Contacts of the helix formed by residues 149 - 164 (chain B) in PDB entry 3QEL
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 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B ILE* 4.3 2.9 - - - -
147B GLY 3.8 2.2 + - - -
148B PRO* 1.3 75.6 - - - +
150B ILE* 1.3 66.3 + - - +
151B GLU* 3.7 7.6 + - - +
152B GLN* 3.3 24.8 + - - +
153B GLN* 3.1 22.2 + - - +
356B TYR* 3.3 57.9 + - - -
357B GLN 4.8 0.2 + - - -
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Residues in contact with ILE 150 (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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133B ILE* 3.6 28.6 - - + +
135B ALA* 3.6 20.9 - - + +
148B PRO 3.8 0.8 + - - -
149B SER* 1.3 73.5 - - - +
151B GLU* 1.3 62.5 + - - +
153B GLN* 3.5 11.2 + - - +
154B ALA* 3.1 20.4 + - - +
177B PRO 4.2 0.2 - - - +
178B GLY* 3.3 43.5 - - - +
181B ASP* 4.3 8.1 - - + +
182B PHE* 3.9 26.1 - - + +
231B TYR* 3.5 21.8 - - + +
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Residues in contact with GLU 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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149B SER* 3.1 7.6 + - - +
150B ILE* 1.3 81.2 - - - +
152B GLN* 1.3 57.6 + - - +
154B ALA 3.3 0.9 + - - -
155B SER* 3.0 24.6 + - - -
181B ASP* 5.1 6.5 - - + +
185B LYS* 3.5 46.3 + - + +
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Residues in contact with GLN 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 PRO* 4.5 8.7 - - + -
149B SER* 3.2 25.5 + - - +
151B GLU* 1.3 73.8 - - - +
153B GLN* 1.3 66.1 + - - +
154B ALA 3.1 1.6 - - - -
155B SER* 3.1 7.7 + - - -
156B VAL* 2.8 38.2 + - + +
185B LYS* 5.4 0.9 - - - +
356B TYR* 5.7 2.4 - - - -
357B GLN 5.3 2.6 + - - -
358B MET 4.3 14.2 + - - +
359B HIS* 5.7 0.2 - - - -
360B PRO* 4.2 21.1 - - - +
362B LEU* 4.7 1.1 - - + +
379B TRP* 3.2 29.1 + - + +
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Residues in contact with GLN 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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133B ILE* 4.1 18.4 - - - +
148B PRO* 3.5 38.8 + - + +
149B SER 3.1 15.1 + - - +
150B ILE* 3.8 7.2 - - - +
152B GLN* 1.3 76.6 - - - +
154B ALA* 1.3 57.7 + - - +
156B VAL* 3.3 9.7 + - - +
157B MET* 3.0 35.6 + - - +
182B PHE* 5.8 2.0 - - + -
231B TYR* 6.0 1.4 - - - -
259B PRO* 3.7 17.8 - - + +
260B SER* 2.9 38.5 + - - +
261B LEU* 5.4 1.8 - - - +
280B VAL* 4.1 18.1 - - + +
362B LEU* 5.1 0.2 - - + -
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Residues in contact with ALA 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 ILE 3.1 13.9 + - - +
151B GLU 3.5 9.0 - - - +
152B GLN 3.1 0.6 - - - -
153B GLN* 1.3 74.5 - - - +
155B SER* 1.3 64.6 + - - +
157B MET* 3.2 6.7 + - - +
158B LEU* 3.2 24.9 + - - +
182B PHE* 3.8 23.5 - - + -
185B LYS* 4.2 12.8 - - + -
186B ILE* 3.5 27.0 - - + +
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Residues in contact with SER 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 GLU 3.0 13.8 + - - -
152B GLN* 3.1 12.2 + - - -
154B ALA* 1.3 74.3 - - - +
156B VAL* 1.3 65.3 + - - +
158B LEU* 3.1 14.3 + - - +
159B ASN* 3.0 34.8 + - - +
185B LYS* 4.6 15.8 - - - +
189B THR* 5.5 2.2 - - - -
379B TRP* 4.4 8.1 - - - -
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Residues in contact with VAL 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 GLN* 2.8 28.3 + - + +
153B GLN* 3.5 9.0 - - - +
155B SER* 1.3 72.0 - - - +
157B MET* 1.3 61.9 + - - +
159B ASN* 3.2 10.5 + - - +
160B ILE* 3.1 24.9 + - + +
280B VAL* 4.3 22.0 - - + -
362B LEU* 4.0 15.3 - - + -
364B ILE* 4.7 5.4 - - + -
379B TRP* 3.8 47.3 - - + -
384B LEU* 4.5 9.4 - - + -
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Residues in contact with MET 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 GLN* 3.0 19.0 + - - +
