Contacts of the helix formed by residues 177 - 194 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLY 4.0 1.0 + - - -
164A PHE* 3.8 15.5 - - - +
165A LEU 4.8 5.3 + - - -
175A ASP 4.0 0.2 + - - -
176A LEU* 1.3 73.1 - - - +
178A ALA* 1.3 66.2 + - - +
179A GLY 3.1 3.1 - - - -
180A LEU* 3.0 29.8 + - + -
181A LEU* 3.0 11.4 + - + +
304A LEU 4.4 0.3 - - - +
305A PRO* 3.2 12.1 - - - +
306A VAL* 2.8 51.5 + - - +
308A ASP* 2.9 29.7 + - - +
311A LEU* 4.9 3.4 - - + -
312A VAL* 3.9 8.5 - - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 4.9 4.5 - - - -
64A ARG 4.1 8.5 - - - +
158A ARG* 3.9 27.9 + - - +
162A LEU 4.3 4.3 - - - +
163A GLY* 3.0 15.0 + - - +
175A ASP 4.0 12.5 + - - +
176A LEU 3.1 5.1 + - - -
177A ASN* 1.3 75.7 - - - +
179A GLY* 1.3 57.2 + - - +
181A LEU* 3.1 12.1 + - - +
182A ASP* 2.8 33.6 + - - +
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 3.5 12.3 - - - +
158A ARG 3.3 27.4 - - - -
163A GLY* 2.9 11.9 + - - -
164A PHE* 3.7 9.6 - - - -
177A ASN 3.1 0.4 - - - -
178A ALA* 1.3 76.8 - - - +
180A LEU* 1.3 59.5 + - - +
182A ASP* 3.3 24.6 - - - +
183A GLN* 3.3 7.4 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 4.2 7.0 - - + -
164A PHE* 3.7 11.7 - - + -
177A ASN* 3.0 16.8 + - + +
179A GLY* 1.3 73.0 - - - +
181A LEU* 1.3 61.5 + - - +
183A GLN* 3.0 19.2 + - - +
184A ARG* 2.9 30.0 + - - +
215A SER* 3.5 31.9 - - - +
218A TYR* 3.7 37.5 - - + -
219A HIS* 4.3 4.1 - - + +
305A PRO* 4.2 14.6 - - + -
311A LEU* 3.8 14.6 - - + -
312A VAL* 4.3 14.8 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.9 14.4 - - + -
66A PRO* 3.5 20.1 - - + +
175A ASP* 3.8 24.2 - - + +
176A LEU 3.6 18.8 - - - +
177A ASN 3.0 14.2 + - - +
178A ALA* 3.1 8.5 + - - +
180A LEU* 1.3 71.9 - - - +
182A ASP* 1.3 66.1 + - - +
184A ARG* 3.2 10.3 + - + +
185A LYS 2.9 18.7 + - - -
223A TYR* 4.5 14.1 - - - +
308A ASP* 5.7 1.1 - - - +
311A LEU* 4.0 23.1 - - + -
2901A SO4 5.1 0.4 - - - +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.3 25.7 - - - +
66A PRO* 3.4 17.0 - - - +
102A LEU* 3.5 11.5 - - - +
157A TYR* 3.7 6.7 - - + -
158A ARG* 2.8 65.3 + - - +
178A ALA 2.8 14.5 + - - +
179A GLY 3.3 8.7 - - - +
181A LEU* 1.3 77.2 - - - +
183A GLN* 1.3 62.8 + - - +
185A LYS* 3.1 2.3 + - - -
186A ALA* 2.9 19.2 + - - +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 3.6 12.5 - - - +
129A TYR* 4.9 0.4 - - - -
155A PHE* 3.8 26.9 - - + -
157A TYR* 3.5 35.8 - - + -
179A GLY 3.3 9.0 + - - +
180A LEU* 3.0 20.2 + - - +
182A ASP* 1.3 77.6 - - - +
184A ARG* 1.3 56.5 + - - +
186A ALA* 3.2 2.3 + - - +
187A LEU* 2.9 33.7 + - + +
215A SER* 3.0 33.1 + - - -
219A HIS* 2.8 29.5 + - - +
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU 2.9 18.2 + - - +
181A LEU* 3.2 16.6 + - + +
183A GLN* 1.3 74.7 - - - +
185A LYS* 1.3 62.7 + - - +
187A LEU* 3.3 12.9 + - - +
188A ARG* 3.0 29.1 + - - +
219A HIS* 3.1 42.0 + - - +
222A ALA* 3.5 24.1 - - - +
223A TYR* 3.8 9.5 - - - -
228A GLU* 4.3 10.5 - - - +
230A LEU* 3.9 19.9 - - - +
231A PHE* 5.0 2.2 - - - -
311A LEU* 3.8 20.0 - - + +
326A ILE* 6.2 0.2 - - - +
2901A SO4 2.8 51.2 + - - +
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.7 25.8 - - + +
54A ALA* 4.4 0.2 - - + -
66A PRO* 3.6 28.8 + - + +
67A GLN* 3.9 7.5 - - - +
68A ASP* 2.7 47.8 + - - +
69A PRO* 5.0 0.9 - - - -
181A LEU 2.9 12.9 + - - +
182A ASP 3.1 8.7 + - - +
184A ARG* 1.3 77.2 - - - +
186A ALA* 1.3 56.8 + - - +
188A ARG* 3.3 8.1 + - + +
189A TRP* 2.8 28.1 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.6 17.4 - - + -
