Contacts of the helix formed by residues 150 - 168 (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 SER 150 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0R NAD 4.7 5.6 - - - -
122R PRO* 3.7 23.1 - - - +
149R ALA* 1.3 77.1 - - - +
151R GLY* 1.3 65.7 + - - +
152R THR* 3.4 8.8 + - - -
153R THR* 2.7 30.1 + - - -
154R ASN* 2.7 26.3 + - - -
211R THR* 4.9 3.3 + - - -
213R ALA* 4.1 5.5 + - - +
320R TYR* 3.4 8.3 - - - -
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Residues in contact with GLY 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0R NAD 3.8 12.8 - - - -
150R SER* 1.3 74.9 - - - +
152R THR* 1.3 63.2 + - - +
154R ASN* 3.2 6.5 + - - +
155R SER 2.9 17.2 + - - -
178R HIS* 5.9 1.1 - - - -
289R GLY 4.9 0.2 - - - +
314R TYR* 3.5 23.7 - - - +
316R ASN* 4.7 4.0 - - - -
320R TYR* 3.5 25.2 - - - -
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Residues in contact with THR 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150R SER* 3.2 5.0 + - - -
151R GLY* 1.3 76.4 - - - +
153R THR* 1.3 63.0 + - - +
155R SER* 2.7 22.4 + - - -
156R LEU* 3.0 7.8 + - - +
174R MET* 4.0 15.7 - - + -
176R THR* 3.9 19.1 - - + +
178R HIS* 3.7 14.1 + - - -
211R THR* 4.4 7.9 + - - +
213R ALA* 3.5 23.6 - - + -
243R THR* 4.1 7.9 - - + +
314R TYR* 2.7 26.8 + - - +
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Residues in contact with THR 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R PRO* 5.1 2.9 - - - +
129R THR* 5.5 1.1 - - + -
131R VAL* 3.8 17.5 - - + -
149R ALA* 3.7 18.7 - - + +
150R SER* 2.7 25.2 + - - -
151R GLY 3.3 0.2 - - - -
152R THR* 1.3 76.9 - - - +
154R ASN* 1.3 55.9 + - - +
156R LEU* 3.8 3.0 - - - +
157R ALA* 2.9 31.7 + - - +
213R ALA* 3.6 21.8 - - - +
216R ALA 5.6 1.6 - - - +
217R ILE* 4.0 17.5 - - + -
220R VAL* 4.0 14.4 - - + -
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Residues in contact with ASN 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R ILE 4.7 0.3 - - - +
131R VAL* 3.4 21.4 - - - +
148R GLY 3.3 22.1 + - - +
149R ALA* 3.8 6.5 - - - +
150R SER 2.7 21.8 + - - +
151R GLY* 3.2 9.2 + - - +
153R THR* 1.3 77.8 - - - +
155R SER* 1.3 60.8 + - - +
158R PRO* 3.3 17.7 - - - +
289R GLY* 3.6 9.9 - - - +
290R SER* 3.6 7.8 - - - -
320R TYR* 3.5 12.2 - - + -
323R GLN* 3.1 47.0 + - + +
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Residues in contact with SER 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151R GLY 2.9 7.4 + - - -
152R THR 2.7 18.3 + - - -
154R ASN* 1.3 78.2 - - - +
156R LEU* 1.3 59.0 + - - +
158R PRO* 4.1 0.3 - - - +
159R VAL* 3.8 9.7 - - - +
243R THR* 2.7 27.0 + - - +
289R GLY 3.7 2.2 + - - -
290R SER* 2.6 31.1 + - - -
312R ALA* 3.9 5.8 - - - +
314R TYR* 3.3 37.7 - - - -
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Residues in contact with LEU 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R THR 3.0 13.8 + - - +
153R THR* 3.2 2.0 + - - +
155R SER* 1.3 80.9 - - - +
157R ALA* 1.3 56.8 + - - +
158R PRO 3.3 2.0 - - - -
159R VAL* 3.0 9.3 + - + +
160R ALA* 2.8 38.6 + - + +
174R MET* 4.2 12.1 - - - -
213R ALA* 4.2 5.6 - - + +
214R ALA* 4.0 26.0 - - + +
217R ILE* 3.6 25.6 - - + -
228R LEU* 4.3 5.4 - - + -
243R THR* 4.5 18.2 - - + -
245R LEU* 3.6 40.2 - - + -
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Residues in contact with ALA 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R VAL* 3.9 11.9 - - + -
134R THR* 3.8 22.0 - - + +
153R THR 2.9 16.9 + - - +
156R LEU* 1.3 76.4 - - - +
158R PRO* 1.3 69.7 - - + +
159R VAL 3.1 0.2 + - - -
160R ALA* 3.2 1.3 + - - -
161R LYS* 2.8 21.7 + - - +
217R ILE* 4.1 10.3 - - + -
220R VAL* 4.0 13.9 - - + -
221R ILE* 3.5 14.7 - - + +
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Residues in contact with PRO 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R VAL* 4.6 2.7 - - + -
133R ASN 6.0 0.4 - - - +
134R THR* 3.9 14.6 - - - +
154R ASN 3.3 22.2 - - - +
156R LEU 3.6 1.6 - - - -
157R ALA* 1.3 94.5 - - + +
159R VAL* 1.3 61.4 + - - +
161R LYS* 3.5 5.9 + - + +
162R VAL* 3.3 28.1 + - - +
270R SER* 5.4 2.9 - - - +
271R PHE* 3.7 43.0 - - + -
290R SER* 3.8 9.9 - - - +
