Contacts of the helix formed by residues 152 - 168 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G PHE* 4.6 2.2 - - - -
150G PRO 3.4 2.8 - - - -
151G TRP* 1.3 76.3 - - - +
153G GLN* 1.3 67.7 + - - -
155G SER* 3.0 7.1 + - - -
156G PHE 2.9 17.5 + - - -
279G ASN* 3.0 19.7 - - - -
281G ILE 3.2 13.7 - - - -
282G GLU* 4.2 0.7 - - - -
283G ALA* 3.4 10.5 - - - +
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Residues in contact with GLN 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G GLY* 1.3 71.6 - - - +
154G MET* 1.3 70.3 + - + +
155G SER 2.8 1.2 + - - -
156G PHE* 3.0 8.7 + - - +
157G TRP* 3.3 29.6 + - - -
278G ASP* 3.3 12.7 + - + +
279G ASN* 3.1 2.0 + - - -
281G ILE* 2.9 39.9 + - + +
282G GLU 3.7 3.4 - - - +
283G ALA* 3.6 0.7 - - - +
284G ASN* 2.9 38.4 + - - +
287G ARG* 3.4 23.0 + - - +
289G PRO* 3.3 37.1 - - + +
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Residues in contact with MET 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G TYR* 3.5 32.0 - - + +
153G GLN* 1.3 77.3 - - - +
155G SER* 1.3 57.7 + - - +
157G TRP* 5.2 1.3 - - + -
158G GLY* 2.9 30.1 + - - +
276G HIS* 3.7 42.0 - - + +
278G ASP* 3.6 22.0 - - + -
279G ASN* 3.0 12.1 + - - +
289G PRO* 3.7 26.7 - - + -
292G ILE* 3.9 29.2 - - + -
293G VAL 4.0 7.9 - - - +
503G SMA 3.9 8.0 - - - +
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Residues in contact with SER 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G TYR* 2.7 26.6 + - - -
148G VAL* 3.3 30.2 + - - +
150G PRO* 4.2 0.7 - - - +
151G TRP* 3.7 4.4 + - - -
152G GLY 3.1 23.0 + - - -
153G GLN 2.8 1.6 + - - -
154G MET* 1.3 78.3 - - - +
156G PHE* 1.3 63.6 + - - +
158G GLY 4.0 0.2 - - - -
159G ALA* 3.1 20.3 + - - +
279G ASN* 2.9 23.8 + - - +
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Residues in contact with PHE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G TRP* 3.9 25.5 - + + -
152G GLY 2.9 11.8 + - - +
153G GLN 3.0 5.6 + - - +
155G SER* 1.3 73.7 - - - +
157G TRP* 1.3 104.1 + + + +
159G ALA* 2.8 17.8 + - - +
160G THR* 2.9 17.0 + - - -
185G ALA* 6.1 0.2 - - + -
186G VAL* 3.1 50.7 - - + -
283G ALA* 3.8 14.8 - - + +
284G ASN 4.0 7.4 - - - -
285G PRO* 3.2 42.2 - - + -
69L GLY 4.8 5.2 - - - -
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Residues in contact with TRP 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G GLN* 3.3 21.1 + - - +
154G MET* 4.6 0.4 - - + +
156G PHE* 1.3 90.5 - + - +
158G GLY* 1.3 66.5 + - - +
160G THR* 2.8 33.9 + - + -
161G VAL* 2.8 16.2 + - - +
284G ASN 3.3 19.3 + - - -
285G PRO 3.6 17.3 - - - -
287G ARG 2.6 37.1 + - - -
288G THR* 3.3 23.8 - - + -
289G PRO* 3.4 22.9 - - + -
292G ILE* 3.8 20.4 - - + -
71L PRO* 5.0 4.5 - - + -
133L GLY 4.1 5.8 - - - -
134L CYS* 3.8 24.7 - - - -
135L SER* 3.9 11.9 - - - -
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Residues in contact with GLY 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PHE* 4.4 1.3 - - - -
147G TYR* 6.2 0.7 - - - -
154G MET 2.9 16.0 + - - -
155G SER 4.0 0.4 - - - -
157G TRP* 1.3 76.7 - - - +
159G ALA* 1.3 55.1 + - - +
161G VAL* 3.3 2.6 + - - +
162G ILE* 2.9 38.8 + - - +
292G ILE* 4.9 0.4 - - - +
503G SMA 3.2 35.6 + - - -
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Residues in contact with ALA 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PHE* 3.8 16.3 - - + -
148G VAL* 4.1 22.2 - - + +
155G SER 3.1 13.4 + - - +
156G PHE* 2.8 10.6 + - - +
158G GLY* 1.3 72.3 - - - +
160G THR* 1.3 58.7 + - - +
162G ILE* 4.2 0.2 - - - +
163G THR* 2.7 40.0 + - + +
186G VAL* 4.1 17.3 - - + -
190G THR* 5.8 0.7 - - + -
194G PHE* 4.5 7.2 - - + -
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Residues in contact with THR 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G PHE* 2.9 19.0 + - - -
