Contacts of the helix formed by residues 188 - 201 (chain A) in PDB entry 1EJD
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 GLU 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A VAL* 5.0 4.1 - - - +
163A VAL* 3.4 30.6 - - + +
186A ALA* 3.4 5.3 - - - +
187A ARG* 1.3 86.6 + - - +
189A PRO* 1.3 65.3 - - - +
190A GLU* 3.5 13.7 - - + +
191A ILE* 2.8 33.4 + - + +
192A VAL* 3.3 3.8 + - - +
232A ARG* 3.5 8.5 - - - +
298A PRO* 5.5 1.6 - - - +
299A HIS* 4.0 9.1 + - + +
2431A PO4 2.6 44.5 + - - +
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Residues in contact with PRO 189 (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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187A ARG 3.6 0.4 - - - +
188A GLU* 1.3 85.1 - - + +
190A GLU* 1.3 56.4 + - - +
192A VAL* 3.2 13.0 + - + +
193A ASP* 2.9 27.5 + - - +
229A LEU* 3.8 15.3 - - + +
232A ARG* 3.6 33.4 - - - +
258A THR* 3.8 28.0 - - + -
299A HIS* 3.5 35.0 - - + +
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Residues in contact with GLU 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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21A ALA* 4.6 9.7 - - + +
23A ASN* 3.6 46.2 + - + +
24A ALA* 3.8 12.2 - - + +
27A PRO* 5.4 1.1 - - + -
163A VAL* 5.7 6.1 - - + -
167A VAL* 5.9 0.2 - - - -
188A GLU* 3.1 10.4 - - + +
189A PRO* 1.3 76.3 - - - +
191A ILE* 1.3 61.6 + - + +
193A ASP* 3.8 7.0 - - - +
194A THR* 2.9 32.7 + - - -
229A LEU* 4.6 5.5 - - + +
230A PRO 5.4 0.3 - - - +
232A ARG* 2.9 50.4 + - - +
233A ILE* 6.0 0.2 - - - +
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Residues in contact with ILE 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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163A VAL* 3.7 22.2 - - + +
166A THR* 4.0 14.4 - - + -
167A VAL* 3.4 29.8 - - + -
170A MET* 3.9 7.8 - - + +
186A ALA* 3.6 33.7 - - + +
187A ARG 4.6 0.9 - - - -
188A GLU* 2.8 20.9 + - + +
190A GLU* 1.3 74.2 - - - +
192A VAL* 1.3 61.8 + - - +
194A THR* 3.3 5.2 + - - -
195A ALA* 2.9 28.1 + - - +
208A GLN* 4.9 4.5 - - + -
209A GLY 5.0 2.9 - - - +
213A ILE* 4.0 21.8 - - + -
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Residues in contact with VAL 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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187A ARG 4.3 2.2 - - - +
188A GLU 3.3 9.4 + - - +
189A PRO* 3.2 12.8 + - + +
191A ILE* 1.3 77.1 - - - +
193A ASP* 1.3 57.8 + - - +
195A ALA* 3.3 1.9 + - - +
196A ASN* 2.8 45.9 + - - +
208A GLN* 3.9 17.3 - - + +
209A GLY* 3.5 35.7 - - - +
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Residues in contact with ASP 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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24A ALA* 3.8 5.4 - - + +
28A ILE* 3.6 10.1 - - - +
189A PRO 2.9 17.4 + - - +
190A GLU 3.8 5.2 - - - +
191A ILE 3.2 0.2 - - - -
192A VAL* 1.3 77.7 - - - +
194A THR* 1.3 58.2 + - - +
196A ASN* 3.3 2.9 + - - +
197A PHE* 2.9 27.2 + - - +
226A TYR* 2.7 35.1 + - - -
227A ARG 4.4 1.0 - - - +
228A VAL* 3.5 8.7 - - - -
229A LEU* 2.9 52.0 + - + +
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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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24A ALA 4.4 0.5 + - - -
27A PRO* 3.4 43.6 - - + +
28A ILE* 4.0 13.7 - - + +
31A ALA* 4.7 2.9 - - + -
167A VAL* 4.5 6.6 - - + +
170A MET* 4.0 15.5 - - + -
171A SER* 4.2 14.4 - - - +
