Contacts of the strand formed by residues 198 - 208 (chain Q) in PDB entry 2AK4
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193Q PRO* 3.7 4.3 - - - +
194Q VAL* 3.2 25.5 + - + +
195Q SER* 3.2 28.4 + - - +
197Q HIS* 1.3 102.5 + - + +
199Q ALA* 1.3 64.5 + - - +
248Q VAL* 4.0 19.7 - - + +
249Q VAL 3.2 12.7 - - - +
250Q PRO* 4.3 10.8 - - + +
251Q SER* 3.5 8.9 + - - -
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Residues in contact with ALA 199 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q HIS* 3.2 39.0 - - + +
192Q HIS 3.5 9.0 - - - +
193Q PRO* 3.9 3.6 - - + -
194Q VAL* 3.6 6.9 - - - +
198Q GLU* 1.3 77.6 - - - +
200Q THR* 1.3 61.6 - - - +
248Q VAL* 3.5 0.6 - - - -
249Q VAL* 2.7 47.1 + - + +
251Q SER* 4.4 4.7 - - - +
254Q GLU* 4.4 6.1 - - - +
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Residues in contact with THR 200 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Q THR 3.6 0.9 - - - +
191Q HIS* 3.4 6.1 - - - -
192Q HIS* 2.6 52.9 + - + +
194Q VAL* 4.0 16.0 - - - +
199Q ALA* 1.3 71.4 - - - +
201Q LEU* 1.3 65.7 + - - +
202Q ARG* 3.9 28.2 + - - +
229Q GLU* 5.5 1.3 - - - +
246Q ALA* 3.9 17.5 - - + -
247Q VAL 3.3 11.7 - - - +
248Q VAL* 4.3 10.1 - - + +
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Residues in contact with LEU 201 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Q VAL* 4.3 2.2 - - + -
190Q THR 3.4 4.7 - - - +
191Q HIS* 3.7 24.9 - - + -
199Q ALA 3.7 0.4 + - - -
200Q THR* 1.3 72.1 - - - +
202Q ARG* 1.3 59.4 + - - +
217Q TRP* 3.7 23.3 - - + -
246Q ALA* 3.2 4.0 - - - +
247Q VAL* 2.8 37.5 + - + -
249Q VAL* 3.9 26.2 - - + -
254Q GLU* 4.0 13.5 - - + +
257Q TYR* 3.8 30.1 - - + -
274Q TRP* 3.5 33.9 - - + +
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Residues in contact with ARG 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188Q HIS 3.8 0.9 - - - +
189Q VAL* 3.2 5.7 - - - -
190Q THR* 2.9 46.3 + - - +
192Q HIS* 3.2 30.8 - - + -
200Q THR* 3.9 18.6 - - + +
201Q LEU* 1.3 74.6 - - - +
203Q CYS* 1.3 60.9 + - - +
204Q TRP* 3.6 19.5 + - - +
217Q TRP* 4.2 2.5 - - - -
229Q GLU* 4.2 7.9 + - - -
244Q TRP* 3.4 57.4 - - + -
245Q ALA 3.4 1.8 - - - +
246Q ALA* 4.0 1.7 - - + +
98R ASP* 2.9 31.4 + - - +
99R MET* 4.2 16.5 - - - +
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Residues in contact with CYS 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Q THR* 5.8 0.2 - - - -
188Q HIS 3.8 2.9 - - - -
189Q VAL* 4.4 9.9 - - - -
202Q ARG* 1.3 71.8 - - - +
204Q TRP* 1.3 65.8 + - - +
215Q LEU* 3.6 7.8 - - + +
217Q TRP* 3.7 13.4 - - + +
244Q TRP* 3.1 7.2 - - - -
245Q ALA* 2.6 39.6 + - + +
259Q CYS* 2.0 50.3 - - - -
261Q VAL* 4.5 10.5 - - - -
272Q LEU* 4.9 5.2 - - - -
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Residues in contact with TRP 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Q LYS 4.3 0.2 - - - -
187Q THR* 3.2 27.9 - - - +
188Q HIS* 2.9 50.4 + + + +
190Q THR* 3.4 29.6 + - + +
192Q HIS* 5.2 0.2 + - - -
202Q ARG* 3.6 23.7 - - + +
203Q CYS* 1.3 75.1 - - - +
205Q ALA* 1.3 59.3 + - - +
206Q LEU* 3.8 30.3 - - + -
215Q LEU* 4.7 1.3 - - - -
234Q ARG* 3.6 12.6 - - - -
242Q GLN* 4.9 1.1 - - + -
243Q LYS 3.9 5.2 - - - -
244Q TRP* 3.5 21.5 - + + -
97R ARG 4.8 3.8 - - - -
98R ASP* 3.2 28.6 + - - +
99R MET 3.2 28.9 - - - -
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Residues in contact with ALA 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Q PRO* 3.9 8.3 - - + -
186Q LYS 3.6 3.4 - - - -
187Q THR* 4.3 6.1 - - + -
203Q CYS 4.1 0.2 + - - -
204Q TRP* 1.3 72.6 - - - +
206Q LEU* 1.3 64.9 + - - +
208Q PHE* 3.3 20.6 - - + -
213Q ILE* 3.9 17.3 - - + -
215Q LEU* 3.9 15.7 - - + +
242Q GLN* 3.4 1.9 - - - -
243Q LYS 2.9 37.9 + - - +
261Q VAL* 5.1 0.4 - - + -
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Residues in contact with LEU 206 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Q PRO* 3.4 1.2 - - - +
186Q LYS* 2.8 46.3 + - + +
188Q HIS* 4.2 20.9 - - + +
204Q TRP* 3.8 27.6 - - + -
205Q ALA* 1.3 79.5 - - - +
207Q GLY* 1.3 64.4 + - - +
208Q PHE* 3.4 4.7 + - - -
241Q PHE 3.8 2.2 - - - -
242Q GLN* 3.7 35.4 - - + +
12R ARG 5.6 0.4 - - - +
14R PRO* 4.0 31.2 - - + -
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Residues in contact with GLY 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183Q ASP* 3.9 13.0 - - - +
184Q PRO 4.0 5.5 - - - +
186Q LYS* 5.8 2.9 - - - +
206Q LEU* 1.3 74.5 - - - +
208Q PHE* 1.3 59.2 + - - +
236Q ALA* 5.8 0.4 - - - +
240Q THR* 3.4 33.8 + - - +
241Q PHE 3.1 7.7 + - - -
242Q GLN* 4.9 2.4 - - - +
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Residues in contact with PHE 208 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183Q ASP 3.3 14.4 - - - +
184Q PRO 4.4 0.2 - - - -
185Q PRO* 3.7 24.0 - - + -
205Q ALA* 3.3 24.7 - - + -
207Q GLY* 1.3 79.2 - - - +
209Q TYR* 1.3 62.0 + - - +
210Q PRO 3.3 18.8 - - - -
211Q ALA 3.3 23.1 - - - -
213Q ILE* 3.7 37.2 - - + -
233Q THR* 4.2 2.2 - - + -
240Q THR* 3.5 2.9 - - - -
241Q PHE* 2.9 60.5 + - + -
242Q GLN* 3.8 12.1 - - - -
243Q LYS* 4.2 0.9 - - + -
263Q HIS* 3.6 12.6 - + - +
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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