Contacts of the helix formed by residues 152 - 168 (chain M) in PDB entry 2QJK
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 GLY 152 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M PHE* 4.5 2.5 - - - -
150M PRO 3.4 3.2 - - - -
151M TRP* 1.3 77.2 - - - +
153M GLN* 1.3 67.2 + - - -
155M SER* 3.1 7.4 + - - -
156M PHE 2.9 17.5 + - - -
279M ASN* 3.0 20.0 - - - -
281M ILE 3.1 15.5 - - - -
282M GLU* 4.2 1.1 - - - -
283M ALA* 3.4 11.6 - - - +
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Residues in contact with GLN 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152M GLY* 1.3 71.8 - - - +
154M MET* 1.3 69.4 + - + +
155M SER 2.9 1.4 + - - -
156M PHE* 3.0 9.9 + - - +
157M TRP* 3.2 30.0 + - - -
278M ASP* 3.2 11.8 + - + +
279M ASN* 3.2 2.0 + - - -
281M ILE* 2.9 40.6 + - + +
282M GLU 3.8 2.0 - - - +
283M ALA* 3.6 0.7 - - - +
284M ASN* 2.9 37.9 + - - +
287M ARG* 3.3 28.5 + - - +
289M PRO* 3.3 30.8 - - + +
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Residues in contact with MET 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M TYR* 3.4 33.8 - - + +
153M GLN* 1.3 76.9 - - - +
155M SER* 1.3 58.1 + - - +
157M TRP* 5.2 1.1 - - - -
158M GLY* 2.9 30.0 + - - +
276M HIS* 3.6 43.5 - - + +
278M ASP* 3.6 21.7 + - + +
279M ASN* 3.0 11.1 + - - +
289M PRO* 3.7 26.7 - - + -
292M ILE* 3.9 25.4 - - + -
293M VAL 4.0 4.3 - - - +
503M SMA 3.9 15.3 - - - +
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Residues in contact with SER 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M TYR* 2.7 26.4 + - - -
148M VAL* 3.3 29.4 + - - +
150M PRO* 4.2 0.9 - - - +
151M TRP* 3.7 4.4 + - - -
152M GLY 3.2 22.8 + - - -
153M GLN 2.9 1.4 + - - -
154M MET* 1.3 76.9 - - - +
156M PHE* 1.3 63.9 + - - +
158M GLY* 4.1 0.2 - - - -
159M ALA* 3.1 21.0 + - - +
279M ASN* 2.9 20.5 + - - +
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Residues in contact with PHE 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M TRP* 3.9 23.3 - + + -
152M GLY 2.9 11.8 + - - +
153M GLN 3.0 5.4 + - - +
155M SER* 1.3 73.7 - - - +
157M TRP* 1.3 106.6 + + + +
159M ALA* 2.8 17.3 + - - +
160M THR* 2.9 15.7 + - - -
185M ALA* 6.2 0.2 - - + -
186M VAL* 3.1 50.5 - - + -
283M ALA* 3.8 15.0 - - + +
284M ASN 3.9 7.6 - - - -
285M PRO* 3.2 42.4 - - + -
69R GLY 5.0 4.9 - - - -
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Residues in contact with TRP 157 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153M GLN* 3.2 21.9 + - - +
154M MET 4.6 0.2 - - - +
156M PHE* 1.3 91.2 - + - +
158M GLY* 1.3 66.9 + - - +
160M THR* 2.8 35.2 + - + -
161M VAL* 2.9 17.1 + - - +
284M ASN 3.3 22.5 + - - -
285M PRO 3.6 17.3 - - - -
287M ARG 2.6 33.0 + - - -
288M THR* 3.3 23.3 - - + -
289M PRO* 3.4 22.0 - - + -
292M ILE* 3.7 20.9 - - + -
71R PRO* 4.9 5.4 - - + -
133R GLY 4.1 6.7 - - - -
134R CYS* 3.9 21.5 - - - -
135R SER* 4.1 10.5 - - - -
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Residues in contact with GLY 158 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M PHE* 4.4 2.2 - - - -
147M TYR* 6.2 0.7 - - - -
154M MET 2.9 24.6 + - - -
155M SER 4.1 0.2 - - - -
157M TRP* 1.3 73.7 - - - +
159M ALA* 1.3 55.6 + - - +
161M VAL* 3.3 1.2 + - - +
162M ILE* 2.8 39.4 + - - +
292M ILE* 4.8 0.2 - - - +
503M SMA 3.5 30.6 + - - -
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Residues in contact with ALA 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M PHE* 3.8 16.0 - - + -
148M VAL* 4.0 22.7 - - + -
155M SER 3.1 13.8 + - - +
156M PHE* 2.8 10.4 + - - +
158M GLY* 1.3 71.9 - - - +
160M THR* 1.3 58.7 + - - +
162M ILE* 3.8 0.3 - - - +
163M THR* 2.8 39.5 + - + +
186M VAL* 4.1 16.8 - - + -
190M THR* 5.8 1.3 - - + -
194M PHE* 4.5 7.0 - - + -
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Residues in contact with THR 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M PHE* 2.9 18.4 + - - -
