Contacts of the helix formed by residues 177 - 194 (chain B) in PDB entry 1UKC
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 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLY 4.1 1.0 + - - -
164B PHE* 3.9 13.2 - - - +
165B LEU 4.8 5.3 + - - -
166B ALA* 6.2 0.4 - - - +
175B ASP 4.0 0.2 + - - -
176B LEU* 1.3 71.6 - - - +
178B ALA* 1.3 66.5 + - - +
179B GLY 3.2 3.6 - - - -
180B LEU* 2.9 31.1 + - + +
181B LEU* 3.0 11.1 + - - +
304B LEU 4.4 0.2 - - - +
305B PRO* 3.2 13.0 - - - +
306B VAL* 2.8 51.4 + - - +
308B ASP* 2.9 30.9 + - - +
311B LEU* 4.8 3.8 - - + -
312B VAL* 3.8 7.3 - - - +
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B PHE* 4.8 4.7 - - - -
64B ARG 4.1 9.0 - - - +
158B ARG* 3.9 27.0 + - - +
162B LEU 4.4 3.6 - - - +
163B GLY 3.1 14.4 + - - +
175B ASP 3.9 13.4 + - - +
176B LEU 3.1 4.0 + - - -
177B ASN* 1.3 75.3 - - - +
179B GLY* 1.3 57.2 + - - +
181B LEU* 3.0 11.8 + - - +
182B ASP* 2.9 33.3 + - - +
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B TYR* 3.6 6.9 - - - +
158B ARG* 3.3 26.7 - - - -
163B GLY* 2.9 11.9 + - - -
164B PHE* 3.8 10.1 - - - -
177B ASN 3.2 0.2 - - - -
178B ALA* 1.3 76.3 - - - +
180B LEU* 1.3 61.2 + - - +
182B ASP* 3.4 22.8 - - - +
183B GLN* 3.4 13.3 + - - +
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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
----------------------------------------------------------
129B TYR* 4.3 7.6 - - + -
164B PHE* 3.8 12.1 - - + -
177B ASN* 2.9 19.3 + - + +
179B GLY* 1.3 74.1 - - - +
181B LEU* 1.3 59.5 + - - +
183B GLN* 3.1 18.1 + - - +
184B ARG* 3.0 31.1 + - - +
215B SER* 3.6 30.5 - - - +
218B TYR* 3.7 37.0 - - + -
219B HIS* 4.3 4.2 - - + +
305B PRO* 4.1 18.4 - - + -
311B LEU* 3.8 14.1 - - + -
312B VAL* 4.3 11.2 - - + -
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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
----------------------------------------------------------
65B ALA* 4.0 12.8 - - + -
66B PRO* 3.6 21.3 - - + +
175B ASP* 3.7 24.2 - - + +
176B LEU 3.6 19.3 - - - +
177B ASN 3.0 12.9 + - - +
178B ALA* 3.0 9.2 + - - +
180B LEU* 1.3 75.2 - - - +
182B ASP* 1.3 63.8 + - - +
184B ARG* 3.2 11.9 + - + +
185B LYS 3.0 18.5 + - - -
223B TYR* 4.5 13.2 - - - +
311B LEU* 4.0 22.7 - - + -
2951B SO4 5.1 0.7 - - - +
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Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.2 27.6 + - - +
66B PRO* 3.4 17.1 - - - +
102B LEU* 3.7 11.6 - - - +
157B TYR* 3.7 6.5 - - + -
158B ARG* 2.8 65.8 + - - +
178B ALA 2.9 14.5 + - - +
179B GLY* 3.4 9.3 - - - +
181B LEU* 1.3 75.8 - - - +
183B GLN* 1.3 57.2 + - - +
185B LYS* 3.2 1.7 + - - -
186B ALA* 2.9 24.1 + - - +
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Residues in contact with GLN 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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124B ILE* 3.6 11.8 - - - +
129B TYR* 5.0 0.2 - - - -
155B PHE* 3.8 28.5 - - + -
157B TYR* 3.5 36.2 - - + -
164B PHE* 5.8 0.2 - - - -
179B GLY 3.4 9.0 + - - +
180B LEU* 3.1 21.2 + - - +
182B ASP* 1.3 72.9 - - - +
184B ARG* 1.3 60.9 + - - +
186B ALA* 3.2 0.9 + - - +
187B LEU* 2.8 34.5 + - - +
215B SER* 2.9 34.3 + - - -
219B HIS* 2.7 36.7 + - - +
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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
----------------------------------------------------------
180B LEU 3.0 18.0 + - - +
181B LEU* 3.5 16.8 - - + +
183B GLN* 1.3 77.0 - - - +
185B LYS* 1.3 56.6 + - - +
187B LEU* 3.4 8.3 + - - +
188B ARG* 2.9 34.6 + - - +
219B HIS* 3.2 42.6 + - - +
222B ALA* 3.5 25.5 - - - +
223B TYR* 3.8 10.1 - - - -
226B LYS 5.9 0.2 + - - -
228B GLU* 4.4 10.1 - - - +
230B LEU* 4.0 24.1 - - + +
231B PHE* 5.0 2.2 - - - -
311B LEU* 3.8 19.3 - - + +
2951B SO4 2.9 50.5 + - - +
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.8 25.1 - - + +
54B ALA* 4.5 0.9 - - + -
66B PRO* 3.7 28.3 + - + +
67B GLN* 4.0 6.7 - - - +
68B ASP* 2.9 47.5 + - - +
69B PRO* 5.0 0.7 - - - -
181B LEU 3.0 12.7 + - - +
182B ASP 3.2 8.9 + - - +
184B ARG* 1.3 76.5 - - - +
186B ALA* 1.3 51.2 + - - +
188B ARG* 3.2 9.2 + - + +
189B TRP* 2.8 34.5 + - - +
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.7 18.3 - - + -
104B ILE* 4.2 5.0 - - + +
122B LEU* 5.2 0.7 - - - -
155B PHE* 3.6 42.0 - - + -