190A GLU 2.9 17.8 + - - -
191A ILE* 3.7 6.1 - - - -
193A ASP* 1.3 75.3 - - - +
195A ALA* 1.3 65.6 + - - +
197A PHE* 3.2 2.9 + - - +
198A LEU* 3.0 26.9 + - + +
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Residues in contact with ALA 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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170A MET* 3.7 22.3 - - - +
191A ILE 2.9 17.4 + - - +
192A VAL 3.6 1.6 - - - +
194A THR* 1.3 74.9 - - - +
196A ASN* 1.3 60.6 + - - +
198A LEU* 3.1 4.6 + - - +
199A VAL* 2.9 32.2 + - - +
205A ILE* 3.9 10.2 - - + +
208A GLN* 3.5 35.4 - - + +
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Residues in contact with ASN 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* 2.8 36.0 + - - +
193A ASP* 3.8 1.6 + - - +
195A ALA* 1.3 77.5 - - - +
197A PHE* 1.3 59.9 + - - +
199A VAL* 3.4 8.1 + - - +
200A ALA* 3.0 22.2 + - - +
208A GLN* 2.9 25.6 + - - +
226A TYR* 3.2 27.7 + - + +
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Residues in contact with PHE 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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28A ILE* 3.6 39.0 - - + -
31A ALA* 3.8 20.0 - - + -
32A ALA* 4.0 9.4 - - - -
39A VAL* 3.8 15.9 - - + -
41A ILE* 3.3 28.9 - - + -
193A ASP 2.9 14.5 + - - +
194A THR 3.5 8.3 - - - +
196A ASN* 1.3 75.7 - - - +
198A LEU* 1.3 66.5 + - - +
200A ALA* 3.1 14.8 + - + +
201A LEU* 3.2 43.9 + - + +
224A GLY 6.4 0.2 - - - -
226A TYR* 3.5 38.3 - + + -
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Residues in contact with LEU 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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31A ALA* 3.9 19.7 - - + -
34A LEU* 3.6 30.1 - - + -
170A MET* 4.2 12.6 - - + -
171A SER* 3.9 28.0 - - - +
174A THR* 4.0 4.7 - - + -
194A THR* 3.0 20.8 + - + +
195A ALA 3.1 6.3 + - - +
197A PHE* 1.3 78.2 - - + +
199A VAL* 1.3 59.5 + - - +
201A LEU* 3.1 20.1 + - + +
202A GLY 3.3 0.3 + - - -
203A ALA* 2.9 27.4 + - + +
205A ILE* 3.7 24.7 - - + -
221A LEU* 4.3 9.8 - - + +
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Residues in contact with VAL 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 ALA 2.9 21.9 + - - +
196A ASN* 3.7 8.5 - - - +
197A PHE 3.2 0.4 - - - -
198A LEU* 1.3 75.8 - - - +
200A ALA* 1.3 64.0 + - - +
202A GLY* 2.9 15.4 + - - -
203A ALA 3.5 21.9 + - - +
204A LYS* 5.0 0.2 - - - -
205A ILE* 4.0 32.5 - - + +
208A GLN* 4.6 6.5 - - - +
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Residues in contact with ALA 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 ASN 3.0 13.6 + - - +
197A PHE* 3.1 11.8 + - + +
199A VAL* 1.3 76.9 - - - +
201A LEU* 1.3 61.4 + - + +
202A GLY 3.5 0.5 + - - -
223A GLY 4.0 9.8 - - - +
224A GLY* 5.6 2.3 - - - -
225A VAL 4.9 8.3 - - - +
226A TYR* 4.2 19.3 - - + -
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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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31A ALA 4.6 7.6 - - - +
35A ALA* 4.2 15.0 - - + -
39A VAL* 3.8 15.7 - - + -
197A PHE* 3.2 45.5 + - + +
198A LEU* 3.1 11.7 + - + +
200A ALA* 1.3 78.3 - - + +
202A GLY* 1.3 58.1 + - - +
203A ALA 3.7 0.2 - - - -
221A LEU* 3.6 30.2 - - + -
222A GLY* 2.9 29.8 + - - +
223A GLY* 3.7 33.4 - - - -
224A GLY* 5.2 1.1 - - - -
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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