Contacts of the helix formed by residues 146 - 158 (chain B) in PDB entry 3Q41
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B SER* 5.6 0.4 - - - -
142B PRO* 4.3 7.9 - - + +
143B PRO* 3.1 31.9 + - + +
144B TYR 3.0 0.8 - - - -
145B SER* 1.3 80.7 - - - +
147B GLN* 1.3 55.9 + - - +
148B SER 2.9 6.3 - - - -
149B SER* 2.9 27.1 + - - -
150B VAL* 3.9 2.6 + - - +
179B ARG* 3.0 44.4 + - - +
341B ASN* 3.9 16.4 + - - -
345B ASP* 3.4 32.5 + - + -
346B ARG 4.7 5.4 + - - -
351B TYR* 3.8 18.3 + - - +
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Residues in contact with GLN 147 (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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124B ARG* 3.5 18.2 + - - +
143B PRO 4.8 0.2 - - - +
144B TYR* 3.0 31.4 + - - +
146B HIS* 1.3 78.1 - - - +
148B SER* 1.3 56.2 + - - +
149B SER 3.2 0.2 - - - -
150B VAL* 3.3 13.5 + - - +
151B TRP* 3.2 45.5 + - + +
250B GLY* 3.6 18.4 - - - -
251B GLU* 3.2 40.3 + - - +
253B GLU* 4.4 4.0 + - - -
269B LEU* 4.3 11.4 - - + +
351B TYR* 4.0 21.2 - - + -
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TYR 4.4 0.4 + - - -
145B SER 2.5 25.1 + - - -
147B GLN* 1.3 76.8 - - - +
149B SER* 1.3 59.5 + - - +
150B VAL 3.2 0.9 - - - -
151B TRP* 3.4 27.3 - - - +
152B PHE* 3.0 28.1 + - - +
176B ALA 3.8 17.0 - - - -
179B ARG* 3.2 20.1 - - - +
180B LEU* 3.8 14.1 - - - +
183B LEU* 3.8 3.8 - - - +
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Residues in contact with SER 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 12.3 + - - -
148B SER* 1.3 79.1 + - - +
150B VAL* 1.3 60.9 + - - +
152B PHE* 3.7 3.9 + - - +
153B GLU* 3.5 17.2 + - - +
179B ARG* 2.8 36.5 + - - -
183B LEU* 4.1 16.2 - - - +
367B TYR* 3.6 20.6 + - - -
370B THR* 6.3 0.7 - - - -
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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
----------------------------------------------------------
146B HIS 4.5 1.1 - - - +
147B GLN* 3.3 12.1 + - - +
148B SER 3.2 0.4 - - - -
149B SER* 1.3 75.0 - - - +
151B TRP* 1.3 60.1 + - + +
152B PHE 3.1 1.3 - - - -
153B GLU* 3.0 4.5 + - - +
154B MET* 2.8 41.8 + - - +
269B LEU* 3.5 27.4 - - + -
351B TYR* 3.6 25.6 - - + -
353B ILE* 4.7 3.1 - - + -
367B TYR* 3.6 50.7 - - + -
372B VAL* 5.1 0.7 - - + -
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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 5.5 0.9 - - - -
147B GLN* 3.2 22.7 + - + -
148B SER* 3.4 31.4 + - - +
150B VAL* 1.3 77.3 - - + +
152B PHE* 1.3 56.8 + - - +
154B MET* 3.4 8.7 - - + +
155B MET* 2.9 35.9 + - - +
165B LEU* 5.0 3.8 - - + -
167B VAL* 6.2 0.2 - - + -
176B ALA* 4.3 22.4 - - + -
180B LEU* 4.3 15.7 - - + -
220B ILE* 3.5 27.8 - - + -
221B LEU 3.7 20.9 - - - -
222B SER* 4.6 5.6 - - - -
248B LEU* 3.8 28.6 - - + +
249B VAL 3.1 21.5 + - - -
250B GLY* 3.7 21.8 - - - -
253B GLU* 5.1 1.3 - - - -
269B LEU* 3.6 15.2 - - + +
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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 SER 3.0 17.3 + - - +