182B ASP 2.9 12.0 + - - +
183B GLN 3.2 7.2 + - - +
185B LYS* 1.3 76.3 - - - +
187B LEU* 1.3 61.9 + - - +
189B TRP* 3.2 6.2 + - - +
190B VAL* 3.0 28.3 + - - +
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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
----------------------------------------------------------
122B LEU* 3.7 30.0 - - + +
124B ILE* 4.4 15.7 - - + -
155B PHE* 4.7 6.3 - - + -
183B GLN 2.8 28.1 + - - +
184B ARG* 3.6 7.4 - - - +
186B ALA* 1.3 71.9 - - - +
188B ARG* 1.3 58.1 + - - +
190B VAL* 3.4 3.8 + - - +
191B LYS* 3.0 26.5 + - - +
204B ILE* 5.2 0.3 - - - +
206B ILE* 4.2 11.7 - - + -
219B HIS* 3.9 30.3 - - + +
230B LEU* 4.3 27.3 - - + +
231B PHE* 4.0 25.1 - - + -
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Residues in contact with ARG 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG 2.9 18.0 + - - +
185B LYS* 3.6 9.4 - - + +
187B LEU* 1.3 74.3 - - - +
189B TRP* 1.3 58.2 + - - +
191B LYS* 3.3 6.8 + - + +
192B GLN* 2.9 32.3 + - - +
228B GLU* 3.8 31.9 + - - +
230B LEU* 3.9 27.5 - - + +
2951B SO4 2.7 44.8 + - - -
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Residues in contact with TRP 189 (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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31B LEU* 3.7 22.0 - - + -
33B TYR* 2.9 24.1 + + - -
51B MET* 3.7 20.6 - - + -
52B ARG 3.9 3.0 + - - -
53B TYR* 3.6 32.5 - - + +
69B PRO* 5.1 2.7 - - + -
104B ILE* 3.6 37.0 - - + -
106B VAL* 4.1 13.5 - - + -
185B LYS 2.8 17.7 + - - +
186B ALA* 3.2 8.5 + - - +
188B ARG* 1.3 69.7 - - - +
190B VAL* 1.3 71.3 + - + +
192B GLN* 3.2 2.1 + - - -
193B TYR* 2.8 66.2 + + + +
194B ILE* 4.8 4.7 - - + -
197B PHE* 3.7 24.0 - + - -
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Residues in contact with VAL 190 (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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104B ILE* 3.9 20.4 - - + -
120B VAL* 4.2 15.0 - - + -
122B LEU* 3.9 22.2 - - + -
153B VAL* 4.0 13.7 - - + -
186B ALA 3.0 18.4 + - - +
187B LEU 3.7 7.2 - - - +
189B TRP* 1.3 82.2 - - + +
191B LYS* 1.3 62.4 + - - +
194B ILE* 3.0 49.0 + - + +
204B ILE* 3.6 22.0 - - + -
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Residues in contact with LYS 191 (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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187B LEU 3.0 17.6 + - - +
188B ARG* 3.6 5.8 - - - +
189B TRP 3.3 0.2 - - - -
190B VAL* 1.3 77.5 - - - +
192B GLN* 1.3 61.6 + - - +
194B ILE 4.8 0.2 + - - -
195B GLU* 5.7 0.5 + - - +
201B PRO* 3.0 47.4 + - + +
202B ASP* 3.1 21.3 + - - +
204B ILE* 4.2 10.3 - - + +
228B GLU 5.5 1.1 - - - -
229B GLY* 2.7 32.0 + - - +
230B LEU* 4.0 19.7 - - + -
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Residues in contact with GLN 192 (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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188B ARG 2.9 17.5 + - - +
189B TRP* 3.8 3.8 - - - +
191B LYS* 1.3 79.4 - - - +
193B TYR* 1.3 100.1 + - + +
195B GLU* 5.3 4.4 + - - +
196B GLN* 6.0 0.2 - - - +
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Residues in contact with TYR 193 (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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31B LEU* 3.4 45.8 - - + -
33B TYR* 3.5 24.9 + + - +
69B PRO* 5.9 2.1 - - + +
189B TRP* 2.8 68.8 + + + +
192B GLN* 1.3 116.0 + - + +
194B ILE* 1.3 64.2 + - - +
195B GLU* 3.1 4.0 - - - -
196B GLN* 3.0 26.5 + - + +
197B PHE* 3.5 6.5 - - - -
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Residues in contact with ILE 194 (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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106B VAL* 4.0 20.2 - - + -
120B VAL* 3.9 29.6 - - + -
151B VAL* 3.9 15.7 - - + -
153B VAL* 3.7 26.7 - - + -
189B TRP* 4.8 4.9 - - + -
190B VAL* 3.0 39.5 + - + +
191B LYS 4.8 0.2 + - - -
192B GLN 3.9 0.2 - - - -
193B TYR* 1.3 77.1 - - - +
195B GLU* 1.3 60.2 + - - +
197B PHE* 2.8 25.7 + - + -
199B GLY* 3.1 16.6 + - - -
201B PRO* 4.0 26.2 - - + -
204B ILE* 4.7 0.2 - - + -
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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
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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