Contacts of the helix formed by residues 172 - 188 (chain B) in PDB entry 3U7X
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 ASN 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP* 2.7 34.2 + - - +
168B THR* 4.7 2.2 - - - +
169B GLU* 3.2 33.6 + - - +
170B CYS 4.9 0.4 - - - -
171B GLU* 1.3 73.6 - - - +
173B ARG* 1.3 65.2 + - - +
174B GLU 3.3 2.4 + - - -
175B ALA* 3.4 8.2 + - + +
176B VAL* 3.0 26.2 + - + +
220B SO4 3.8 10.7 + - - +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU 3.0 4.7 + - - +
172B ASN* 1.3 71.3 - - - +
174B GLU* 1.3 62.0 + - + +
176B VAL* 4.0 0.3 - - - +
177B THR* 3.0 44.9 + - + +
214B ARG 5.4 1.0 + - - -
215B PHE* 3.5 48.1 - - + -
220B SO4 2.9 24.3 + - - +
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 3.2 26.8 + - + +
173B ARG* 1.3 74.3 - - + +
175B ALA* 1.3 64.8 + - - +
177B THR* 2.9 20.0 + - - +
178B HIS* 2.9 14.6 + - - +
220B SO4 2.9 22.5 + - - +
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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
----------------------------------------------------------
145B TYR* 3.3 34.4 - - + -
148B ASP* 3.5 33.2 - - + +
172B ASN* 3.4 11.6 + - + +
174B GLU* 1.3 78.0 - - - +
176B VAL* 1.3 57.8 + - - +
178B HIS* 3.4 2.1 + - - +
179B ILE* 2.9 36.7 + - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 2.9 31.6 + - + +
148B ASP* 5.2 1.3 - - - +
167B THR* 4.0 17.5 - - - +
169B GLU 3.7 19.5 - - - +
170B CYS* 4.7 0.2 - - - -
172B ASN* 3.0 24.3 + - + +
173B ARG 4.0 2.7 - - - +
175B ALA* 1.3 77.6 - - + +
177B THR* 1.3 57.2 + - - +
179B ILE* 3.5 5.4 + - + +
180B GLY 3.0 11.3 + - - -
197B TYR* 3.6 29.8 - - + -
215B PHE* 3.5 33.7 - - + -
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 4.4 6.3 - - - -
173B ARG* 3.0 34.6 + - + +
174B GLU* 2.9 23.0 + - - +
176B VAL* 1.3 74.6 - - - +
178B HIS* 1.3 56.2 + - - +
180B GLY* 3.4 1.2 + - - -
181B ARG* 3.0 42.9 + - - +
215B PHE* 4.1 25.6 - - + -
216B VAL 5.9 0.9 - - - +
217B VAL* 4.1 6.5 - - + +
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Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PHE* 3.5 14.8 - - + -
143B ASP* 2.6 31.3 + - + +
145B TYR* 3.4 35.8 - + + -
174B GLU 2.9 18.7 + - - +
175B ALA 3.7 0.4 - - - +
177B THR* 1.3 74.4 + - - +
179B ILE* 1.3 65.1 + - - +
181B ARG* 3.4 11.6 + - - +
182B VAL* 3.2 44.2 + - + +
228B UNX 4.7 7.4 - - - -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 4.1 15.9 - - + +
142B PHE* 3.5 47.6 - - + -
145B TYR* 3.6 23.6 - - + +
148B ASP* 4.0 10.8 - - + -
149B VAL* 4.0 7.2 - - + -
165B ILE* 4.3 16.6 - - + -
167B THR* 3.9 21.8 - - + -
175B ALA 2.9 26.7 + - - +
176B VAL* 3.9 4.7 - - - +
178B HIS* 1.3 72.2 - - - +
180B GLY* 1.3 63.5 + - - +
183B TYR* 3.0 28.1 + - + +
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 3.3 38.3 - - - +
176B VAL 3.0 10.5 + - - -
177B THR 3.8 0.2 - - - -
179B ILE* 1.3 77.8 - - - +
181B ARG* 1.3 55.2 + - - +
183B TYR* 3.8 2.9 - - - +
184B LYS* 3.1 23.2 + - - +
195B ILE* 4.4 2.2 - - - +
217B VAL* 3.4 17.2 - - - +
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 3.0 28.8 + - - +
178B HIS* 4.0 10.9 + - - +
180B GLY* 1.3 73.7 - - - +