157G TRP* 2.8 31.8 + - + -
159G ALA* 1.3 76.2 - - - +
161G VAL* 1.3 57.4 + - + +
163G THR* 2.7 19.1 + - - -
164G GLY* 3.1 9.4 + - - -
177G GLN* 4.4 2.3 + - - -
186G VAL* 3.6 20.6 - - + +
132L LEU 3.4 5.0 - - - +
133L GLY* 3.9 32.8 - - - +
134L CYS 4.5 0.2 - - - +
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Residues in contact with VAL 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G TRP 2.8 11.8 + - - +
158G GLY 3.6 7.4 - - - +
160G THR* 1.3 76.9 - - - +
162G ILE* 1.3 63.7 + - - +
164G GLY* 2.9 14.9 + - - -
165G LEU* 3.0 13.5 + - + +
292G ILE* 5.5 0.2 - - + -
503G SMA 3.3 50.3 - - + +
132L LEU* 3.8 34.6 - - + +
134L CYS* 3.7 31.2 - - - +
151L CYS* 4.4 1.3 - - - -
152L HIS* 4.2 2.7 - - + -
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Residues in contact with ILE 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PHE* 3.3 48.5 - - + -
158G GLY 2.9 23.6 + - - +
161G VAL* 1.3 73.1 - - + +
163G THR* 1.3 66.0 + - - +
165G LEU* 3.4 17.1 + - + +
166G PHE* 3.3 17.8 - - - -
298G PHE* 5.3 0.4 - - + -
503G SMA 3.6 90.2 - - + +
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Residues in contact with THR 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PHE* 5.3 2.0 - - + -
159G ALA 2.7 17.5 + - - +
160G THR* 2.7 26.2 + - - -
162G ILE* 1.3 77.3 - - - +
164G GLY* 1.3 61.0 + - - +
166G PHE* 3.1 17.9 + - - +
177G GLN* 2.9 29.4 + - - +
180G LEU* 4.4 20.6 - - + +
181G LEU* 3.6 34.5 - - + +
186G VAL* 4.8 0.9 - - + -
190G THR* 4.8 0.9 - - + -
194G PHE* 4.5 20.6 - - + -
503G SMA 6.5 0.2 - - - -
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Residues in contact with GLY 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G THR 3.1 11.6 + - - -
161G VAL 2.9 9.4 + - - -
163G THR* 1.3 73.6 + - - +
165G LEU* 1.3 58.6 + - - +
166G PHE 2.9 2.2 - - - -
167G GLY* 2.5 25.1 + - - -
168G ALA 3.2 6.2 + - - -
177G GLN* 3.6 13.9 - - - +
329G LYS* 5.1 1.2 - - - -
132L LEU* 3.7 23.0 - - - +
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Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G VAL* 3.0 11.2 + - + +
162G ILE* 3.6 30.5 - - + +
163G THR 3.3 0.6 - - - -
164G GLY* 1.3 73.9 - - - +
166G PHE* 1.3 67.4 + - + +
168G ALA* 3.1 19.1 + - - +
169G ILE* 4.0 4.2 + - - +
305G LEU* 4.0 19.5 - - + -
333G VAL* 4.0 17.1 - - + +
336G MET* 3.7 25.8 - - + -
337G PHE* 4.5 16.2 - - + -
503G SMA 4.7 13.9 - - + +
132L LEU* 3.7 30.5 - - + -
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Residues in contact with PHE 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G ILE* 3.3 21.8 - - + -
163G THR 3.5 8.7 - - - +
164G GLY 2.7 3.0 + - - -
165G LEU* 1.3 78.3 - - + +
167G GLY* 1.3 62.7 + - - +
168G ALA 2.9 5.6 + - - -
169G ILE* 2.8 37.4 + - + +
173G GLY* 3.3 12.5 - - - -
176G ILE* 3.7 30.1 - - + -
177G GLN* 4.7 3.6 - - + -
180G LEU* 4.0 16.8 - - + -
337G PHE* 4.6 17.7 - + - -
503G SMA 4.0 38.6 - - + -
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Residues in contact with GLY 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G THR 3.6 3.2 + - - -
164G GLY 2.5 17.9 + - - -
166G PHE* 1.3 73.8 - - - +
168G ALA* 1.3 59.1 + - - -
169G ILE 3.4 7.5 + - - +
173G GLY* 3.5 17.3 - - - -
174G HIS* 4.6 2.6 + - - -
177G GLN* 3.9 17.4 - - - +
329G LYS* 4.7 10.1 + - - -
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Residues in contact with ALA 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G GLY 3.2 3.1 + - - +
165G LEU* 3.1 17.9 + - - +
166G PHE 2.9 1.0 - - - -
167G GLY* 1.3 77.2 - - - +
169G ILE* 1.3 66.1 + - - +
170G PRO* 3.2 5.4 - - - +
329G LYS* 4.1 26.0 - - + +
330G PHE* 3.5 24.2 - - + +
333G VAL* 3.5 25.1 - - + -
132L 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