Contacts of the helix formed by residues 152 - 168 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A PHE* 4.7 1.8 - - - -
150A PRO 3.4 3.0 - - - -
151A TRP* 1.3 76.0 - - - +
153A GLN* 1.3 68.7 + - - +
155A SER* 3.0 7.7 + - - -
156A PHE 2.9 15.2 + - - -
279A ASN* 3.0 20.6 - - - -
281A ILE 3.3 14.4 - - - -
282A GLU* 4.5 0.7 - - - -
283A ALA* 3.4 12.3 - - - +
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLY* 1.3 72.3 - - - +
154A MET* 1.3 70.7 + - + +
155A SER 2.8 1.7 + - - -
156A PHE* 3.0 8.5 + - - +
157A TRP* 3.3 28.7 + - - -
278A ASP 3.2 12.9 + - - +
279A ASN* 3.1 2.4 + - - -
281A ILE* 3.0 41.2 + - + +
282A GLU 3.7 3.1 - - - +
283A ALA* 3.6 0.7 - - - +
284A ASN* 2.8 38.4 + - - +
287A ARG* 3.5 19.8 + - - +
289A PRO* 3.4 35.1 - - + +
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Residues in contact with MET 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 3.7 9.2 - - - +
147A TYR* 3.5 30.5 - - + +
153A GLN* 1.3 75.8 - - - +
155A SER* 1.3 63.8 + - - +
157A TRP* 5.2 1.1 - - + -
158A GLY* 3.0 23.1 + - - +
276A HIS* 3.7 42.4 - - + +
278A ASP* 3.6 22.9 - - + +
279A ASN* 2.9 14.3 + - - +
289A PRO* 3.7 26.9 - - + -
292A ILE* 3.8 29.2 - - + -
293A VAL 3.9 8.5 - - - +
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 2.7 25.6 + - - -
148A VAL* 3.3 31.0 + - - +
150A PRO* 4.1 1.0 - - - +
151A TRP* 3.7 3.8 + - - -
152A GLY 3.1 23.7 + - - -
153A GLN 2.8 2.4 + - - -
154A MET* 1.3 78.1 - - - +
156A PHE* 1.3 65.6 - - - +
158A GLY* 4.0 0.3 - - - -
159A ALA* 3.1 19.9 + - - +
279A ASN* 2.9 22.3 + - - +
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TRP* 3.9 24.4 - + + -
152A GLY 2.9 12.0 + - - +
153A GLN 3.8 5.8 - - - +
155A SER* 1.3 75.1 - - - +
157A TRP* 1.3 94.1 + + + +
159A ALA* 2.7 28.9 + - - +
160A THR* 2.9 17.3 + - - -
186A VAL* 3.1 50.5 - - + -
283A ALA* 3.8 15.5 - - + +
284A ASN 4.0 5.6 - - - -
285A PRO* 3.3 42.4 - - + -
69F GLY 4.9 5.6 - - - -
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Residues in contact with TRP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLN* 3.3 21.5 + - - +
154A MET 4.7 0.2 - - - +
156A PHE* 1.3 90.8 - + - +
158A GLY* 1.3 65.5 + - - +
160A THR* 2.8 24.6 + - + -
161A VAL* 2.8 26.8 + - - +
284A ASN 3.4 19.1 + - - -
285A PRO 3.6 16.8 - - - -
287A ARG 2.6 36.7 + - - -
288A THR* 3.2 24.7 - - + -
289A PRO* 3.5 22.0 - - + -
292A ILE* 3.8 21.5 - - + -
71F PRO* 5.0 5.4 - - + -
133F GLY 4.2 6.7 - - - -
134F CYS* 3.9 23.3 - - - -
135F SER* 4.0 11.4 - - - -
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Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SMA 3.1 37.5 + - - -
144A PHE* 4.4 2.9 - - - -
147A TYR* 6.2 0.7 - - - -
154A MET 3.0 15.6 + - - -
155A SER 4.0 0.2 - - - -
157A TRP* 1.3 75.4 - - - +
159A ALA* 1.3 57.2 + - - +
161A VAL* 3.3 1.7 + - - +
162A ILE* 2.9 37.5 + - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.8 16.0 - - + -
148A VAL* 4.1 21.1 - - + -
155A SER 3.1 12.7 + - - +
156A PHE* 2.7 20.6 + - - +
158A GLY* 1.3 67.9 - - - +
160A THR* 1.3 54.5 + - - +
162A ILE* 3.9 0.3 - - - +
163A THR* 2.7 40.8 + - + +
186A VAL* 4.1 16.8 - - + -
190A THR* 5.8 1.1 - - + -
194A PHE* 4.6 6.3 - - + -
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 2.9 20.0 + - - -