149B SER 3.7 7.4 - - - +
150B VAL 3.1 0.2 - - - -
151B TRP* 1.3 78.2 - - - +
153B GLU* 1.3 64.7 + - + +
155B MET* 2.8 24.6 + - + +
180B LEU* 4.4 5.3 - - + +
183B LEU* 3.2 60.3 - - + -
184B LEU* 3.6 22.4 - - + -
186B GLU* 4.6 4.0 - - - -
187B ARG* 3.2 47.5 + - + -
189B SER* 5.5 0.2 - - - -
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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 SER 3.5 5.2 + - - +
150B VAL 3.0 7.9 + - - +
152B PHE* 1.3 83.2 - - + +
154B MET* 1.3 60.1 + - - +
155B MET 2.8 14.6 - - - +
156B ARG* 2.8 45.1 + - - +
157B VAL* 3.3 23.0 + - - +
187B ARG* 5.9 0.9 + - - -
367B TYR* 3.8 13.2 - - + +
370B THR* 5.0 4.0 - - + -
371B HIS* 3.4 41.1 + - - +
372B VAL* 3.7 16.3 + - + -
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Residues in contact with MET 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* 2.8 22.9 + - - +
151B TRP* 3.4 15.5 - - - +
153B GLU* 1.3 72.4 - - - +
155B MET* 1.3 61.8 + - - +
157B VAL* 3.3 2.7 + - - +
158B TYR* 3.2 54.5 + - + +
160B TRP* 3.8 10.4 + - + -
248B LEU* 4.1 20.9 - - + -
267B ILE* 3.7 31.0 - - + -
269B LEU* 6.4 1.6 - - + -
353B ILE* 3.8 27.1 - - + -
372B VAL* 3.9 25.9 - - + +
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Residues in contact with MET 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TRP 2.9 21.6 + - - +
152B PHE* 2.8 16.8 - - + +
153B GLU 2.8 11.4 - - - +
154B MET* 1.3 73.7 - - - +
156B ARG* 1.3 68.7 + - - +
157B VAL 3.4 0.2 - - - -
160B TRP* 3.4 30.7 - - + +
161B ASN* 4.2 8.3 - - - -
163B ILE* 3.7 29.2 - - + -
180B LEU* 4.3 11.0 - - - -
184B LEU* 3.7 41.7 - - + -
187B ARG* 4.3 2.1 + - - +
189B SER* 4.0 17.7 - - - +
220B ILE* 4.4 11.0 - - + -
248B LEU* 5.1 2.2 - - + -
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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 4.6 0.9 - - - +
153B GLU* 2.8 35.7 + - - +
155B MET* 1.3 78.3 - - - +
157B VAL* 1.3 90.7 + - - +
158B TYR 3.1 11.6 + - - -
159B ASN* 3.6 29.4 + - - +
160B TRP 3.7 5.7 + - - -
161B ASN* 5.6 4.2 - - + +
187B ARG* 3.1 34.8 - - - +
189B SER* 5.9 0.9 - - - +
371B HIS* 3.7 21.2 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLU* 3.3 26.9 - - - +
154B MET* 3.3 6.7 + - - +
156B ARG* 1.3 105.6 - - - +
158B TYR* 1.3 84.6 + - + +
159B ASN 4.1 0.7 + - - -
372B VAL* 4.0 28.5 - - + +
374B PRO* 5.0 7.2 - - + -
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Residues in contact with TYR 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 MET* 3.2 40.9 + - + +
156B ARG 3.1 12.1 + - - -
157B VAL* 1.3 92.3 - - + +
159B ASN* 1.3 52.1 + - - +
160B TRP* 2.6 58.7 + + + -
353B ILE* 6.0 1.0 - - - +
364B VAL* 5.0 2.8 + - - +
365B GLY* 5.9 0.5 - - - -
372B VAL* 5.1 3.6 - - + +
374B PRO* 3.6 23.9 - - + +
379B ILE* 3.4 33.5 - - + +
381B TRP* 4.3 13.5 - + - -
388B LYS* 3.7 14.4 - - + -
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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