Contacts of the strand formed by residues 169 - 179 (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 169 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160O ALA* 5.1 4.9 - - + +
163O LEU* 5.1 5.4 - - + -
164O ASN* 2.9 32.1 + - + +
168O GLY* 1.3 70.4 - - - +
170O VAL* 1.3 62.7 + - - +
171O GLU* 3.8 27.6 - - - +
224O ILE* 4.0 33.9 - - + -
227O LYS* 3.2 32.1 + - + -
228O LEU* 4.0 21.3 - - + -
245O LEU* 6.1 0.2 - - + -
247O VAL* 3.8 26.0 - - + -
248O VAL 4.0 2.7 - - - +
249O LEU* 4.2 7.6 - - + -
250O GLU* 4.6 4.2 + - - +
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Residues in contact with VAL 170 (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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169O LEU* 1.3 77.0 - - - +
171O GLU* 1.3 68.2 + - + +
227O LYS* 3.6 18.9 - - - +
248O VAL* 2.8 27.6 + - + +
249O LEU 3.6 21.3 - - - +
250O GLU* 3.7 17.7 - - + +
302P VAL* 3.9 15.5 - - + +
305P ARG* 3.8 47.3 - - + +
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Residues in contact with GLU 171 (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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169O LEU* 3.7 9.0 - - - +
170O VAL* 1.3 84.4 - - + +
172O GLY* 1.3 55.5 + - - +
227O LYS 3.3 13.7 - - - +
247O VAL* 3.4 2.9 - - - +
248O VAL* 2.7 44.9 + - + +
300P MET* 3.5 13.0 - - + +
302P VAL* 3.3 18.7 + - + +
305P ARG* 2.5 49.3 + - - +
306P GLN 3.3 10.9 + - - +
307P LEU* 3.8 21.8 + - + +
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Residues in contact with GLY 172 (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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171O GLU* 1.3 75.9 - - - +
173O LEU* 1.3 68.9 + - - +
227O LYS 2.9 8.6 + - - +
228O LEU* 3.4 36.5 - - - +
229O ASP 3.4 3.6 + - - -
246O THR 3.1 13.2 - - - -
247O VAL* 3.9 3.8 - - - -
300P MET* 4.0 3.3 - - - +
307P LEU* 3.8 5.6 - - - -
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Residues in contact with LEU 173 (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* 1.3 78.8 - - - +
174O MET* 1.3 60.1 + - - +
229O ASP* 3.2 29.8 - - + +
230O GLY* 4.3 3.1 - - - +
244O GLU 4.1 0.3 - - - +
245O LEU* 3.5 3.2 - - - -
246O THR* 2.8 35.1 + - - +
246P THR* 4.2 15.9 - - + -
298P ARG* 4.6 12.8 - - + +
299P VAL 5.6 0.2 - - - -
300P MET* 3.8 19.7 - - + +
307P LEU* 3.9 32.7 - - + +
309P LYS* 3.7 40.8 - - + +
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Residues in contact with MET 174 (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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152O THR* 3.9 21.5 - - + -
156O LEU* 4.0 15.0 - - - -
173O LEU* 1.3 74.2 - - - +
175O THR* 1.3 64.1 + - - +
176O THR* 4.5 1.1 - - + -
211O THR* 3.5 32.5 - - + -
213O ALA* 4.1 3.1 - - + -
214O ALA* 3.9 30.3 - - + +
229O ASP 2.9 12.0 + - - +
230O GLY* 3.1 16.8 - - - +
231O GLY 3.1 18.1 + - - +
243O THR* 3.9 15.5 - - + -
244O GLU 3.2 11.4 - - - +
245O LEU* 4.1 12.3 - - + -
309P LYS* 2.7 24.1 + - - -
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Residues in contact with THR 175 (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 4.4 0.2 + - - -
174O MET* 1.3 72.0 + - - +
176O THR* 1.3 69.9 + - - +
177O ILE* 4.0 12.4 + - + +
231O GLY 3.3 9.0 + - - +
232O ALA* 4.8 0.7 - - - -
233O GLN* 4.1 15.0 - - + +
244O GLU* 2.7 52.9 + - - +
175P THR* 6.3 0.7 - - + -
177P ILE* 5.0 2.0 - - + -
244P GLU* 2.5 38.6 + - - +
309P LYS* 2.8 21.1 + - - -
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Residues in contact with THR 176 (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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152O THR* 3.8 23.6 - - + +
174O MET* 4.3 1.3 - - + +
175O THR* 1.3 74.3 - - - +
177O ILE* 1.3 63.1 + - - +
178O HIS* 3.3 9.8 + - + -
211O THR* 4.3 6.7 - - + -
231O GLY 2.9 14.9 + - - +
232O ALA* 3.3 21.9 - - + +
233O GLN 2.9 26.0 + - - -
242O LEU 2.9 13.7 + - - -
243O THR* 3.8 10.8 - - - -
314O TYR* 2.6 25.9 + - - +
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Residues in contact with ILE 177 (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* 4.2 13.2 - - + +
176O THR* 1.3 72.1 - - - +
178O HIS* 1.3 57.4 + - - +
233O GLN* 3.5 4.5 - - + +
235O VAL* 3.8 33.0 - - + -
241O SER* 3.3 4.0 - - - -
242O LEU* 2.8 49.7 + - + +
244O GLU* 4.0 30.1 - - + +
175P THR* 5.2 0.9 - - + -
177P ILE* 4.1 23.8 - - + -
206P ILE* 3.7 18.6 - - + +
233P GLN* 4.1 17.7 - - + -
235P VAL* 4.0 12.1 - - + -
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Residues in contact with HIS 178 (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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0O NAD 4.6 2.2 + - - -
151O GLY* 5.9 0.4 - - - -
152O THR* 3.7 11.5 + - - -
176O THR* 3.8 14.1 - - + +
177O ILE* 1.3 74.4 - - - +
179O ALA* 1.3 90.6 + - - +
181O THR* 3.9 13.5 - - + -
232O ALA* 4.8 3.1 - - + -
233O GLN 2.9 8.8 + - - +
234O ARG* 3.2 28.3 + - - +
235O VAL* 2.9 29.9 + - - +
240O GLY 4.4 0.7 - - - -
241O SER* 3.3 4.5 - - - -
314O TYR* 3.2 24.7 + - - -
316O ASN* 3.7 35.5 - - + +
206P ILE* 5.0 0.2 - - - -
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Residues in contact with ALA 179 (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* 1.3 99.0 + - - +
180O TYR* 1.3 62.5 + - - +
181O THR* 3.8 0.2 - - - +
234O ARG* 3.4 4.7 - - - -
235O VAL 3.9 0.7 - - - -
237O VAL* 3.0 27.4 - - + +
239O THR* 3.3 30.1 - - - +
240O GLY 3.4 13.6 + - - +
241O SER* 3.0 9.1 + - - -
316O ASN* 3.7 7.4 - - - +
337O GOL 3.7 4.7 - - - +
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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