Contacts of the strand formed by residues 228 - 235 (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 228 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q MET* 3.4 5.8 - - - +
156R LEU* 4.3 19.5 - - + -
160R ALA* 4.0 26.0 - - + -
169R LEU* 3.9 20.2 - - + -
172R GLY* 3.6 33.0 - - - +
214R ALA* 3.3 31.1 + - + +
215R LYS* 3.6 8.3 - - - +
217R ILE* 3.9 19.9 - - + +
224R ILE* 4.1 6.1 + - + -
226R GLY* 3.4 5.3 - - - +
227R LYS* 1.3 80.7 - - - +
229R ASP* 1.3 64.9 + - - +
245R LEU* 3.9 15.9 - - + -
247R VAL* 4.5 0.9 - - + -
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Residues in contact with ASP 229 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298Q ARG* 5.6 8.3 - - - +
299Q VAL 5.8 0.3 - - - +
300Q MET* 3.0 27.5 - - + +
172R GLY 3.4 2.8 + - - -
173R LEU* 3.3 15.1 - - + -
174R MET* 2.9 21.5 + - - +
211R THR 5.1 1.4 - - - +
214R ALA* 3.5 15.3 - - - +
215R LYS* 3.3 44.4 + - - +
228R LEU* 1.3 71.8 - - - +
230R GLY* 1.3 79.9 + - - +
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Residues in contact with GLY 230 (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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298Q ARG* 5.9 8.6 + - - -
309Q LYS* 4.4 5.2 - - - -
173R LEU* 4.5 4.0 - - - -
174R MET* 3.1 22.7 - - - -
210R SER* 5.4 0.7 - - - -
211R THR 3.9 14.0 + - - +
214R ALA* 3.9 2.4 - - - +
229R ASP* 1.3 94.6 + - - +
231R GLY* 1.3 57.9 + - - -
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Residues in contact with GLY 231 (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* 4.5 3.6 - - - +
174R MET* 3.1 14.8 + - - +
175R THR* 3.4 7.2 - - - -
176R THR* 2.9 22.0 + - - +
209R ASN 3.9 7.0 - - - -
210R SER* 4.8 1.8 - - - -
211R THR* 3.8 12.6 - - - -
230R GLY* 1.3 74.1 - - - -
232R ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 232 (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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175R THR* 4.9 0.9 - - - -
176R THR* 3.3 25.4 - - + +
178R HIS* 4.8 6.5 - - + -
208R PRO* 3.3 4.5 - - - +
209R ASN* 2.8 46.2 + - + +
210R SER 4.6 2.9 - - - +
211R THR* 4.4 7.9 - - + -
231R GLY* 1.3 74.7 - - - -
233R GLN* 1.3 69.4 + - - +
234R ARG* 4.9 7.4 - - - +
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Residues in contact with GLN 233 (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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177Q ILE* 4.2 17.0 - - + -
242Q LEU* 3.4 14.4 - - - +
244Q GLU* 2.7 29.7 + - - +
296Q GLN* 3.3 21.0 - - - +
175R THR* 4.2 10.1 - - + -
176R THR 2.9 9.5 + - - +
177R ILE* 3.5 6.3 - - - -
178R HIS 2.8 26.4 + - - -
206R ILE* 3.7 14.7 - - + +
207R ILE 3.4 2.3 - - - -
208R PRO* 3.1 30.5 - - - +
232R ALA* 1.3 82.1 + - - +
234R ARG* 1.3 64.0 + - - +
235R VAL* 3.6 6.7 + - + +
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Residues in contact with ARG 234 (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* 3.3 28.4 + - - +
179R ALA 3.5 15.7 - - - -
180R TYR* 4.8 1.6 - - - -
181R THR* 3.0 31.5 + - - +
183R ASP* 3.8 12.7 + - - -
184R GLN* 2.7 56.9 + - - +
198R ARG* 4.8 4.0 - - + +
202R ALA 5.7 0.4 - - - -
205R ASN 3.4 4.7 - - - +
207R ILE* 2.7 43.5 + - + +
209R ASN* 4.3 22.4 + - + +
210R SER 5.6 3.8 + - - -
232R ALA* 4.9 7.3 - - + +
233R GLN* 1.3 72.5 - - - +
235R VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 235 (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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177Q ILE* 4.1 9.9 - - + -
206Q ILE* 3.8 22.7 - - + -
235Q VAL* 4.0 23.3 - - + -
236Q PRO* 5.1 0.2 - - + -
177R ILE* 3.8 27.8 - - + -
178R HIS 2.9 18.7 + - - +
180R TYR* 3.5 16.7 + - - +
202R ALA 4.6 1.8 - - - -
205R ASN 3.8 1.1 - - - -
206R ILE* 4.2 9.9 - - + -
233R GLN 3.8 9.9 - - - +
234R ARG* 1.3 81.1 - - - +
236R PRO* 1.3 71.7 - - + +
237R VAL 2.8 15.5 + - - +
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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