Contacts of the strand formed by residues 202 - 213 (chain A) in PDB entry 1E8U
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 SER 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ARG* 4.3 4.6 + - - -
190A ASN* 3.2 30.6 + - - -
191A VAL 3.1 18.6 - - - -
192A ILE* 3.3 12.3 - - - -
193A LEU* 6.5 0.2 - - - -
200A SER 3.5 2.2 + - - -
201A HIS* 1.3 90.5 + - - +
203A HIS* 1.3 60.1 + - - +
231A ASP 5.5 0.5 - - - +
233A GLN 4.5 10.4 - - - +
234A ASN* 3.5 23.5 + - - +
235A ARG 4.4 2.6 + - - +
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Residues in contact with HIS 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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167A THR* 3.9 14.3 - - - +
190A ASN* 3.7 4.6 + - - -
191A VAL* 2.8 62.5 + - + +
193A LEU* 3.3 34.2 - - + +
201A HIS* 5.3 2.3 + - + -
202A SER* 1.3 77.0 - - - +
204A GLN* 1.3 58.9 + - - +
205A TYR* 5.8 0.2 - - + -
228A SER* 3.1 24.9 - - - -
229A LEU 3.1 23.1 - - - +
230A ASP* 4.0 21.8 + - + +
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Residues in contact with GLN 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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175A ILE 4.8 3.4 + - - -
188A THR* 2.7 29.8 + - - +
189A HIS* 3.3 20.1 + - - +
190A ASN* 3.1 29.7 + - - +
203A HIS* 1.3 74.2 - - - +
205A TYR* 1.3 59.5 + - - +
227A ILE 3.8 0.7 - - - +
228A SER* 3.6 2.2 - - - -
229A LEU* 2.8 49.4 + - + +
235A ARG* 4.5 14.5 - - + +
236A LYS* 5.6 0.5 - - - -
238A CYS* 3.7 32.4 + - - +
249A MET* 4.0 18.4 - - + -
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Residues in contact with TYR 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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162A PHE 4.2 6.1 + - - -
164A PRO* 3.2 40.1 - - + +
187A TYR* 4.1 14.4 - + - -
188A THR* 2.6 27.0 + - - -
189A HIS* 2.9 49.9 + + + +
191A VAL* 4.3 8.1 - - + -
203A HIS* 4.0 1.0 + - + -
204A GLN* 1.3 72.8 - - - +
206A LEU* 1.3 56.3 + - - +
207A ALA* 3.5 29.7 - - + +
223A THR* 4.3 5.5 - - - +
226A SER* 3.7 24.4 + - - -
227A ILE 3.6 11.9 - - - -
228A SER* 4.4 10.5 - - - +
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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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187A TYR 3.5 15.5 - - - +
188A THR* 3.9 14.8 - - - +
204A GLN 4.1 1.8 + - - +
205A TYR* 1.3 76.4 - - - +
207A ALA* 1.3 62.4 + - - +
226A SER* 3.1 4.1 - - - -
227A ILE* 2.9 41.9 + - + +
229A LEU* 5.3 2.0 - - + -
240A VAL* 3.9 21.5 - - + -
247A CYS* 4.4 9.9 - - + +
249A MET* 4.1 24.0 - - + -
275A LEU* 3.7 23.8 - - + +
281A TYR* 3.6 36.8 - - + -
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Residues in contact with ALA 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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162A PHE* 6.3 0.2 - - + -
185A TYR* 4.1 2.4 - - + +
186A CYS* 3.4 5.4 - - - -
187A TYR* 2.7 45.6 + - + +
205A TYR* 3.5 29.8 - - + +
206A LEU* 1.3 76.9 - - - +
208A LEU* 1.3 60.8 + - - +
223A THR* 4.0 14.4 - - + +
225A ARG 3.4 9.9 - - - +
226A SER* 4.0 1.3 - - - -
247A CYS* 3.7 4.8 - - - +
275A LEU* 4.0 4.3 - - - -
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Residues in contact with LEU 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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126A PRO* 4.9 3.1 - - + -
184A HIS* 3.1 30.7 - - + -
185A TYR* 3.6 5.4 - - - +
207A ALA* 1.3 72.8 - - - +
209A GLY* 1.3 68.8 + - - +
223A THR* 3.7 3.1 - - - -
224A LEU* 2.8 38.3 + - + -
225A ARG* 2.7 32.7 + - + +
246A GLY* 4.2 6.1 - - - -
247A CYS* 3.1 29.6 - - - -
275A LEU* 3.8 16.3 - - + +
277A PHE* 4.2 27.4 - - + -
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Residues in contact with GLY 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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184A HIS* 3.2 5.7 - - - +
185A TYR* 2.9 45.7 + - - -
208A LEU* 1.3 78.7 - - - +
210A VAL* 1.3 71.3 + - - +
222A SER 3.1 13.9 - - - -
223A THR* 3.9 0.2 - - - -
224A LEU* 3.8 4.5 - - - -
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Residues in contact with VAL 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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126A PRO* 3.9 9.2 - - + -
127A ILE 3.7 19.5 - - - +
128A HIS* 3.5 10.3 - - - +
183A THR 3.6 17.3 - - - +
184A HIS* 4.2 3.8 - - + -
185A TYR* 3.2 9.9 - - - -
208A LEU* 5.3 0.2 - - + -
209A GLY* 1.3 81.3 - - - +
211A LEU* 1.3 61.4 + - - +
212A ARG* 3.4 40.6 - - + +
222A SER* 2.8 33.7 + - - +
224A LEU* 3.7 18.6 - - + -
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Residues in contact with LEU 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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128A HIS* 2.7 20.9 + - + +
129A ASP 3.0 24.6 + - - -
132A PHE* 3.7 24.5 - - + -
136A ILE* 3.7 21.8 - - + -
180A MET* 3.6 34.5 - - + -
210A VAL* 1.3 72.7 - - - +
212A ARG* 1.3 64.4 + - - +
219A ILE* 4.2 16.4 - - + -
220A PHE 3.9 2.0 - - - +
221A PHE* 3.3 43.7 - - + -
532A PHE* 4.1 9.9 - - + -
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Residues in contact with ARG 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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126A PRO* 5.2 4.6 + - - +
127A ILE 5.3 2.4 + - - -
129A ASP* 3.1 25.2 + - - +
132A PHE* 3.6 4.1 - - - -
210A VAL* 3.4 21.6 - - + +
211A LEU* 1.3 84.2 - - - +
213A THR* 1.3 72.8 + - - +
219A ILE* 3.5 1.7 - - - -
220A PHE* 2.9 56.6 + - + +
222A SER* 3.1 29.2 + - - -
224A LEU* 3.8 24.6 - - - +
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Residues in contact with THR 213 (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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129A ASP* 2.8 16.8 + - - +
131A ASP* 3.9 27.3 + - + +
132A PHE* 3.4 25.6 - - + -
212A ARG* 1.3 81.9 - - - +
214A THR* 1.3 69.6 + - - +
217A GLY* 4.2 12.5 - - - +
218A ARG 3.1 10.1 - - - +
219A ILE* 4.3 10.1 - - + -
220A PHE* 3.7 8.3 - - - -
534A VAL* 5.5 4.5 - - + -
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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