Contacts of the helix formed by residues 146 - 158 (chain A) 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 HIS 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.2 10.7 - - + +
143A PRO* 2.9 37.2 + - + +
145A SER* 1.3 78.6 + - - +
147A GLN* 1.3 61.4 + - - +
148A ALA 2.9 6.3 - - - -
149A LEU* 2.9 41.4 + - + +
150A VAL* 4.1 1.9 + - - +
179A LYS* 3.4 29.8 + - + +
362A ASN* 3.5 28.1 + - + -
364A ASP* 5.5 2.0 + - - -
366A ASP* 4.1 16.6 + - + -
367A ARG 4.2 12.7 + - - -
368A LYS* 5.8 2.9 - - + +
372A TYR* 4.3 7.7 + - - +
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Residues in contact with GLN 147 (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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124A ARG* 3.8 12.4 + - - +
143A PRO 4.3 0.2 + - - -
144A TYR* 2.8 33.1 + - - +
146A HIS* 1.3 77.3 - - - +
148A ALA* 1.3 56.9 + - - +
150A VAL* 2.8 25.3 + - - +
151A TRP* 3.1 29.2 + - + -
271A GLY* 3.6 18.9 - - - -
272A GLU* 2.9 32.7 + - - +
273A ARG* 6.2 0.2 - - - +
274A GLU* 5.0 2.6 + - - -
290A LEU* 3.6 24.9 - - + +
372A TYR* 4.0 19.9 + - + +
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Residues in contact with ALA 148 (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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145A SER 3.1 15.7 + - - +
146A HIS 2.9 0.2 - - - -
147A GLN* 1.3 78.4 - - - +
149A LEU* 1.3 51.6 + - - +
151A TRP* 3.2 19.7 + - + +
152A PHE* 2.8 36.2 + - - +
176A ALA 4.4 2.9 - - - +
179A LYS* 3.6 17.5 - - + -
180A LEU* 3.9 29.6 - - + +
183A LEU* 3.6 4.1 - - + +
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Residues in contact with LEU 149 (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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146A HIS* 2.9 38.0 + - + +
148A ALA* 1.3 76.1 - - - +
150A VAL* 1.3 65.1 + - + +
152A PHE* 3.7 2.9 + - - +
153A GLU* 3.2 29.3 + - - +
179A LYS* 3.3 30.1 - - - +
183A LEU* 3.7 25.0 - - + +
372A TYR* 5.8 3.4 - - + +
388A PHE* 5.0 11.7 - - + -
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Residues in contact with VAL 150 (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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146A HIS 4.7 1.1 - - - +
147A GLN* 2.8 10.7 + - - +
149A LEU* 1.3 77.3 - - + +
151A TRP* 1.3 65.9 + - - +
153A GLU* 3.0 7.0 + - - +
154A MET* 2.8 42.8 + - + +
290A LEU* 3.7 22.7 - - + -
372A TYR* 3.6 38.8 - - + -
374A ILE* 4.8 3.8 - - + -
388A PHE* 3.9 32.5 - - + -
393A ILE* 4.6 1.5 - - + +
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Residues in contact with TRP 151 (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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147A GLN* 3.1 24.2 + - + -
148A ALA* 3.6 24.9 - - + +
150A VAL* 1.3 75.3 - - - +
152A PHE* 1.3 52.8 - - - +
154A MET* 3.0 6.2 + - + +
155A MET* 2.7 42.9 + - - +
165A LEU* 4.8 6.5 - - + -
176A ALA* 4.7 15.3 - - + -
180A LEU* 4.6 15.5 - - + -
241A ILE* 3.4 31.6 - - + -
242A LEU 3.9 12.6 - - - -
243A SER* 4.4 12.3 - - - -
269A LEU* 3.3 35.5 - - + +
270A VAL 3.0 36.9 + - - -
271A GLY* 3.9 8.3 - - - -
274A GLU* 6.0 0.2 - - - -
290A LEU* 3.8 13.5 - - + +
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Residues in contact with PHE 152 (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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148A ALA 2.8 17.5 + - - +
149A LEU 3.8 3.8 - - - +
150A VAL 3.1 0.2 - - - -
151A TRP* 1.3 76.6 - - - +
153A GLU* 1.3 79.7 + - - +
155A MET* 3.2 12.1 + - + +
156A ARG* 3.2 45.3 + - + +
180A LEU* 4.5 3.1 - - + +
183A LEU* 3.3 56.5 - - + -
184A LEU* 3.8 22.7 - - + -
210A PRO* 4.3 16.4 - - + -
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Residues in contact with GLU 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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149A LEU 3.2 14.3 + - - +
150A VAL 3.0 7.7 + - - +
152A PHE* 1.3 98.8 - - - +
154A MET* 1.3 57.1 + - - +
156A ARG* 3.3 32.2 + - - +
157A LEU* 3.2 21.8 + - - +
183A LEU* 6.1 0.2 - - - +
388A PHE* 3.5 26.9 - - + -
391A SER 4.8 7.1 - - - +
393A ILE* 3.5 23.3 - - + +
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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
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150A VAL* 2.8 34.7 + - + +
151A TRP* 3.1 11.2 - - + +
153A GLU* 1.3 77.6 - - - +
155A MET* 1.3 59.0 + - - +
157A LEU* 4.4 1.1 - - - -
158A PHE* 3.1 53.6 + - + +
160A TRP* 3.6 24.2 - - + -
269A LEU* 3.8 23.6 - - + -
288A ILE* 4.7 4.3 - - - -
290A LEU* 4.5 5.6 - - + -
374A ILE* 4.1 35.0 - - + -
393A ILE* 3.7 10.5 - - + +
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Residues in contact with MET 155 (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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151A TRP 2.7 23.1 + - - +
152A PHE* 3.2 15.7 + - + +
154A MET* 1.3 71.4 - - - +
156A ARG* 1.3 63.8 + - - +
159A ASN* 3.1 3.6 + - - -
160A TRP* 2.9 58.7 + - + +
161A ASN* 5.5 0.9 - - - +
163A VAL* 3.9 20.4 - - + -
180A LEU* 4.4 9.4 - - - -
184A LEU* 4.0 18.6 - - + -
210A PRO* 3.7 31.7 - - + +
211A LYS 5.0 0.7 - - - +
239A VAL* 5.8 0.2 - - + -
241A ILE* 4.1 22.4 - - + -
269A LEU* 4.9 3.6 - - + -
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Residues in contact with ARG 156 (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 PHE* 3.2 43.1 + - + +
153A GLU* 3.3 30.1 + - - +
154A MET 3.3 0.2 - - - -
155A MET* 1.3 74.4 - - - +
157A LEU* 1.3 68.8 + - - +
159A ASN* 2.9 24.7 + - - +
210A PRO* 5.0 13.0 - - + -
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Residues in contact with LEU 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 GLU 3.2 14.9 + - - +
154A MET 3.4 5.1 + - - +
156A ARG* 1.3 86.1 - - - +
158A PHE* 1.3 85.1 + - + +
159A ASN* 3.3 10.0 + - - +
393A ILE* 3.5 41.1 - - + +
395A GLN* 4.2 17.3 - - + +
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Residues in contact with PHE 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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154A MET* 3.1 35.1 + - + +
157A LEU* 1.3 93.9 - - + +
159A ASN* 1.3 69.8 + - - +
160A TRP* 3.3 45.7 + + + +
393A ILE* 5.9 0.7 - - + -
395A GLN* 3.9 28.7 - - + -
400A ILE* 3.7 24.5 - - + -
402A TRP* 4.1 19.7 - + + -
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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