104A ILE* 4.2 6.9 - - + +
122A LEU* 5.1 0.7 - - - -
155A PHE* 3.5 43.5 - - + -
182A ASP 2.9 9.1 + - - +
183A GLN 3.2 7.4 + - - +
185A LYS* 1.3 73.9 - - - +
187A LEU* 1.3 65.7 + - - +
189A TRP* 3.1 6.3 + - - +
190A VAL* 3.0 29.1 + - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.6 28.7 - - + +
124A ILE* 4.4 16.8 - - + -
155A PHE* 4.9 4.9 - - + -
183A GLN 2.9 22.1 + - - +
184A ARG* 3.6 11.0 - - - +
186A ALA* 1.3 72.5 - - - +
188A ARG* 1.3 58.8 + - - +
190A VAL* 3.4 3.3 + - - +
191A LYS* 3.1 26.3 + - - +
204A ILE* 5.2 0.5 - - - +
206A ILE* 4.3 11.0 - - + -
219A HIS* 3.9 25.4 - - + +
230A LEU* 4.2 28.7 - - + +
231A PHE* 3.9 29.8 - - + -
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ARG 3.0 21.6 + - - +
185A LYS* 3.7 7.9 - - + +
187A LEU* 1.3 72.6 - - - +
189A TRP* 1.3 60.6 + - - +
191A LYS* 3.4 7.0 + - - +
192A GLN* 2.9 32.4 + - - +
228A GLU* 3.4 36.6 + - - +
230A LEU* 4.0 26.7 - - + +
2901A SO4 2.8 42.5 + - - -
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Residues in contact with TRP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.5 20.6 - - + -
33A TYR* 3.0 23.9 + + - -
51A MET* 3.8 28.7 - - + -
52A ARG 3.8 2.8 + - - -
53A TYR* 3.5 31.0 - - + +
69A PRO* 5.1 2.7 - - + -
104A ILE* 3.5 38.6 - - + -
106A VAL* 4.1 12.1 - - + -
185A LYS 2.8 14.7 + - - +
186A ALA* 3.1 8.3 + - - +
188A ARG* 1.3 76.6 - - - +
190A VAL* 1.3 68.2 + - + +
192A GLN* 3.3 1.7 + - - -
193A TYR* 2.8 67.1 + + + +
194A ILE* 4.8 4.3 - - + -
197A PHE* 3.8 17.3 - + - -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 3.9 20.9 - - + -
120A VAL* 4.1 14.1 - - + -
122A LEU* 3.9 19.3 - - + -
153A VAL* 3.9 15.7 - - + -
186A ALA 3.0 13.7 + - - +
187A LEU 3.7 6.5 - - - +
189A TRP* 1.3 78.8 - - + +
191A LYS* 1.3 66.7 - - - +
194A ILE* 2.9 52.9 + - + +
204A ILE* 3.8 18.6 - - + -
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU 3.1 15.1 + - - +
188A ARG* 3.6 7.6 - - - +
189A TRP 3.3 0.2 - - - -
190A VAL* 1.3 77.9 - - - +
192A GLN* 1.3 61.3 + - - +
194A ILE 4.6 0.5 + - - -
195A GLU* 5.5 0.7 + - - +
201A PRO* 3.0 47.4 + - + +
202A ASP* 3.2 20.3 + - - +
204A ILE* 4.1 11.6 - - + +
228A GLU 5.4 1.6 - - - -
229A GLY* 2.7 32.8 + - - +
230A LEU* 4.0 18.4 - - + -
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Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG 2.9 18.3 + - - +
189A TRP* 3.9 3.1 - - - +
191A LYS* 1.3 79.9 - - - +
193A TYR* 1.3 103.1 + - + +
195A GLU* 5.2 4.1 + - - +
196A GLN* 6.0 0.3 - - - +
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Residues in contact with TYR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.4 49.1 + - + -
33A TYR* 3.4 24.1 - + - +
69A PRO* 5.9 2.4 - - + +
189A TRP* 2.8 66.3 + + + +
192A GLN* 1.3 117.0 + - + +
194A ILE* 1.3 63.9 + - - +
195A GLU* 3.1 4.0 - - - -
196A GLN* 3.0 27.6 + - + +
197A PHE* 3.6 5.5 - - - -
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Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 4.0 20.2 - - + -
120A VAL* 3.9 29.8 - - + -
151A VAL* 4.0 12.8 - - + -
153A VAL* 3.8 26.0 - - + -
189A TRP* 4.2 6.0 + - + -
190A VAL* 2.9 44.4 + - + +
191A LYS 4.6 0.2 + - - -
192A GLN 3.9 0.2 - - - -
193A TYR* 1.3 72.2 - - - +
195A GLU* 1.3 64.6 + - - +
197A PHE* 2.9 19.0 + - + -
199A GLY* 2.9 21.4 + - - -
201A PRO* 4.0 24.2 - - + -
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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
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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