Contacts of the helix formed by residues 168 - 185 (chain B) in PDB entry 5U07
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 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ARG 3.9 0.2 + - - -
167B GLN* 1.3 72.2 - - - +
169B LEU* 1.3 66.2 + - - +
170B ASP* 3.4 9.5 + - - +
171B GLY* 2.6 34.4 + - - -
172B VAL* 3.0 26.3 + - - +
202B TRP* 4.5 3.6 - - - -
206B PRO* 5.6 3.8 - - - -
33F LYS* 4.7 21.4 - - - +
34F GLU* 5.7 6.8 + - + +
196F GLY 6.3 1.0 - - - -
198F THR* 4.1 17.1 - - - +
307G SER* 6.1 0.9 - - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 4.6 23.3 - - + +
79B ARG* 4.2 23.3 - - + -
168B ASN* 1.3 76.2 - - - +
170B ASP* 1.3 62.3 - - + +
172B VAL* 3.1 6.8 - - - +
173B HIS* 2.9 46.4 - - + +
199B LEU 3.9 9.2 - - - +
202B TRP* 3.6 37.8 + - + +
203B GLY* 4.7 4.7 - - - +
206B PRO* 5.8 1.0 - - - +
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 4.7 15.3 + - - +
168B ASN* 3.2 10.9 + - - +
169B LEU* 1.3 84.3 - - + +
171B GLY* 1.3 62.8 + - - +
172B VAL 3.4 0.2 - - - -
173B HIS* 3.8 5.0 + - - +
174B ARG* 3.3 27.6 + - - +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLN* 3.4 21.8 - - - -
168B ASN* 2.6 23.7 + - - -
170B ASP* 1.3 74.0 - - - +
172B VAL* 1.3 64.2 + - - +
174B ARG* 3.0 26.5 - - - +
175B HIS* 3.0 16.5 + - - +
198F THR* 4.6 1.6 - - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 4.4 12.6 - - + +
167B GLN* 3.9 10.3 - - + -
168B ASN 3.0 13.0 + - - +
169B LEU* 3.1 21.3 - - + +
171B GLY* 1.3 77.7 - - - +
173B HIS* 1.3 68.1 + - + +
175B HIS* 5.1 0.2 - - - -
176B LEU* 2.5 44.2 + - + +
199B LEU* 4.3 7.2 - - + -
202B TRP* 3.3 57.2 - - + +
213B TRP* 6.1 0.4 - - + -
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Residues in contact with HIS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 5.7 4.5 - - - +
79B ARG* 3.4 46.8 + - + +
80B ALA* 3.5 30.3 - - - -
83B ALA* 3.0 22.5 - - + +
169B LEU* 2.9 41.1 - - + +
170B ASP 3.8 5.3 + - - +
171B GLY 3.2 0.6 - - - -
172B VAL* 1.3 85.4 - - + +
174B ARG* 1.3 56.2 + - - +
176B LEU* 4.4 4.5 - - - -
177B PRO* 3.2 18.3 - - - +
199B LEU* 3.6 24.6 - - + +
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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
----------------------------------------------------------
79B ARG* 6.1 0.7 - - - +
170B ASP* 3.3 24.3 + - - +
171B GLY* 3.0 25.4 - - - +
173B HIS* 1.3 78.9 - - - +
175B HIS* 1.3 72.3 + - + +
176B LEU 3.5 0.2 - - - -
177B PRO* 3.6 12.4 - - - +
178B ARG* 5.6 1.4 - - - +
29E VAL* 3.0 50.4 - - + +
198F THR* 2.9 36.4 + - - +
200F GLU* 4.8 5.3 + - - +
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Residues in contact with HIS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ARG* 4.9 0.3 - - - -
163B LEU* 3.6 29.6 - - + +
164B ILE* 4.0 16.3 - - + +
167B GLN* 3.0 43.2 + - + -
171B GLY 3.0 15.0 + - - +
172B VAL 4.5 0.7 - - - +
174B ARG* 1.3 89.2 + - + +
176B LEU* 1.3 64.8 + - - +
177B PRO* 3.5 1.3 - - - -
178B ARG* 3.3 40.2 + - - +
179B LEU* 4.3 0.9 + - - +
198F THR* 4.0 7.7 + - - -
199F VAL 3.7 19.3 + - - -
200F GLU* 4.4 15.0 - - + -
201F VAL 5.0 1.1 - - - -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.8 13.2 - - + -
139B LEU* 4.8 0.4 - - + -
164B ILE* 4.1 15.0 - - + +
172B VAL* 2.5 24.0 + - + +
173B HIS* 4.4 3.4 - - - -
175B HIS* 1.3 76.4 - - - +
177B PRO* 1.3 67.6 - - + +
178B ARG 3.1 1.0 + - - -
179B LEU* 3.2 14.9 + - + +
180B VAL* 2.9 69.0 + - + +
195B LEU* 4.8 8.7 - - + -
199B LEU* 4.7 21.3 - - + -
213B TRP* 4.3 25.6 - - + -