157A TRP* 2.8 32.9 + - + -
159A ALA* 1.3 76.8 - - - +
161A VAL* 1.3 57.5 + - - +
163A THR* 2.8 19.0 + - - -
164A GLY* 3.1 10.6 + - - -
177A GLN* 4.5 2.3 - - - +
186A VAL* 3.7 19.2 - - + +
132F LEU 3.4 5.4 - - - +
133F GLY* 4.0 30.7 - - - +
134F CYS 4.5 0.7 - - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 3.4 50.7 - - + +
157A TRP 2.8 16.1 + - - +
158A GLY 3.6 7.0 - - - +
160A THR* 1.3 73.1 - - - +
162A ILE* 1.3 62.1 + - - +
164A GLY* 2.9 15.6 + - - -
165A LEU* 3.0 13.7 + - + +
132F LEU* 3.8 34.4 - - + +
134F CYS* 3.6 31.2 - - - +
151F CYS* 4.4 1.3 - - - -
152F HIS* 4.1 1.8 - - + -
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SMA 3.2 98.3 - - + +
144A PHE* 3.6 33.7 - - + -
158A GLY 2.9 19.7 + - - +
161A VAL* 1.3 72.6 - - - +
163A THR* 1.3 66.1 + - - +
164A GLY 3.3 0.2 + - - -
165A LEU* 3.3 19.7 + - + +
166A PHE* 3.3 15.0 - - + -
298A PHE* 5.4 0.2 - - + -
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Residues in contact with THR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SMA 5.4 1.3 - - + -
144A PHE* 5.3 1.6 - - + -
159A ALA 2.7 25.1 + - - +
160A THR* 2.8 17.2 + - - -
162A ILE* 1.3 77.6 - - - +
164A GLY* 1.3 61.9 + - - +
166A PHE* 3.1 18.6 + - - +
177A GLN* 3.0 26.7 + - - +
180A LEU* 4.3 21.0 - - + +
181A LEU* 3.6 35.1 - - + +
186A VAL* 4.1 1.1 - - + +
190A THR* 4.8 1.1 - - + -
194A PHE* 4.4 20.4 - - + -
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A THR 3.1 11.8 + - - -
161A VAL 2.9 11.1 + - - -
163A THR* 1.3 74.2 + - - +
165A LEU* 1.3 56.1 + - - +
166A PHE 2.9 2.5 - - - -
167A GLY* 2.5 29.3 + - - -
168A ALA 3.2 3.5 + - - -
177A GLN* 3.5 13.2 - - - -
329A LYS* 5.1 1.6 - - - -
132F LEU* 3.8 23.1 - - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SMA 4.6 16.4 - - + +
161A VAL* 3.0 11.0 + - + +
162A ILE* 3.6 28.0 - - + +
163A THR 3.3 0.6 - - - -
164A GLY* 1.3 73.2 - - - +
166A PHE* 1.3 69.5 + - + +
168A ALA* 3.1 19.2 + - - +
169A ILE* 4.0 4.3 + - - +
305A LEU* 4.0 19.7 - - + -
333A VAL* 4.1 16.4 - - + +
336A MET* 3.7 26.5 - - + -
337A PHE* 4.5 15.0 - - + -
132F LEU* 3.8 31.2 - - + -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SMA 4.3 33.2 - - + -
162A ILE 3.3 20.9 - - - -
163A THR 3.5 8.3 - - - +
164A GLY 2.9 1.2 - - - -
165A LEU* 1.3 79.0 - - + +
167A GLY* 1.3 61.6 + - - +
168A ALA 2.9 5.6 - - - -
169A ILE* 2.8 34.0 + - + +
173A GLY* 3.3 11.6 - - - -
176A ILE* 3.6 29.8 - - + -
177A GLN* 4.8 3.6 - - + +
180A LEU* 4.0 20.6 - - + -
337A PHE* 4.7 17.0 - + - -
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A THR 3.6 2.6 + - - -
164A GLY 2.5 18.1 + - - -
166A PHE* 1.3 74.0 - - - +
168A ALA* 1.3 57.8 + - - -
169A ILE 3.4 7.5 + - - +
173A GLY* 3.5 18.5 + - - -
174A HIS* 4.6 2.5 + - - -
177A GLN* 4.0 18.5 - - - +
329A LYS* 4.6 10.8 + - - -
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY 3.2 3.1 + - - +
165A LEU* 3.1 17.2 + - - +
166A PHE 2.9 0.8 - - - -
167A GLY* 1.3 77.6 - - - +
169A ILE* 1.3 65.2 + - - +
170A PRO* 3.3 5.0 - - - +
329A LYS* 4.2 26.2 - - + +
330A PHE* 3.5 23.0 - - + +
333A VAL* 3.5 26.2 - - + -
132F 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
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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