182B VAL* 1.3 65.9 + - + +
184B LYS* 3.6 4.4 + - - +
185B GLU* 3.1 23.4 + - - +
217B VAL* 3.8 21.5 - - + -
228B UNX 4.2 17.9 - - - -
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER* 3.5 25.1 - - - +
142B PHE* 3.6 17.3 - - + -
143B ASP* 4.7 1.6 - - - +
178B HIS* 3.2 42.7 + - + +
181B ARG* 1.3 71.9 - - - +
183B TYR* 1.3 61.7 + - - +
185B GLU* 3.1 7.5 + - - +
186B ARG* 2.8 42.6 + - + +
228B UNX 4.4 10.8 - - - -
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 4.4 20.2 - + + -
115B ILE* 4.0 25.2 - - + +
132B GLU* 5.4 0.4 - - + -
133B THR* 2.8 35.8 + - - +
136B CYS* 4.5 11.2 - - - -
142B PHE* 3.7 9.6 - - + -
163B ILE* 3.3 20.4 - - - +
165B ILE* 3.6 41.9 + - + +
179B ILE* 3.0 20.1 + - + +
180B GLY 3.8 2.5 - - - +
182B VAL* 1.3 77.3 - - - +
184B LYS* 1.3 53.2 + - - +
186B ARG* 3.1 5.3 + - - -
187B LEU* 2.8 59.2 + - + +
195B ILE* 4.7 4.0 - - + -
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLY 3.1 16.6 + - - +
181B ARG* 3.8 5.2 - - - +
183B TYR* 1.3 78.3 - - - +
185B GLU* 1.3 61.6 + - - +
187B LEU* 3.5 9.6 + - - +
188B GLY 3.2 16.5 + - - -
189B LEU* 3.4 27.9 + - + +
190B PRO 3.9 10.8 - - - -
191B PRO* 2.7 35.6 + - - -
193B ILE 2.8 22.7 + - - +
194B VAL* 4.3 1.4 - - - +
195B ILE* 4.4 7.6 - - + -
217B VAL* 2.7 44.7 + - + +
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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 ARG 3.1 16.9 + - - +
182B VAL* 3.1 7.9 + - - +
184B LYS* 1.3 75.0 - - - +
186B ARG* 1.3 64.3 + - + +
188B GLY* 3.2 14.6 + - - -
189B LEU 5.9 0.4 - - - -
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Residues in contact with ARG 186 (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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132B GLU* 2.9 45.1 + - + +
135B LEU* 4.3 5.3 + - - +
136B CYS* 3.8 33.0 - - - +
141B SER* 3.1 33.6 + - - -
182B VAL* 2.8 29.9 + - + +
183B TYR* 3.6 3.6 - - + +
185B GLU* 1.3 78.2 - - + +
187B LEU* 1.3 63.5 + - - +
188B GLY* 3.4 0.7 + - - -
54D TYR 5.4 0.8 + - - -
55D ASP* 5.1 5.3 - - - +
56D ARG* 3.8 33.4 - - - +
59D LEU* 5.6 0.2 - - - +
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Residues in contact with LEU 187 (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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115B ILE* 3.6 34.3 - - + -
128B ARG* 5.0 7.1 + - - -
129B PHE* 3.5 64.9 - - + +
132B GLU* 4.3 8.1 - - + -
133B THR* 4.2 0.9 - - - +
183B TYR* 2.8 50.6 + - + +
184B LYS* 3.7 6.5 - - - +
186B ARG* 1.3 72.5 - - - +
188B GLY* 1.3 60.7 + - - +
189B LEU* 3.9 22.0 - - + -
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Residues in contact with GLY 188 (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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129B PHE* 5.7 0.2 - - - -
184B LYS 3.2 1.8 + - - -
185B GLU* 3.2 18.2 + - - -
186B ARG 3.2 0.6 - - - -
187B LEU* 1.3 77.5 - - - +
189B LEU* 1.3 66.4 + - - +
190B PRO* 3.5 4.3 - - - +
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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
------------------------------------------------------------
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