Contacts of the helix formed by residues 150 - 168 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P PRO* 3.7 14.1 - - - +
149P ALA* 1.3 78.3 - - - +
151P GLY* 1.3 66.1 + - - +
152P THR* 3.5 7.3 + - - -
153P THR* 2.6 31.2 + - - -
154P ASN* 2.9 25.8 + - - -
211P THR* 5.0 2.5 + - - -
213P ALA* 4.1 5.0 + - - +
320P TYR* 3.5 6.3 - - - -
337P GOL 3.4 28.9 - - - -
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Residues in contact with GLY 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150P SER* 1.3 69.6 - - - +
152P THR* 1.3 64.4 + - - +
154P ASN* 3.0 6.1 + - - +
155P SER 2.8 19.1 + - - -
289P GLY 5.0 0.2 - - - +
314P TYR* 3.4 18.7 - - - -
316P ASN 4.7 1.3 - - - -
320P TYR* 3.4 26.4 - - - -
337P GOL 2.9 22.3 - - - -
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Residues in contact with THR 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150P SER* 3.3 4.2 + - - -
151P GLY* 1.3 75.9 - - - +
153P THR* 1.3 62.0 + - - +
155P SER* 2.7 20.0 + - - +
156P LEU* 3.0 8.1 + - - +
174P MET* 3.9 13.5 - - + -
176P THR* 3.9 18.8 - - + +
178P HIS* 3.8 6.8 - - - -
211P THR* 4.4 7.3 + - - +
213P ALA* 3.5 24.9 - - + -
243P THR* 3.9 9.6 - - - +
314P TYR* 2.7 27.9 + - - +
337P GOL 3.0 14.1 + - - -
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Residues in contact with THR 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P PRO* 5.1 2.9 - - - +
129P THR* 5.5 1.3 - - + -
131P VAL* 3.9 17.3 - - + -
149P ALA* 3.8 11.8 - - + +
150P SER* 2.6 31.5 + - - -
152P THR* 1.3 74.3 - - - +
154P ASN* 1.3 57.6 + - - +
156P LEU* 3.1 4.2 + - - +
157P ALA* 2.9 31.2 + - - +
213P ALA* 3.7 21.1 - - - +
216P ALA 5.7 1.6 - - - +
217P ILE* 3.8 24.2 - - + -
220P VAL* 3.9 11.0 - - + -
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Residues in contact with ASN 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ILE 4.7 0.2 - - - +
131P VAL* 3.3 22.2 - - - +
148P GLY 3.2 23.7 + - - +
149P ALA* 3.9 6.5 - - - +
150P SER 2.9 23.6 + - - +
151P GLY* 3.0 10.8 + - - +
153P THR* 1.3 75.2 - - - +
155P SER* 1.3 61.4 + - - +
158P PRO* 3.3 17.0 - - - +
289P GLY* 3.7 10.3 - - - +
290P SER* 3.6 7.8 - - - -
320P TYR* 3.6 11.3 - - + -
323P GLN* 3.0 47.5 + - + +
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Residues in contact with SER 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P GLY 2.8 6.6 + - - -
152P THR 2.7 15.2 + - - -
154P ASN* 1.3 78.2 - - - +
156P LEU* 1.3 58.3 + - - +
158P PRO* 4.0 1.1 - - - +
159P VAL* 3.7 9.7 - - - +
243P THR* 2.7 29.5 + - - +
289P GLY 3.8 2.4 + - - -
290P SER* 2.7 29.7 + - - -
312P ALA* 4.1 6.7 - - - +
313P TRP 4.9 0.2 - - - -
314P TYR* 3.2 38.9 - - - -
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Residues in contact with LEU 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152P THR 3.0 14.1 + - - +
153P THR 3.1 2.9 + - - +
155P SER* 1.3 81.0 - - - +
157P ALA* 1.3 61.9 + - - +
158P PRO 3.3 1.3 - - - -
159P VAL* 3.1 7.4 + - + +
160P ALA* 2.8 33.6 + - + +
174P MET* 4.1 12.8 - - - -
213P ALA* 3.8 24.7 - - + +
214P ALA* 3.9 17.0 - - + -
217P ILE* 4.1 15.7 - - + -
228P LEU* 4.4 4.9 - - + -
243P THR* 4.5 16.8 - - + -
245P LEU* 3.7 37.9 - - + -
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Residues in contact with ALA 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P VAL* 3.9 18.2 - - + -
134P THR* 3.9 15.3 - - + +
153P THR 2.9 16.8 + - - +
156P LEU* 1.3 77.7 - - - +
158P PRO* 1.3 65.5 - - + +
160P ALA* 4.7 0.2 - - - -
161P LYS* 2.9 27.2 + - - +
217P ILE* 4.2 10.3 - - + -
220P VAL* 4.0 13.2 - - + -
221P ILE* 3.4 14.2 - - + +
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Residues in contact with PRO 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P VAL* 4.6 2.7 - - + -
133P ASN 6.0 0.2 - - - +
134P THR* 3.9 15.9 - - - +
154P ASN 3.3 15.3 - - - +
155P SER 4.1 0.4 - - - +
156P LEU 3.6 1.1 - - - -
157P ALA* 1.3 95.2 - - + +
159P VAL* 1.3 60.5 + - - +
161P LYS* 3.8 5.9 - - + +
162P VAL* 3.2 27.7 + - - +
270P SER* 5.4 2.0 - - - +
271P PHE* 3.7 33.3 - - + -
290P SER* 3.7 27.6 - - - +
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Residues in contact with VAL 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155P SER 3.7 15.9 - - - +
