Contacts of the strand formed by residues 169 - 179 (chain Q) in PDB entry 3K9Q
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 LEU 169 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160Q ALA* 5.0 4.9 - - + +
163Q LEU* 5.0 4.9 - - + -
164Q ASN* 2.9 32.4 + - + +
168Q GLY* 1.3 72.5 - - - +
170Q VAL* 1.3 61.8 + - - +
171Q GLU* 3.8 27.6 - - - +
224Q ILE* 3.8 37.7 - - + -
227Q LYS* 3.0 31.6 + - + +
228Q LEU* 3.9 20.0 - - + -
247Q VAL* 3.8 25.6 - - + -
248Q VAL 4.0 2.7 - - - +
249Q LEU* 4.2 7.6 - - + -
250Q GLU* 4.1 4.3 - - - +
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Residues in contact with VAL 170 (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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169Q LEU* 1.3 73.8 - - - +
171Q GLU* 1.3 74.3 + - + +
227Q LYS* 3.4 23.5 - - - +
248Q VAL* 2.9 26.7 + - + +
249Q LEU 3.7 3.8 - - - +
250Q GLU* 3.4 46.0 - - - +
302R VAL* 3.8 15.2 - - + +
305R ARG* 3.8 39.0 - - + +
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Residues in contact with GLU 171 (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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169Q LEU* 3.7 6.8 - - - +
170Q VAL* 1.3 87.3 - - + +
172Q GLY* 1.3 58.7 + - - +
227Q LYS* 3.2 15.0 - - - +
247Q VAL* 3.4 3.1 - - - +
248Q VAL* 2.8 39.8 + - + +
300R MET* 3.6 15.9 - - + +
302R VAL* 3.5 14.9 + - + +
305R ARG* 2.5 47.3 - - - +
306R GLN 3.3 11.4 + - - +
307R LEU* 3.8 23.1 - - + +
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Residues in contact with GLY 172 (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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171Q GLU* 1.3 78.3 - - - +
173Q LEU* 1.3 68.1 + - - +
227Q LYS 2.8 11.2 + - - +
228Q LEU* 3.5 16.8 - - - +
229Q ASP 3.4 19.4 + - - -
246Q THR 3.1 12.8 - - - -
247Q VAL* 4.0 3.1 - - - -
300R MET* 4.0 3.6 - - - +
307R LEU* 3.7 6.5 - - - -
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Residues in contact with LEU 173 (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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172Q GLY* 1.3 79.8 - - - +
174Q MET* 1.3 59.8 + - - +
229Q ASP* 3.3 27.8 - - + +
244Q GLU 3.9 0.5 - - - +
245Q LEU* 3.5 4.4 - - - +
246Q THR* 2.7 44.5 + - - +
246R THR* 4.1 14.4 - - + +
298R ARG* 3.9 21.3 - - + +
300R MET* 3.9 17.5 - - + -
307R LEU* 3.9 32.7 - - + +
309R LYS* 3.7 44.6 - - + +
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Residues in contact with MET 174 (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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152Q THR* 3.8 26.9 - - + -
156Q LEU* 4.1 19.7 - - - -
173Q LEU* 1.3 75.1 - - - +
175Q THR* 1.3 71.4 + - - +
176Q THR* 4.4 2.0 - - + -
211Q THR* 3.7 30.5 - - + -
213Q ALA* 4.1 3.8 - - + -
214Q ALA* 4.1 17.3 - - + +
229Q ASP 2.8 13.3 + - - +
230Q GLY* 3.1 14.4 - - - +
231Q GLY 3.2 18.5 + - - +
243Q THR* 3.9 16.4 - - + -
244Q GLU 3.2 10.3 - - - +
245Q LEU* 4.1 11.7 - - + -
309R LYS* 2.9 16.1 + - - -
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Residues in contact with THR 175 (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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173Q LEU 4.3 0.2 - - - -
174Q MET* 1.3 72.7 + - - +
176Q THR* 1.3 71.7 + - - +
177Q ILE* 3.9 13.1 + - + -
231Q GLY 3.5 8.1 + - - +
232Q ALA 4.9 0.9 - - - -
233Q GLN* 4.1 21.8 - - + +
243Q THR* 3.7 0.2 - - - -
244Q GLU* 2.7 47.8 + - - +
175R THR* 6.3 0.7 - - + -
177R ILE* 5.1 2.0 - - + -
244R GLU* 2.5 33.7 + - - +
309R LYS* 2.9 19.9 + - - -
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Residues in contact with THR 176 (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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152Q THR* 3.9 25.1 - - + +
174Q MET* 4.2 2.3 - - + +
175Q THR* 1.3 74.9 - - - +
177Q ILE* 1.3 62.7 + - - +
178Q HIS* 3.4 8.1 + - + +
211Q THR* 4.3 5.6 - - + -
231Q GLY 3.1 15.7 + - - +
232Q ALA* 3.3 14.7 - - + +
233Q GLN 2.9 24.3 + - - -
242Q LEU 2.9 16.1 + - - -
243Q THR* 3.6 10.5 + - - -
314Q TYR* 2.8 24.9 + - - +
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Residues in contact with ILE 177 (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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175Q THR* 4.1 13.9 - - + +
176Q THR* 1.3 71.2 - - - +
178Q HIS* 1.3 58.9 + - - +
233Q GLN* 3.5 5.8 - - + +
235Q VAL* 3.7 33.7 - - + -
241Q SER* 3.4 4.0 - - - -
242Q LEU* 2.7 46.2 + - + +
244Q GLU* 3.9 33.2 - - + +
175R THR* 5.2 1.1 - - + -
177R ILE* 4.1 22.9 - - + -
206R ILE* 3.6 21.4 - - + +
233R GLN* 4.2 14.6 - - + -
235R VAL* 4.1 12.1 - - + -
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Residues in contact with HIS 178 (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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152Q THR* 3.8 7.2 - - - -
176Q THR* 3.9 15.0 - - + +
177Q ILE* 1.3 76.0 - - - +
179Q ALA* 1.3 93.9 + - - +
181Q THR* 3.9 12.1 - - + -
232Q ALA* 4.9 2.2 - - + -
233Q GLN 2.8 14.0 + - - +
234Q ARG* 3.2 22.7 + - - +
235Q VAL* 2.9 26.1 + - - -
240Q GLY 4.4 0.4 - - - -
241Q SER* 3.4 4.7 - - - -
314Q TYR* 3.2 24.3 + - - -
316Q ASN* 3.7 23.6 - - - +
337Q GOL 2.9 37.7 + - - -
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Residues in contact with ALA 179 (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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178Q HIS* 1.3 99.3 + - - +
180Q TYR* 1.3 61.8 + - - +
234Q ARG* 3.6 4.3 - - - -
235Q VAL 4.0 1.1 - - - -
237Q VAL* 3.0 25.6 - - + +
238Q ALA 3.8 2.2 - - - +
239Q THR* 3.3 24.9 - - - +
240Q GLY 3.3 21.5 + - - +
241Q SER* 3.0 8.3 + - - -
316Q ASN* 3.7 10.3 - - - +
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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