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Residues in contact with VAL 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R SER 3.8 15.9 - - - +
156R LEU* 3.0 9.5 + - + +
158R PRO* 1.3 74.1 - - - +
160R ALA* 1.3 66.5 + - - +
161R LYS 3.2 0.3 + - - -
162R VAL 3.3 1.9 + - - -
163R LEU* 3.0 29.2 + - + +
245R LEU* 4.2 6.7 - - + -
263R MET* 3.6 17.7 - - + +
271R PHE* 3.7 26.5 - - + -
292R PHE* 4.1 6.3 - - + -
310R VAL* 3.5 31.4 - - + -
311R ALA 6.2 0.2 - - - -
312R ALA* 3.9 16.2 - - + +
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Residues in contact with ALA 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R LEU* 2.8 26.1 + - + +
157R ALA* 3.8 4.0 - - - +
159R VAL* 1.3 75.6 - - - +
161R LYS* 1.3 61.2 + - - +
163R LEU* 3.5 10.8 + - - +
164R ASN* 3.0 24.3 + - - +
169R LEU* 5.2 3.6 - - + +
217R ILE* 4.8 0.9 - - + -
221R ILE* 4.3 5.2 - - + -
224R ILE* 3.9 24.4 - - + +
228R LEU* 4.0 18.6 - - + -
245R LEU* 4.7 2.0 - - + -
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Residues in contact with LYS 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R THR* 4.5 26.9 + - + +
157R ALA 2.8 18.9 + - - +
158R PRO* 3.9 7.4 - - + +
159R VAL 3.2 0.4 - - - -
160R ALA* 1.3 69.8 - - - +
162R VAL* 1.3 58.8 + - + +
164R ASN* 3.2 4.6 + - - +
165R ASP* 2.7 59.5 + - - +
221R ILE* 3.9 18.0 - - + +
223R GLU* 3.4 23.7 + - - +
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Residues in contact with VAL 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R PRO 3.3 12.5 + - - +
159R VAL 3.3 7.0 + - - +
161R LYS* 1.3 78.7 - - + +
163R LEU* 1.3 67.4 + - - +
165R ASP* 4.6 5.4 - - - +
166R ASP* 2.9 29.7 + - + +
167R PHE* 5.0 2.0 - - + -
262R ALA* 3.7 35.7 - - + +
263R MET* 3.7 23.8 - - + -
266R ALA* 3.4 33.2 - - + -
271R PHE* 4.5 0.9 - - + -
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Residues in contact with LEU 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R VAL* 3.0 28.2 + - + +
160R ALA* 3.8 4.7 - - - +
162R VAL* 1.3 75.6 - - - +
164R ASN* 1.3 57.3 + - - +
167R PHE* 2.9 47.7 + - + +
168R GLY 3.4 4.5 + - - -
169R LEU* 4.3 8.9 + - + -
245R LEU* 3.7 30.5 - - + -
247R VAL* 4.2 18.8 - - + -
249R LEU* 4.3 22.3 - - + +
259R VAL* 4.6 13.0 - - + -
263R MET* 3.8 14.6 - - + -
308R VAL* 4.8 5.8 - - + -
310R VAL* 4.2 8.5 - - + -
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Residues in contact with ASN 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160R ALA 3.0 18.0 + - - +
161R LYS* 3.8 3.6 - - - +
163R LEU* 1.3 74.5 - - - +
165R ASP* 1.3 70.7 + - - +
168R GLY* 2.9 21.8 + - - -
169R LEU* 3.0 31.6 + - + +
221R ILE* 5.3 1.1 - - + +
223R GLU* 3.4 27.5 + - - +
224R ILE* 3.4 32.2 - - + +
227R LYS* 4.7 3.8 + - - -
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Residues in contact with ASP 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161R LYS* 2.7 59.3 + - - +
162R VAL* 4.0 2.9 - - - +
164R ASN* 1.3 78.6 + - - +
166R ASP* 1.3 70.9 + - - +
168R GLY 4.9 0.2 + - - -
223R GLU* 4.5 6.6 - - - +
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Residues in contact with ASP 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R VAL* 2.9 19.4 + - - +
165R ASP* 1.3 88.7 - - - +
167R PHE* 1.3 82.0 + - + +
251R LYS* 2.8 25.7 + - - -
262R ALA* 3.3 24.7 - - + +
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Residues in contact with PHE 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R VAL* 4.7 3.6 - - + -
163R LEU* 2.9 31.6 + - + +
166R ASP* 1.3 101.2 - - + +
168R GLY* 1.3 67.4 + - - +
249R LEU* 3.6 23.3 - - + -
250R GLU* 3.3 2.1 + - - +
251R LYS* 3.0 46.4 + - + +
254R VAL* 3.9 28.3 - - + -
258R GLN* 3.7 39.7 - - + -
259R VAL* 4.1 14.1 - - + -
262R ALA* 4.2 11.7 - - + -
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Residues in contact with GLY 168 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163R LEU 3.4 0.8 + - - -
164R ASN* 2.9 19.5 + - - -
165R ASP 4.9 0.2 + - - -
166R ASP 3.9 0.2 - - - -
167R PHE* 1.3 75.2 - - - +
169R LEU* 1.3 62.7 + - - +
249R LEU* 3.2 7.8 - - - -
250R GLU* 2.8 46.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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