Contacts of the strand formed by residues 198 - 208 (chain D) in PDB entry 3HAE
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 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D ALA* 4.0 1.2 - - - -
194D VAL* 3.2 37.8 + - + +
195D SER* 3.4 18.9 + - - +
197D HIS* 1.3 85.4 - - + +
199D ALA* 1.3 62.8 + - - +
248D VAL* 3.7 31.3 - - + +
249D VAL 3.4 13.2 - - - +
250D PRO* 4.6 2.2 - - + -
251D SER* 3.5 5.6 + - - -
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D HIS* 3.9 28.5 - - + +
192D HIS 3.3 14.4 - - - +
193D ALA* 4.4 2.5 - - + -
194D VAL* 4.0 3.1 - - - +
198D GLU* 1.3 76.2 - - - +
200D THR* 1.3 60.8 + - - +
201D LEU* 5.3 0.2 - - + -
248D VAL* 3.2 5.8 - - - -
249D VAL* 2.8 51.3 + - + +
251D SER* 5.1 2.7 - - - +
254D GLU* 4.3 6.3 - - - +
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Residues in contact with THR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D THR 3.8 0.5 - - - +
191D HIS* 3.4 5.9 - - - +
192D HIS* 2.9 41.0 + - - -
194D VAL* 3.9 16.6 - - - +
199D ALA* 1.3 72.9 - - - +
201D LEU* 1.3 69.0 + - - +
202D ARG* 3.8 26.5 + - - +
246D ALA* 3.7 26.5 - - + -
247D VAL 3.3 7.7 + - - +
248D VAL* 4.4 7.6 - - - +
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Residues in contact with LEU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D MET* 4.5 4.0 - - - -
190D THR 3.5 4.5 - - - +
191D HIS* 3.5 35.9 - - + +
199D ALA* 5.3 0.2 - - + -
200D THR* 1.3 78.6 - - - +
202D ARG* 1.3 60.6 + - - +
217D TRP* 3.3 24.3 - - + -
246D ALA* 3.1 22.0 - - - -
247D VAL* 2.9 16.0 + - + +
249D VAL* 4.4 16.6 - - + -
254D GLU* 4.3 21.8 - - + +
257D TYR* 4.3 24.5 - - + +
274D TRP* 4.3 21.1 - - + -
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Residues in contact with ARG 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D MET* 3.1 9.1 - - - -
190D THR* 2.9 45.0 + - - +
192D HIS* 3.6 28.5 + - + -
200D THR* 3.8 22.4 + - - +
201D LEU* 1.3 73.2 - - - +
203D CYS* 1.3 63.0 + - - +
204D TRP* 3.6 31.1 - - - +
229D GLU* 5.5 1.6 + - - -
244D TRP* 3.4 52.8 - - + -
245D ALA 3.4 2.2 - - - -
246D ALA* 4.2 3.3 - - + +
99E MET* 3.8 31.3 + - - +
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Residues in contact with CYS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D HIS 3.8 2.7 - - - -
189D MET* 4.5 2.9 - - - -
201D LEU 4.0 0.4 + - - -
202D ARG* 1.3 72.8 - - - +
204D TRP* 1.3 63.9 + - - +
215D LEU* 3.8 6.2 - - + +
217D TRP* 3.7 10.1 - - + +
244D TRP* 3.2 7.2 - - - -
245D ALA* 2.7 37.7 + - + +
259D CYS* 2.0 52.9 - - - -
261D VAL* 4.7 10.5 - - - -
272D LEU* 4.5 13.7 - - - -
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Residues in contact with TRP 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D THR* 3.2 29.9 - - - +
188D HIS* 2.8 56.2 + + + +
190D THR* 3.9 5.2 + - + -
202D ARG* 3.6 38.4 - - + +
203D CYS* 1.3 77.1 - - - +
205D ALA* 1.3 59.4 + - - +
206D LEU* 3.8 28.0 - - + -
215D LEU* 5.3 0.2 - - - -
234D ARG* 3.8 24.0 - - - -
242D GLN* 5.1 0.9 - - + -
243D LYS 4.0 5.6 - - - -
244D TRP* 3.5 30.5 - + + -
99E MET* 3.4 44.6 + - + -
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Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PRO* 4.2 2.9 - - + -
186D LYS 3.7 3.8 - - - -
187D THR* 4.1 9.9 - - + -
204D TRP* 1.3 74.2 - - - +
206D LEU* 1.3 61.2 + - - +
208D PHE* 3.3 7.6 - - + -
213D ILE* 3.9 28.3 - - + -
215D LEU* 4.1 15.9 - - + -
242D GLN* 3.2 6.2 - - - -
243D LYS* 2.9 38.8 + - + +
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PRO* 3.6 2.3 - - - +
186D LYS* 2.8 44.7 + - + +
188D HIS* 4.6 19.3 - - + +
204D TRP* 3.8 28.5 - - + -
205D ALA* 1.3 78.9 - - - +
207D SER* 1.3 73.0 + - - +
208D PHE* 3.4 2.9 + - - -
241D PHE 3.6 1.3 - - - -
242D GLN* 3.8 31.6 - - + +
12E ARG 5.9 0.2 - - - +
14E PRO* 4.1 29.8 - - + -
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Residues in contact with SER 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ASP* 3.9 5.7 - - - +
184D ALA 3.5 11.4 - - - +
186D LYS* 3.3 26.9 - - - +
206D LEU* 1.3 78.4 + - - +
208D PHE* 1.3 56.6 + - - +
236D ALA* 5.4 2.9 - - - -
238D ASP* 5.5 2.2 - - - -
240D THR* 3.5 28.6 - - - +
241D PHE 2.9 12.7 + - - +
242D GLN* 4.5 5.5 + - - +
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Residues in contact with PHE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ASP* 3.2 15.3 - - - +
185D PRO* 3.7 26.0 - - + -
205D ALA* 3.3 31.0 - - + -
206D LEU 4.1 0.2 - - - -
207D SER* 1.3 76.9 - - - +
209D TYR* 1.3 61.1 + - - +
210D PRO 3.1 20.4 - - - -
211D ALA 3.5 21.5 - - - -
213D ILE* 3.8 30.7 - - + -
233D THR* 4.0 8.3 - - + -
240D THR* 3.3 7.1 - - - +
241D PHE* 2.9 64.1 + - + -
242D GLN* 3.8 6.5 - - - -
243D LYS 4.0 1.8 - - - -
263D HIS* 3.6 9.2 - + - +
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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