154B ALA* 3.5 8.1 - - - +
155B SER 3.1 0.2 - - - -
156B VAL* 1.3 75.5 - - - +
158B LEU* 1.3 56.6 + - - +
160B ILE* 3.2 12.0 + - - +
161B MET* 3.0 38.8 + - + +
182B PHE* 3.3 42.0 - - + -
229B LEU* 3.3 37.9 - - + -
230B LEU 5.6 0.2 - - - +
257B ILE* 3.6 27.4 - - + +
258B VAL 4.6 16.6 - - - +
259B PRO* 4.8 4.3 - - - -
280B VAL* 4.2 12.6 - - + -
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Residues in contact with LEU 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 ALA 3.2 12.3 + - - +
155B SER* 3.1 12.1 + - - +
157B MET* 1.3 74.4 - - - +
159B ASN* 1.3 62.7 + - - +
161B MET* 3.3 14.8 + - + -
162B GLU* 2.9 26.2 + - - +
169B PHE* 4.3 15.0 - - + -
185B LYS* 4.8 0.4 - - + +
186B ILE* 4.3 25.4 - - + +
189B THR* 3.3 42.0 - - + +
190B ILE* 4.9 2.9 - - + +
197B TRP* 3.3 44.1 - - + -
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Residues in contact with ASN 159 (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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155B SER* 3.0 24.2 + - - +
156B VAL* 3.5 8.4 - - - +
157B MET 3.2 0.2 - - - -
158B LEU* 1.3 74.7 - - - +
160B ILE* 1.3 66.2 + - - +
162B GLU* 3.4 6.0 + - - +
163B GLU* 3.1 23.4 + - - +
379B TRP* 2.8 40.7 - - + -
384B LEU* 3.9 17.6 - - + +
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Residues in contact with ILE 160 (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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156B VAL* 3.1 19.2 + - + +
157B MET* 3.2 13.7 + - - +
159B ASN* 1.3 75.3 - - - +
161B MET* 1.3 66.1 + - - +
163B GLU* 3.2 10.0 + - - +
164B TYR* 3.3 32.1 - - + +
166B TRP* 4.5 15.9 - - + -
257B ILE* 5.0 11.7 - - + -
278B ILE* 4.6 10.8 - - + -
280B VAL* 5.0 6.3 - - + -
364B ILE* 3.8 37.0 - - + -
384B LEU* 4.0 19.7 - - + -
386B MET* 4.7 5.8 - - + -
391B TRP* 5.1 4.7 - - + -
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Residues in contact with MET 161 (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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157B MET* 3.0 38.2 + - + +
158B LEU* 3.6 10.1 - - + +
159B ASN 3.3 0.4 - - - -
160B ILE* 1.3 77.6 - - - +
162B GLU* 1.3 62.5 + - - +
163B GLU 3.2 0.2 + - - -
164B TYR* 3.3 0.9 + - - -
165B ASP 3.0 4.0 + - - -
166B TRP* 2.9 61.5 + - + +
169B PHE* 4.2 14.4 - - - -
197B TRP* 3.7 17.5 - - + -
227B ILE* 4.0 17.9 - - + -
229B LEU* 3.6 35.7 - - + -
257B ILE* 4.3 14.4 - - + -
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Residues in contact with GLU 162 (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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158B LEU 2.9 16.2 + - - +
159B ASN* 3.9 6.5 - - - +
161B MET* 1.3 76.3 - - - +
163B GLU* 1.3 62.7 + - - +
165B ASP* 3.0 21.1 + - - +
167B TYR* 3.5 19.4 + - + +
195B VAL* 5.8 3.4 - - + -
197B TRP* 3.8 13.3 - - + -
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Residues in contact with GLU 163 (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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159B ASN 3.1 15.7 + - - +
160B ILE* 3.7 6.7 - - - +
161B MET 3.2 0.6 - - - -
162B GLU* 1.3 79.8 - - - +
164B TYR* 1.3 80.2 + - + +
165B ASP* 3.5 8.1 + - - +
384B LEU* 5.0 9.7 - - + +
386B MET* 4.3 24.3 + - + +
388B TYR 5.5 1.5 - - - +
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Residues in contact with TYR 164 (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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160B ILE* 3.3 22.7 - - + -
161B MET 3.3 2.0 + - - -
163B GLU* 1.3 85.1 - - + +
165B ASP* 1.3 70.7 + - - +
166B TRP* 2.9 40.7 + + + +
386B MET* 3.3 32.4 - - + +
388B TYR 2.9 23.5 + - - -
389B TYR* 3.5 27.8 - - - -
391B TRP* 3.1 56.2 - + + -
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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