Contacts of the helix formed by residues 147 - 158 (chain B) in PDB entry 3QEK
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 GLN 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B ARG* 3.9 22.6 + - - +
143B PRO 4.2 0.4 + - - -
144B TYR* 3.0 34.4 + - - +
145B SER 3.1 0.4 - - - -
146B HIS* 1.3 77.9 - - - +
148B ALA* 1.3 57.4 + - - +
150B VAL* 2.9 24.4 + - - +
151B TRP* 3.1 30.2 + - + -
271B GLY* 3.4 16.9 - - - -
272B GLU* 2.9 34.1 + - - +
273B ARG* 6.1 0.8 - - - +
274B GLU* 4.8 4.6 + - - -
290B LEU* 3.8 22.3 - - + +
372B TYR* 4.1 11.1 + - + +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B SER 3.2 15.9 + - - +
146B HIS 2.9 0.4 - - - -
147B GLN* 1.3 76.2 - - - +
149B LEU* 1.3 65.0 + - - +
151B TRP* 3.6 21.0 - - + +
152B PHE* 3.0 25.3 + - - +
176B ALA 4.2 3.1 - - - +
179B LYS* 3.7 17.0 - - + -
180B LEU* 3.8 30.4 - - + +
183B LEU* 3.4 4.1 - - + +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B HIS* 2.9 37.8 + - + +
148B ALA* 1.3 79.2 - - - +
150B VAL* 1.3 64.6 + - + +
152B PHE* 3.5 3.3 + - - +
153B GLU* 3.3 27.5 + - - +
179B LYS* 4.1 18.6 - - - +
183B LEU* 3.8 27.9 - - + +
369B PHE 6.4 0.4 - - - +
372B TYR* 5.5 4.5 - - + +
388B PHE* 4.7 16.3 - - + -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN* 2.9 10.9 + - - +
149B LEU* 1.3 77.5 - - + +
151B TRP* 1.3 66.5 + - - +
153B GLU* 3.3 2.1 + - - +
154B MSE 2.9 36.8 + - + +
290B LEU* 3.9 29.4 - - + -
372B TYR* 3.5 40.8 - - + -
374B ILE* 4.6 7.4 - - + -
388B PHE* 3.8 36.1 - - + -
393B ILE* 5.0 1.1 - - + -
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Residues in contact with TRP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TYR 5.6 0.9 - - - -
147B GLN* 3.1 28.1 + - + -
148B ALA* 3.6 27.6 - - + +
150B VAL* 1.3 75.2 - - - +
152B PHE* 1.3 56.9 + - - +
154B MSE 3.1 3.8 + - - +
155B MSE 2.9 34.5 + - - +
165B LEU* 4.6 7.0 - - + -
176B ALA* 4.3 26.9 - - + -
180B LEU* 4.5 12.6 - - + -
241B ILE* 3.6 32.1 - - + -
242B LEU 4.0 17.3 - - - -
243B SER* 4.4 4.5 - - - -
269B LEU* 3.7 35.2 - - + +
270B VAL 3.1 20.5 + - - -
271B GLY* 3.9 18.8 - - - -
274B GLU* 5.6 0.4 - - - -
290B LEU* 3.8 12.7 - - + +
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ALA 3.0 18.2 + - - +
149B LEU* 3.6 5.6 - - - +
151B TRP* 1.3 76.1 - - - +
153B GLU* 1.3 76.2 + - - +
155B MSE 3.4 13.3 + - + +
156B ARG* 3.1 52.5 + - + +
180B LEU* 4.3 3.1 - - + -
183B LEU* 3.8 43.1 - - + -
184B LEU* 3.8 28.7 - - + -
187B LYS* 3.8 32.5 - - + -
210B PRO* 5.4 4.9 - - + -
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU 3.3 16.6 + - - +
150B VAL 3.9 2.2 - - - +
152B PHE* 1.3 89.0 - - - +
154B MSE 1.3 61.2 + - - +
156B ARG* 3.2 30.1 + - - +
157B LEU* 2.8 30.8 + - - +
388B PHE* 3.7 24.7 - - + -
391B SER 4.3 9.8 - - - +
392B TYR* 6.1 1.2 - - - -
393B ILE* 3.6 19.5 - - + +
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Residues in contact with MSE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B VAL* 2.9 29.9 + - + +
151B TRP* 3.1 12.3 + - - +
153B GLU* 1.3 76.6 - - - +
155B MSE 1.3 61.5 + - - +
157B LEU* 3.1 2.1 + - - -
158B PHE* 2.9 54.2 + - + +
160B TRP* 4.0 21.1 - - + -
269B LEU* 4.3 9.4 - - + -
288B ILE* 3.7 42.0 - - + -
290B LEU* 5.9 1.3 - - + -
374B ILE* 4.3 20.9 - - + -
393B ILE* 3.6 22.9 - - + -
400B ILE* 5.3 1.6 - - + -
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Residues in contact with MSE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B TRP 2.9 18.3 + - - +
152B PHE* 3.4 17.5 - - + +
154B MSE 1.3 76.9 - - - +
156B ARG* 1.3 58.0 + - + +
159B ASN* 2.9 25.6 + - - -
160B TRP* 2.9 49.0 + - + +
161B ASN* 5.4 0.5 - - - +
163B VAL* 2.9 41.5 - - + -
180B LEU* 4.3 10.1 - - + -
184B LEU* 4.4 20.2 - - + -
210B PRO* 5.4 7.2 - - + -
241B ILE* 2.8 38.8 - - + -
269B LEU* 5.0 0.7 - - + -
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.1 42.6 + - + +
153B GLU* 3.4 31.3 + - - +
154B MSE 3.2 0.2 - - - -
155B MSE 1.3 73.0 - - + +
157B LEU* 1.3 66.9 + - - +
158B PHE 3.4 0.5 + - - -
159B ASN* 3.5 17.3 + - - +
187B LYS* 3.8 31.0 - - - +
190B LYS* 5.9 2.6 - - - +
210B PRO* 5.7 6.7 - - + -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLU 2.8 17.6 + - - +
154B MSE 3.1 4.9 + - - +
156B ARG* 1.3 78.2 - - - +
158B PHE* 1.3 82.1 + - + +
159B ASN* 3.8 5.7 + - - +
393B ILE* 3.7 35.4 - - + +
395B GLN* 3.6 30.3 - - - +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B MSE 2.9 46.1 + - + +
157B LEU* 1.3 101.4 - - + +
159B ASN* 1.3 72.4 + - - +
160B TRP* 3.2 39.6 + + + +
395B GLN* 4.1 15.5 - - - -
400B ILE* 3.8 23.6 - - + -
402B TRP* 3.7 26.5 - + - -
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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