156P LEU* 3.1 10.0 + - + +
158P PRO* 1.3 75.0 - - - +
160P ALA* 1.3 64.9 + - - +
162P VAL 3.3 1.9 + - - -
163P LEU* 3.1 24.5 + - + +
245P LEU* 4.1 13.2 - - + -
263P MET* 3.4 17.8 - - + +
271P PHE* 3.7 25.1 - - + -
292P PHE* 4.0 6.3 - - + -
310P VAL* 3.6 31.2 - - + -
312P ALA* 3.9 17.0 - - + +
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Residues in contact with ALA 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156P LEU* 2.8 23.0 + - + +
157P ALA* 3.9 3.1 - - - +
159P VAL* 1.3 79.1 - - - +
161P LYS* 1.3 56.6 + - - +
163P LEU* 3.4 12.5 + - - +
164P ASN* 2.9 30.4 + - - +
169P LEU* 5.1 3.8 - - + +
217P ILE* 4.9 0.9 - - + -
221P ILE* 4.3 4.9 - - + -
224P ILE* 3.9 24.3 - - + +
228P LEU* 4.0 19.1 - - + -
245P LEU* 4.6 1.8 - - + -
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Residues in contact with LYS 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P ASN 6.0 0.4 - - - +
134P THR* 4.6 25.4 + - + +
157P ALA 2.9 17.8 + - - +
158P PRO* 3.8 7.4 - - + +
160P ALA* 1.3 75.3 - - - +
162P VAL* 1.3 55.6 + - + +
164P ASN* 3.1 5.2 + - + +
165P ASP* 2.8 55.9 + - - +
221P ILE* 3.8 22.8 - - + +
223P GLU* 3.5 21.8 + - - +
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Residues in contact with VAL 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158P PRO 3.2 14.0 + - - +
159P VAL 3.3 0.2 + - - -
161P LYS* 1.3 76.2 - - + +
163P LEU* 1.3 59.3 + - - +
165P ASP* 4.8 4.3 - - - -
166P ASP* 2.9 37.8 + - + +
167P PHE* 4.9 1.6 - - + -
262P ALA* 3.7 32.3 - - + +
263P MET* 3.6 31.4 - - + -
266P ALA* 3.4 33.2 - - + -
271P PHE* 4.6 0.7 - - + -
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Residues in contact with LEU 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P VAL* 3.1 21.6 + - + +
160P ALA* 3.5 8.3 - - - +
162P VAL* 1.3 76.6 - - - +
164P ASN* 1.3 56.7 + - - +
167P PHE* 3.0 45.4 + - + +
168P GLY* 3.3 6.9 + - - -
169P LEU* 4.8 7.9 - - + -
245P LEU* 3.7 30.3 - - + -
247P VAL* 4.0 22.0 - - + -
249P LEU* 4.3 22.0 - - + +
259P VAL* 4.8 11.2 - - + -
263P MET* 3.7 15.3 - - + -
308P VAL* 4.8 4.7 - - + -
310P VAL* 4.4 8.1 - - + -
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Residues in contact with ASN 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P ALA 2.9 17.7 + - - +
161P LYS* 3.8 3.8 - - - +
163P LEU* 1.3 75.6 - - - +
165P ASP* 1.3 74.3 + - - +
168P GLY* 3.0 19.9 + - - -
169P LEU* 3.0 33.6 + - + +
221P ILE* 5.5 1.3 - - + +
223P GLU* 3.5 31.5 + - - +
224P ILE* 3.4 22.8 - - + +
227P LYS* 4.7 4.2 + - - -
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Residues in contact with ASP 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P LYS* 2.8 51.5 + - - +
162P VAL* 4.1 3.0 - - - +
164P ASN* 1.3 82.9 + - - +
166P ASP* 1.3 70.4 + - - +
168P GLY 5.0 0.3 + - - -
223P GLU* 4.3 10.4 - - - +
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Residues in contact with ASP 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P VAL* 2.9 21.4 + - - +
165P ASP* 1.3 87.8 - - - +
167P PHE* 1.4 81.8 + - + +
251P LYS* 3.4 24.3 + - - +
262P ALA* 3.3 24.6 - - + +
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Residues in contact with PHE 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P VAL* 4.6 3.1 - - + -
163P LEU* 3.0 32.6 + - + +
166P ASP* 1.4 101.9 - - + +
168P GLY* 1.3 62.8 + - - +
249P LEU* 3.7 21.3 - - + -
250P GLU* 3.2 1.6 + - - +
251P LYS* 2.9 53.0 + - + +
254P VAL* 4.0 26.2 - - + -
258P GLN* 3.7 40.8 - - + -
259P VAL* 4.0 13.2 - - + -
262P ALA* 4.1 12.1 - - + -
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Residues in contact with GLY 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P LEU 3.3 2.9 + - - -
164P ASN* 3.0 18.8 + - - -
165P ASP 5.0 0.2 + - - -
166P ASP 4.0 0.2 - - - -
167P PHE* 1.3 75.2 - - - +
169P LEU* 1.3 63.9 + - - -
249P LEU* 3.2 7.0 - - - -
250P GLU* 2.7 48.3 + - - -
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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) + - + + + + + -
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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