Contacts of the strand formed by residues 228 - 235 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156O LEU* 4.3 20.0 - - + -
160O ALA* 4.0 25.8 - - + -
169O LEU* 4.0 20.2 - - + -
172O GLY* 3.4 26.2 - - - +
214O ALA* 3.3 29.4 + - + +
215O LYS* 3.7 7.4 - - - +
217O ILE* 4.0 20.1 - - + +
224O ILE* 4.2 5.7 + - + -
226O GLY* 4.4 5.5 - - - -
227O LYS* 1.3 84.4 - - - +
229O ASP* 1.3 65.0 + - - +
245O LEU* 3.9 16.4 - - + -
247O VAL* 4.6 0.9 - - + -
300P MET* 3.3 6.6 - - - +
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Residues in contact with ASP 229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O GLY 3.4 1.8 + - - -
173O LEU* 3.2 16.0 - - + +
174O MET* 2.9 24.1 + - - +
211O THR 5.1 1.2 - - - +
214O ALA* 3.5 11.7 - - - -
215O LYS* 3.3 45.0 + - + +
228O LEU* 1.3 77.0 - - - +
230O GLY* 1.3 81.2 + - - +
298P ARG* 4.4 17.8 + - - +
299P VAL 5.7 1.0 - - - +
300P MET* 3.2 20.5 - - + +
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Residues in contact with GLY 230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O LEU* 4.6 3.1 - - - -
174O MET* 3.1 23.3 - - - -
210O SER* 5.5 0.5 - - - -
211O THR 3.9 14.6 + - - +
214O ALA* 3.9 2.0 - - - +
229O ASP* 1.3 94.9 + - - +
231O GLY* 1.3 57.2 + - - -
298P ARG* 4.7 14.9 + - - -
309P LYS* 4.5 4.3 - - - -
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Residues in contact with GLY 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O MET* 3.1 9.5 + - - +
175O THR* 3.3 8.9 - - - -
176O THR* 2.9 25.6 + - - +
209O ASN 3.8 7.9 - - - -
210O SER* 4.9 1.6 - - - -
211O THR* 3.9 12.8 - - - -
230O GLY* 1.3 73.5 - - - -
232O ALA* 1.3 60.7 + - - -
298P ARG* 5.6 4.7 - - - -
309P LYS* 4.6 2.8 - - - +
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Residues in contact with ALA 232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O THR* 4.8 0.4 - - - -
176O THR* 3.3 26.2 - - + +
178O HIS* 4.8 6.7 - - + -
208O PRO* 3.3 4.5 - - - +
209O ASN* 2.8 45.7 + - + +
210O SER 4.8 1.6 - - - +
211O THR* 4.3 9.9 - - + -
231O GLY* 1.3 75.6 - - - -
233O GLN* 1.3 71.6 + - - +
234O ARG* 4.1 7.2 - - - +
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Residues in contact with GLN 233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O THR* 4.1 7.9 - - + -
176O THR 2.9 8.0 + - - +
177O ILE* 3.5 6.2 - - - -
178O HIS* 2.9 24.2 + - - -
206O ILE* 3.7 15.3 - - + +
207O ILE 3.4 2.3 - - - -
208O PRO* 3.2 28.2 - - - +
232O ALA* 1.3 81.9 + - - +
234O ARG* 1.3 64.4 + - - +
235O VAL* 3.6 6.8 + - + +
177P ILE* 4.0 20.4 - - + -
242P LEU* 3.3 22.3 - - - +
244P GLU* 2.9 27.3 + - - +
296P GLN* 3.4 13.9 + - - -
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Residues in contact with ARG 234 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O HIS* 3.2 32.3 + - - +
179O ALA 3.4 15.0 - - - -
180O TYR* 4.7 2.2 - - - -
181O THR* 3.1 27.1 + - - +
183O ASP* 5.4 0.6 - - - +
184O GLN* 2.6 58.2 + - - +
198O ARG* 4.8 10.6 - - + +
202O ALA 5.7 0.4 - - - -
205O ASN 3.4 4.4 - - - +
207O ILE* 2.7 43.4 + - + +
209O ASN* 4.5 20.9 + - + +
232O ALA* 5.0 7.3 - - + +
233O GLN* 1.3 71.8 - - - +
235O VAL* 1.3 59.9 + - - +
338O CL 3.9 14.3 - - - +
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Residues in contact with VAL 235 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O ILE* 3.8 27.8 - - + -
178O HIS 2.9 13.9 + - - +
179O ALA* 3.9 0.2 - - - -
180O TYR* 3.5 12.4 + - - -
202O ALA 4.6 2.2 - - - -
205O ASN 3.9 0.9 - - - -
206O ILE* 4.2 9.6 - - + -
233O GLN* 3.9 11.4 - - + +
234O ARG* 1.3 78.7 - - - +
236O PRO* 1.4 71.4 - - + +
237O VAL* 2.8 22.4 + - + +
177P ILE* 4.0 19.7 - - + -
206P ILE* 3.9 21.3 - - + -
235P VAL* 4.0 15.0 - - + -
236P PRO* 4.8 0.9 - - + -
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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