Contacts of the helix formed by residues 170 - 185 (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 ASP 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASN* 6.2 2.0 - - - +
73A GLN* 5.4 1.1 - - - +
125B MET* 5.4 2.4 - - - +
168B SER* 2.7 35.4 - - - -
169B ASP* 1.3 76.5 - - - +
171B HIS* 1.3 66.9 + - - +
172B GLU* 3.8 15.8 + - - +
173B GLY 3.0 8.4 + - - -
174B ARG* 3.3 24.3 + - - +
199B PRO* 3.7 21.0 - - + +
252B ARG* 5.3 3.3 + - - -
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Residues in contact with HIS 171 (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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70A ASN* 6.0 1.0 - - - +
72A ILE* 4.0 20.2 - - + -
73A GLN* 4.0 7.5 - - - +
76A LEU* 4.3 11.7 - - + -
126B SER* 3.8 13.4 - - - -
127B ILE* 3.5 52.3 + - + +
130B ASP* 3.7 17.8 + - + -
170B ASP* 1.3 75.9 - - - +
172B GLU* 1.3 60.1 + - - +
174B ARG* 3.5 16.9 + - + +
175B ALA* 2.9 35.5 + - + +
178B LYS* 6.1 2.7 - - - -
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Residues in contact with GLU 172 (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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125B MET* 3.4 24.9 - - + +
126B SER* 2.6 49.2 + - - -
127B ILE 4.5 0.3 + - - -
144B TYR* 3.3 28.0 - - + +
145B SER* 3.7 2.9 + - - -
168B SER* 5.5 0.7 - - - +
170B ASP* 3.4 15.0 + - - +
171B HIS* 1.3 79.9 + - - +
173B GLY* 1.3 64.8 + - - +
175B ALA* 3.4 12.9 + - - +
176B ALA* 3.5 5.5 + - - +
222B SER* 4.2 7.7 + - - +
252B ARG* 3.7 24.9 - - - +
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Residues in contact with GLY 173 (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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167B VAL* 3.5 14.4 - - - +
168B SER* 3.4 29.1 - - - -
170B ASP* 3.0 11.2 + - - -
172B GLU* 1.3 76.1 - - - +
174B ARG* 1.3 62.9 + - - +
176B ALA* 3.0 15.2 + - - +
177B GLN 3.2 7.4 + - - -
222B SER* 3.6 11.2 - - - -
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Residues in contact with ARG 174 (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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73A GLN* 3.0 33.1 + - - +
167B VAL* 4.3 0.8 - - + +
169B ASP* 3.2 53.9 + - - +
170B ASP* 3.3 13.5 + - - +
171B HIS* 3.5 19.9 - - + +
173B GLY* 1.3 73.6 - - - +
175B ALA* 1.3 53.3 + - - +
177B GLN* 3.6 24.4 - - - +
178B LYS* 2.7 64.0 + - - +
196B GLN* 4.6 6.7 - - - +
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Residues in contact with ALA 175 (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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126B SER* 3.9 24.9 - - - -
145B SER* 3.4 16.0 - - - -
171B HIS* 2.9 29.9 + - + +
172B GLU 3.5 7.2 - - - +
173B GLY 3.1 0.4 + - - -
174B ARG* 1.3 77.0 - - - +
176B ALA* 1.3 58.3 + - - +
178B LYS* 4.5 6.7 - - - +
179B ARG* 3.6 18.2 + - - +
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Residues in contact with ALA 176 (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 4.7 2.7 - - - +
145B SER* 4.0 26.2 - - - +
148B SER* 3.8 4.2 - - - -
151B TRP* 4.3 23.3 - - + -
165B LEU* 5.5 0.4 - - - +
167B VAL* 4.9 1.8 - - + -
172B GLU* 3.5 4.6 + - - +
173B GLY 3.0 8.7 + - - +
175B ALA* 1.3 77.3 - - - +
177B GLN* 1.3 60.4 + - - +
179B ARG* 4.0 1.1 - - - -
180B LEU* 3.2 28.9 + - - +
222B SER* 4.2 15.3 - - - +
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Residues in contact with GLN 177 (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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165B LEU* 3.9 12.6 - - + +
167B VAL* 3.5 24.5 - - + +
173B GLY 3.2 3.6 + - - -
174B ARG* 3.2 22.2 + - - +
176B ALA* 1.3 74.9 - - - +
