Contacts of the strand formed by residues 169 - 179 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160R ALA* 5.2 4.7 - - + +
163R LEU* 4.3 5.8 + - + -
164R ASN* 3.0 31.6 + - + +
168R GLY* 1.3 71.9 - - - +
170R VAL* 1.3 63.0 + - - +
171R GLU 3.9 17.3 - - - +
224R ILE* 3.9 33.7 - - + -
227R LYS* 3.2 33.8 + - + +
228R LEU* 3.9 21.5 - - + -
245R LEU* 6.1 0.2 - - + -
247R VAL* 3.8 34.1 - - + -
248R VAL 4.0 2.2 - - - +
249R LEU* 4.1 7.0 - - + -
250R GLU* 4.6 4.1 - - - +
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Residues in contact with VAL 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302Q VAL* 4.0 13.5 - - + +
305Q ARG* 3.7 45.5 - - + +
168R GLY 3.4 0.2 + - - -
169R LEU* 1.3 73.0 - - - +
171R GLU* 1.3 75.5 + - + +
227R LYS* 3.5 20.6 - - - +
248R VAL* 2.9 16.9 + - + +
249R LEU 3.7 25.8 - - - +
250R GLU* 3.7 23.8 - - + +
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Residues in contact with GLU 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q MET* 3.8 10.9 - - + +
302Q VAL* 3.5 18.6 + - + +
305Q ARG* 2.6 50.7 + - - +
306Q GLN 3.4 10.8 + - - +
307Q LEU* 4.0 16.7 - - + +
169R LEU* 3.7 7.9 - - - +
170R VAL* 1.3 82.2 - - + +
172R GLY* 1.3 59.9 + - - +
227R LYS* 3.2 16.2 - - - +
247R VAL* 3.3 2.8 - - - +
248R VAL* 2.8 47.2 + - + +
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Residues in contact with GLY 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q MET* 4.0 4.4 - - - +
307Q LEU* 3.8 6.7 - - - -
171R GLU* 1.3 78.1 - - - +
173R LEU* 1.3 65.9 + - - +
227R LYS 2.8 11.6 + - - +
228R LEU* 3.6 17.9 - - - +
229R ASP 3.4 19.4 + - - -
246R THR 3.1 13.0 - - - -
247R VAL* 4.0 3.1 - - - -
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Residues in contact with LEU 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246Q THR* 3.9 14.6 - - + -
298Q ARG* 5.0 11.9 - - + +
299Q VAL 5.8 0.2 - - - -
300Q MET* 3.8 20.0 - - + +
307Q LEU* 3.8 34.8 - - + +
309Q LYS* 3.9 41.1 - - + +
172R GLY* 1.3 79.5 - - - +
174R MET* 1.3 59.8 + - - +
229R ASP* 3.3 28.7 - - + +
230R GLY* 4.3 3.8 - - - +
244R GLU 4.0 0.5 - - - +
245R LEU* 3.5 4.3 - - - +
246R THR* 2.7 37.2 + - - +
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Residues in contact with MET 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309Q LYS* 2.9 16.1 + - - -
152R THR* 4.0 21.3 - - + -
156R LEU* 4.2 13.5 - - - -
173R LEU* 1.3 76.2 - - - +
175R THR* 1.3 70.4 + - - +
176R THR* 4.7 1.3 - - + -
211R THR* 3.6 31.4 - - + -
213R ALA* 4.2 2.2 - - + -
214R ALA* 3.8 30.5 - - + +
229R ASP 2.9 13.0 + - - +
230R GLY* 3.1 1.9 - - - -
231R GLY 3.1 34.6 + - - +
243R THR* 4.0 13.9 - - + -
244R GLU 3.3 11.9 - - - +
245R LEU* 4.1 11.0 - - + -
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Residues in contact with THR 175 (chain R).
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* 6.3 0.7 - - + -
177Q ILE* 5.2 1.8 - - + -
244Q GLU* 2.6 36.3 + - - +
309Q LYS* 2.9 22.2 + - - -
174R MET* 1.3 73.2 - - - +
176R THR* 1.3 73.9 + - - +
177R ILE* 4.0 11.3 + - + -
231R GLY 3.4 7.9 + - - +
232R ALA* 4.9 0.9 - - - -
233R GLN* 4.2 13.9 - - + +
242R LEU 3.9 0.7 - - - +
244R GLU* 2.8 42.3 + - - +
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Residues in contact with THR 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152R THR* 3.9 25.8 - - + +
174R MET* 4.2 1.5 - - + +
175R THR* 1.3 74.9 - - - +
177R ILE* 1.3 64.1 + - - +
178R HIS* 3.4 9.9 + - + -
211R THR* 4.4 5.6 - - + -
231R GLY 2.9 15.4 + - - +
232R ALA* 3.3 21.1 - - + +
233R GLN 2.9 25.8 + - - +
242R LEU 3.1 13.4 + - - -
243R THR* 3.9 10.8 - - - -
314R TYR* 2.7 24.6 + - - +
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Residues in contact with ILE 177 (chain R).
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* 5.1 0.9 - - + -
177Q ILE* 4.1 23.6 - - + -
206Q ILE* 3.6 23.6 - - + +
233Q GLN* 4.2 14.6 - - + -
235Q VAL* 4.2 7.2 - - + -
175R THR* 4.1 12.8 - - + +
176R THR* 1.3 72.6 - - - +
178R HIS* 1.3 58.1 + - - +
233R GLN* 3.5 5.4 - - + +
235R VAL* 3.8 31.2 - - + -
241R SER* 3.4 3.5 - - - -
242R LEU* 2.7 50.2 + - + +
244R GLU* 4.0 32.5 - - + +
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Residues in contact with HIS 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206Q ILE* 4.8 0.2 - - - -
0R NAD 4.3 2.6 - - - -
151R GLY* 5.9 0.8 - - - -
152R THR* 3.7 12.1 + - - -
176R THR* 3.9 14.6 - - + +
177R ILE* 1.3 73.4 - - - +
179R ALA* 1.3 86.1 + - - +
181R THR* 3.9 13.7 - - + -
232R ALA* 4.8 2.7 - - + -
233R GLN 2.8 9.4 + - - +
234R ARG* 3.3 29.4 + - - +
235R VAL* 2.9 29.2 + - - +
240R GLY 4.4 0.2 - - - -
241R SER* 3.3 6.5 - - - -
314R TYR* 3.2 26.2 + - - -
316R ASN* 3.7 33.1 - - + +
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Residues in contact with ALA 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R HIS* 1.3 99.6 + - - +
180R TYR* 1.3 64.0 + - - +
234R ARG* 3.5 4.5 - - - -
235R VAL 4.1 1.1 - - - -
237R VAL* 3.1 26.0 - - + +
238R ALA 3.9 1.8 - - - +
239R THR* 3.4 28.9 - - - +
240R GLY 3.5 15.0 + - - +
241R SER* 3.0 8.1 + - - -
316R ASN* 3.8 9.6 - - - +
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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