - - + -
304A GLU* 3.4 40.6 - - + +
305A THR* 3.9 22.7 - - + -
308A THR* 4.5 7.9 - - - -
365A VAL* 5.0 2.0 - - + -
366A ILE* 4.0 10.5 - - + -
480A PHE* 4.0 9.4 - + - -
481A ALA* 3.7 19.6 - - + +
483A ILE* 4.2 11.4 - - + -
501A NCT 3.2 33.9 - - - -
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Residues in contact with GLN 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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206A LEU* 3.1 44.1 + - + +
207A GLY* 4.2 7.5 - - - +
209A PHE* 1.3 76.9 - - - +
211A PHE* 1.3 65.2 + - - +
213A SER* 2.9 13.5 + - - -
214A THR* 3.3 15.4 + - + +
311A ARG* 6.0 0.2 - - - -
476A LYS* 3.2 30.8 + - - +
477A HIS* 4.0 12.8 - - + +
483A ILE* 3.6 35.6 - - + +
486A ASN* 5.9 1.0 - - - +
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Residues in contact with PHE 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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106A THR* 3.4 32.3 - - + -
207A GLY 3.0 20.2 + - - +
208A ILE 3.8 3.4 - - - +
209A PHE 3.4 0.4 - - - -
210A GLN* 1.3 75.7 - - - +
212A THR* 1.3 59.6 + - + +
214A THR* 2.5 38.7 + - + -
216A THR* 3.7 16.4 - - + -
217A GLY* 3.3 32.8 - - - -
220A TYR* 4.5 4.3 - + + -
233A PRO* 3.8 16.6 - - + -
234A GLN* 3.5 39.0 - - + -
237A ALA* 3.4 27.6 - - + -
238A PHE* 5.6 0.9 - + - -
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Residues in contact with THR 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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104A GLN* 4.1 11.0 - - - +
106A THR* 3.8 36.3 - - + +
107A PHE* 4.3 13.1 - - + -
208A ILE* 3.1 15.3 + - + +
209A PHE* 3.1 14.4 + - - -
211A PHE* 1.3 79.8 - - + +
213A SER* 1.3 57.4 + - - +
214A THR 3.4 0.8 + - - -
217A GLY* 4.3 8.7 - - - -
218A GLN* 3.0 14.6 + - - -
480A PHE* 3.0 44.8 + - - +
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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