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Residues in contact with PRO 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.1 18.8 - - + -
87B ILE* 3.3 26.9 - - + -
173B HIS 3.2 24.7 - - - +
174B ARG* 3.6 11.9 - - - +
175B HIS 3.5 2.7 - - - -
176B LEU* 1.3 91.6 - - + +
178B ARG* 1.3 64.3 + - + +
181B LEU* 2.9 35.3 + - + +
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ARG* 3.4 24.3 - - - +
163B LEU* 3.2 41.8 - - - +
174B ARG 5.6 1.1 - - - +
175B HIS* 3.3 33.0 + - - +
177B PRO* 1.3 79.5 - - + +
179B LEU* 1.3 72.7 + - - +
181B LEU* 4.9 2.7 - - - -
182B TYR* 2.9 52.2 + - + +
20E ASP* 3.3 30.2 + - - -
22E LEU* 3.8 4.3 - - + -
24E SER* 4.5 8.7 - - - +
201F VAL 4.3 12.5 + - - -
203F PHE* 4.1 11.9 - - - -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.3 7.0 - - + -
143B LEU* 4.2 22.5 - - + +
157B THR* 5.5 2.0 - - + -
160B ARG* 3.4 29.4 - - + +
161B LEU* 3.8 24.9 - - + -
164B ILE* 3.3 31.9 - - + -
175B HIS 4.7 0.2 - - - +
176B LEU* 3.2 12.8 + - + +
178B ARG* 1.3 83.3 - - - +
180B VAL* 1.3 90.2 + - + +
183B LEU* 2.8 32.1 + - + +
22E LEU* 3.9 10.0 - - + +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.3 32.3 - - + -
91B GLN* 3.9 0.6 + - - -
139B LEU* 3.7 19.5 - - + -
176B LEU* 2.9 38.5 + - + +
177B PRO 3.5 0.7 - - - +
179B LEU* 1.3 94.0 - - + +
181B LEU* 1.3 58.7 + - - +
183B LEU* 3.3 12.1 + - + +
184B ARG* 2.9 28.6 + - - +
190B ILE* 4.9 4.3 - - + -
195B LEU* 4.1 9.6 - - + -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 6.2 2.5 - - + -
87B ILE* 4.9 7.2 - - + -
90B ALA* 4.7 9.9 - - + +
91B GLN* 3.0 39.4 + - - +
92B PRO* 4.4 14.8 - - + -
177B PRO* 2.9 26.4 + - + +
178B ARG* 4.9 1.1 - - - -
180B VAL* 1.3 79.8 - - + +
182B TYR* 1.3 75.1 + - + +
185B SER* 3.0 24.9 + - - +
201E VAL* 6.2 0.2 - - + -
223E ALA* 5.5 1.1 - - + -
225E GLN* 4.0 27.4 - - + +
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Residues in contact with TYR 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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152B LEU* 5.3 3.4 - - - +
178B ARG* 2.9 31.6 + - + +
179B LEU 4.2 0.4 - - - +
181B LEU* 1.3 89.4 - - + +
183B LEU* 1.3 61.1 + - - +
185B SER* 2.9 35.1 - - - +
186B ASP* 5.3 1.0 - - - +
22E LEU* 3.0 64.4 - - + -
24E SER* 3.5 27.1 + - - -
223E ALA 5.2 2.2 - - - -
225E GLN* 2.3 54.8 + - - +
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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
----------------------------------------------------------
139B LEU* 5.6 0.9 - - + -
142B SER* 4.4 4.3 - - - +
143B LEU* 3.6 41.3 - - + +
146B ALA* 4.5 2.7 - - + -
152B LEU* 5.1 9.6 - - + -
179B LEU* 2.8 22.1 + - + +
180B VAL* 3.4 20.9 - - + +
182B TYR* 1.3 74.7 - - - +
184B ARG* 1.3 63.2 + - - +
185B SER 2.7 17.5 - - - +
188B VAL* 3.0 48.1 - - + +
190B ILE* 3.9 40.4 - - + -
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 3.0 30.2 - - + +
95B ALA* 2.6 52.7 + - + +
96B ARG* 4.4 6.5 - - - +
180B VAL 2.9 11.4 + - - +
183B LEU* 1.3 77.1 - - + +
185B SER* 1.3 63.6 + - - +
187B GLN* 3.1 32.1 + - - +
188B VAL 3.7 14.2 + - - +
189B HIS* 4.5 7.7 - - - +
190B ILE* 3.6 36.1 + - + +
192B TRP* 3.1 40.0 - - - +
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 4.5 0.2 - - - +
92B PRO* 4.5 14.5 - - - +
95B ALA* 5.2 2.9 - - - -
152B LEU* 5.7 1.0 - - - +
181B LEU* 3.0 21.9 + - - +
182B TYR* 2.9 32.6 - - - +
183B LEU* 2.7 20.3 - - - +
184B ARG* 1.3 76.3 - - - +
186B ASP* 1.3 71.9 + - - +
188B VAL* 4.3 0.5 - - - +
222E ASN* 5.9 3.4 - - - +
223E ALA* 5.3 6.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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