178B LYS* 1.3 71.0 + - - +
179B ARG 3.1 1.1 - - - -
180B LEU* 3.3 1.4 + - - +
181B GLU* 3.0 50.8 + - - +
194B VAL* 3.6 26.1 - - + +
196B GLN* 3.2 23.6 + - - +
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Residues in contact with LYS 178 (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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171B HIS* 6.1 2.2 - - - -
174B ARG* 2.7 57.4 + - + +
175B ALA* 4.5 6.1 - - - +
177B GLN* 1.3 77.7 - - - +
179B ARG* 1.3 57.7 + - - +
181B GLU* 4.3 5.0 - - - +
182B THR* 2.8 28.1 + - - -
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Residues in contact with ARG 179 (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* 3.4 19.1 + - - +
146B HIS* 3.0 47.3 + - - +
148B SER* 3.2 13.9 + - - +
149B SER* 2.8 29.1 + - - -
175B ALA 3.6 17.4 + - - +
176B ALA 4.1 0.9 - - - +
177B GLN 3.1 0.8 - - - -
178B LYS* 1.3 75.8 - - - +
180B LEU* 1.3 66.0 + - - +
181B GLU 3.1 1.3 - - - -
182B THR* 3.0 17.7 + - - -
183B LEU* 3.2 22.1 + - + +
341B ASN* 5.5 1.2 - - - +
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Residues in contact with LEU 180 (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* 3.8 29.3 + - - +
151B TRP* 4.3 18.8 - - + -
152B PHE* 4.4 4.7 - - + +
155B MET* 4.3 8.7 - - - -
163B ILE* 3.9 21.3 - - + -
165B LEU* 3.8 33.7 - - + -
176B ALA 3.2 16.8 + - - +
177B GLN 4.0 2.0 - - - +
179B ARG* 1.3 79.2 - - - +
181B GLU* 1.3 57.8 + - - +
183B LEU* 3.3 7.3 + - - +
184B LEU* 3.0 48.1 + - + +
220B ILE* 4.0 7.0 - - + -
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Residues in contact with GLU 181 (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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165B LEU* 5.0 3.8 - - + -
177B GLN* 3.0 42.7 + - - +
178B LYS* 4.4 4.9 - - - +
180B LEU* 1.3 75.9 - - + +
182B THR* 1.3 63.5 + - - +
184B LEU* 3.7 8.7 - - + +
185B GLU* 3.2 30.6 + - - +
191B ALA* 3.3 31.0 - - + +
194B VAL* 3.4 17.9 - - - +
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Residues in contact with THR 182 (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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178B LYS 2.8 18.1 + - - -
179B ARG* 3.0 12.2 + - - -
181B GLU* 1.3 76.2 - - - +
183B LEU* 1.3 67.1 + - + +
185B GLU* 3.4 32.5 + - - +
186B GLU* 5.2 2.1 - - - +
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Residues in contact with LEU 183 (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 3.8 14.1 - - - +
149B SER* 4.1 17.7 - - - +
152B PHE* 3.2 66.1 - - + -
179B ARG* 3.2 24.1 + - + +
180B LEU* 3.7 7.9 - - - +
182B THR* 1.3 80.4 - - + +
184B LEU* 1.3 55.7 + - - +
185B GLU 3.0 13.0 - - - +
186B GLU* 3.9 5.1 - - - +
187B ARG* 4.1 0.3 - - - +
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Residues in contact with LEU 184 (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* 3.6 25.8 - - + -
155B MET* 3.7 26.9 - - + -
163B ILE* 4.8 4.5 - - + -
180B LEU* 3.0 40.0 + - + +
181B GLU* 3.8 12.1 - - + +
182B THR 3.2 0.2 - - - -
183B LEU* 1.3 73.8 - - - +
185B GLU* 1.3 64.4 + - - +
187B ARG* 3.4 10.9 + - - +
189B SER* 2.9 32.7 - - - +
190B LYS* 3.4 41.0 - - - +
191B ALA* 3.9 8.3 - - - +
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Residues in contact with GLU 185 (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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181B GLU* 3.2 20.8 + - - +
182B THR* 3.4 23.2 + - - +
183B LEU 3.0 9.4 - - - +
184B LEU* 1.3 75.9 - - - +
186B GLU* 1.3 76.7 + - + +
187B ARG 2.9 10.9 + - - -
190B LYS* 4.7 13.5 - - - +
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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