157M TRP* 2.8 37.9 + - + -
159M ALA* 1.3 76.6 - - - +
161M VAL* 1.3 57.5 + - + +
163M THR* 2.7 19.1 + - - -
164M GLY* 3.1 9.0 + - - -
177M GLN* 4.2 2.3 + - - -
186M VAL* 3.6 20.7 - - + +
132R LEU 3.6 5.6 - - - +
133R GLY* 4.1 25.1 - - - +
134R CYS 4.7 0.2 - - - +
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Residues in contact with VAL 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157M TRP 2.9 12.4 + - - +
158M GLY 3.5 7.4 - - - +
160M THR* 1.3 75.8 - - - +
162M ILE* 1.3 62.7 + - - +
164M GLY* 2.8 16.5 + - - -
165M LEU* 3.0 14.1 + - + +
292M ILE* 5.6 0.2 - - + -
503M SMA 3.2 51.1 - - + +
132R LEU* 4.0 35.7 - - + +
134R CYS* 3.7 29.6 - - - +
151R CYS* 4.4 0.2 - - - -
152R HIS* 4.3 3.6 - - + -
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Residues in contact with ILE 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M PHE* 3.6 44.4 - - + -
158M GLY 2.8 31.6 + - - +
161M VAL* 1.3 73.2 - - + +
163M THR* 1.3 66.0 + - - +
165M LEU* 3.4 16.8 + - + +
166M PHE* 3.3 17.4 - - + -
298M PHE* 6.0 0.2 - - + -
503M SMA 3.5 92.7 - - + +
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Residues in contact with THR 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M PHE* 5.3 1.3 - - + -
159M ALA 2.8 17.3 + - - +
160M THR* 2.7 26.5 + - - -
162M ILE* 1.3 76.8 - - + +
164M GLY* 1.3 61.7 + - - +
166M PHE* 3.1 20.0 + - - +
177M GLN* 3.2 26.3 + - - +
180M LEU* 4.4 20.5 - - + +
181M LEU* 3.5 33.6 - - + +
186M VAL* 4.8 0.7 - - + -
190M THR* 4.8 1.3 - - + -
194M PHE* 4.4 20.4 - - + -
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Residues in contact with GLY 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160M THR 3.1 11.0 + - - -
161M VAL 2.8 10.8 + - - -
163M THR* 1.3 73.6 - - - +
165M LEU* 1.3 56.6 + - - -
166M PHE 2.9 2.0 - - - -
167M GLY* 2.5 28.8 + - - -
168M ALA 3.2 3.6 + - - -
177M GLN* 2.9 16.8 - - - +
329M LYS* 5.3 1.2 - - - -
132R LEU* 3.8 21.7 - - - +
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Residues in contact with LEU 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161M VAL* 3.0 10.5 + - + +
162M ILE* 3.6 24.0 - - + +
164M GLY* 1.3 72.8 - - - +
166M PHE* 1.3 68.9 + - + +
168M ALA* 3.1 18.9 - - - +
169M ILE* 4.0 4.2 + - - +
305M LEU* 4.0 20.2 - - + -
333M VAL* 4.1 17.2 - - + +
336M MET* 3.8 25.1 - - + -
337M PHE* 4.6 15.0 - - + -
503M SMA 4.5 23.6 - - + +
132R LEU* 3.8 30.7 - - + -
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Residues in contact with PHE 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M ILE* 3.3 21.5 - - + -
163M THR 3.5 8.1 - - - +
164M GLY 2.7 2.4 + - - -
165M LEU* 1.3 77.7 - - + +
167M GLY* 1.3 62.0 + - - +
168M ALA 2.9 5.2 - - - -
169M ILE* 2.9 33.5 + - + +
173M GLY* 3.3 13.4 - - - +
176M ILE* 3.7 29.3 - - + +
177M GLN* 4.8 4.5 - - - +
180M LEU* 4.1 18.2 - - + -
337M PHE* 4.6 14.6 - + - -
503M SMA 4.0 43.3 - - + -
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Residues in contact with GLY 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163M THR 3.6 2.8 + - - -
164M GLY 2.5 18.3 + - - -
166M PHE* 1.3 73.8 - - - +
168M ALA* 1.3 59.3 + - - -
169M ILE 3.4 7.3 + - - +
173M GLY* 3.5 17.4 + - - -
174M HIS* 4.6 3.2 + - - -
177M GLN* 4.1 16.5 - - - +
329M LYS* 4.9 9.2 + - - -
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Residues in contact with ALA 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M GLY 3.2 4.2 + - - +
165M LEU* 3.1 17.9 + - - +
166M PHE 2.9 0.4 - - - -
167M GLY* 1.3 75.7 - - - +
169M ILE* 1.3 67.7 + - - +
170M PRO* 3.2 5.7 - - - +
329M LYS* 4.5 19.9 - - + +
330M PHE* 3.4 28.0 - - + +
333M VAL* 3.5 24.7 - - + -
132R LEU* 5.4 0.7 - - + -
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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
------------------------------------------------------------
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