Contacts of the helix formed by residues 180 - 199 (chain A) in PDB entry 1U1H
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 LEU 180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.6 36.1 - - + -
125A GLY 4.2 14.4 - - - +
126A PRO* 4.7 4.7 - - + -
130A PHE* 4.1 21.1 - - + -
162A LEU* 4.0 10.1 - - + -
175A PHE* 3.7 30.5 - - + -
177A LEU* 2.8 17.1 + - - +
179A SER* 1.3 79.3 - - - +
181A LEU* 1.3 55.9 + - - +
182A PRO* 3.1 4.0 - - - -
183A LYS* 2.7 48.2 + - + +
184A ILE* 3.3 9.6 + - + +
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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
----------------------------------------------------------
158A PRO* 4.4 11.2 - - + -
159A VAL* 4.5 4.3 - - + +
162A LEU* 3.7 22.8 - - + +
178A LEU* 3.6 17.0 + - + +
179A SER 3.4 0.4 - - - -
180A LEU* 1.3 75.6 - - - +
182A PRO* 1.3 69.6 - - + +
183A LYS 3.0 1.4 + - - -
184A ILE* 3.9 10.3 - - + -
185A LEU* 3.0 61.6 + - + +
221A ALA* 3.9 35.9 - - + +
224A GLY 5.8 0.2 - - - -
225A ALA* 4.3 11.4 - - + +
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Residues in contact with PRO 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU 4.8 0.7 - - - +
179A SER 3.3 15.3 - - - +
180A LEU 3.2 4.7 - - - -
181A LEU* 1.3 95.4 - - + +
183A LYS* 1.3 60.0 + - + +
185A LEU* 5.0 3.8 - - + -
186A PRO* 3.2 23.1 - - + +
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Residues in contact with LYS 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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126A PRO* 3.1 30.9 + - - +
128A VAL 4.2 8.5 + - - +
129A ASN* 6.1 0.4 - - - -
130A PHE* 3.6 40.9 - - + +
179A SER 5.9 0.4 - - - +
180A LEU* 2.7 30.7 + - + +
182A PRO* 1.3 78.8 - - + +
184A ILE* 1.3 60.6 + - - +
186A PRO* 3.6 8.3 - - - +
187A ILE* 4.1 8.0 - - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.0 20.4 - - + -
130A PHE* 3.7 42.2 - - + -
158A PRO* 3.7 20.9 - - + +
161A TYR* 4.5 5.4 - - + -
162A LEU* 3.5 41.1 - - + -
180A LEU 3.3 6.0 + - - +
181A LEU* 3.6 16.2 - - + +
183A LYS* 1.3 74.4 - - - +
185A LEU* 1.3 70.3 + - + +
186A PRO* 3.3 2.9 - - - -
187A ILE* 3.0 16.5 + - - +
188A TYR* 3.1 19.0 + - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.6 35.2 - - + -
181A LEU* 3.0 43.1 + - + +
182A PRO* 4.8 2.9 - - + +
184A ILE* 1.3 77.5 - - - +
186A PRO* 1.3 67.5 - - + +
188A TYR* 3.1 7.1 + - + +
189A LYS* 2.9 33.1 + - - +
224A GLY 5.3 0.2 - - - +
225A ALA* 4.1 17.9 - - + -
228A GLU* 4.0 20.0 - - + -
229A LEU* 3.7 25.3 - - + +
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Residues in contact with PRO 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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182A PRO 3.2 26.0 - - - +
183A LYS 3.6 8.5 - - - +
184A ILE 3.3 4.3 - - - -
185A LEU* 1.3 92.6 - - + +
187A ILE* 1.3 62.3 + - + +
189A LYS* 3.1 22.1 + - + +
190A GLU* 3.1 29.8 + - - +
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Residues in contact with ILE 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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74A MSE 3.6 22.2 - - + +
75A LEU* 3.7 20.0 - - + +
130A PHE* 3.5 18.6 - - + -
131A SER* 3.2 36.6 - - - +
132A TYR* 3.8 23.6 - - + +
183A LYS 4.1 9.2 - - - +
184A ILE 3.0 8.1 + - - +
186A PRO* 1.3 74.1 - - + +
188A TYR* 1.3 66.5 + - - +
189A LYS 3.0 1.6 - - - -
190A GLU* 3.2 13.9 + - - +
191A VAL* 3.1 24.9 + - + +
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Residues in contact with TYR 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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71A THR* 4.1 9.0 + - - -
74A MSE 5.2 10.1 - - - -
75A LEU* 4.0 26.7 - - + -
155A LEU* 4.2 26.0 - - + -
156A VAL 2.7 29.8 + - - -
157A GLY 3.5 1.0 + - - -
158A PRO* 3.2 47.8 - - + +
161A TYR* 3.9 9.9 - - - +
184A ILE* 3.1 30.2 + - + -
185A LEU* 3.1 10.2 + - - +
187A ILE* 1.3 77.1 - - - +
189A LYS* 1.3 61.4 + - - +
191A VAL* 3.4 6.5 + - - +
192A ILE* 2.9 40.3 + - + +
205A LEU* 5.1 3.6 - - + -
229A LEU* 4.9 10.5 - - + -
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 2.9 27.7 + - - +
186A PRO* 3.2 18.0 - - + +
187A ILE 3.0 0.2 - - - -
188A TYR* 1.3 77.2 - - - +
190A GLU* 1.3 58.1 + - + +
192A ILE* 3.2 4.2 + - - +
193A THR* 2.9 34.5 + - - +
228A GLU* 2.9 52.1 + - - +
229A LEU* 4.2 9.7 - - + +
231A SER* 5.6 2.9 - - - -
232A THR* 3.6 31.3 - - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 3.9 30.3 + - + +
186A PRO* 3.1 17.5 + - - +
187A ILE* 3.2 17.4 + - - +
189A LYS* 1.3 75.5 - - + +
191A VAL* 1.3 61.8 + - - +
193A THR* 3.3 8.0 + - - -
194A GLU* 3.1 29.4 + - + +
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Residues in contact with VAL 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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74A MSE 3.4 40.4 - - + -
132A TYR* 3.3 44.0 - - + +
137A ALA* 4.6 4.0 - - + -
155A LEU* 4.3 8.1 - - + -
187A ILE* 3.1 15.5 + - + +
188A TYR* 3.7 8.7 - - - +
190A GLU* 1.3 77.1 - - - +
192A ILE* 1.3 57.4 + - - +
194A GLU* 3.4 2.9 + - - +
195A LEU* 3.0 51.4 + - + +
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.7 9.6 - - + -
188A TYR* 2.9 30.4 + - + +
189A LYS 3.7 3.6 - - - +
191A VAL* 1.3 75.8 - - - +
193A THR* 1.3 58.4 + - - +
195A LEU* 3.4 8.1 + - + +
196A LYS* 3.0 28.7 + - + +
203A ILE* 3.8 22.9 - - + -
205A LEU* 5.4 6.5 - - + -
229A LEU* 4.8 12.6 - - + -
232A THR* 3.8 20.4 - - + +
233A LEU* 3.4 26.5 - - + -
236A LEU* 3.7 26.0 - - + -
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Residues in contact with THR 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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189A LYS* 2.9 23.3 + - - +
190A GLU* 3.5 8.9 - - - +
191A VAL 3.2 0.2 - - - -
192A ILE* 1.3 75.1 - - - +
194A GLU* 1.3 61.4 + - + +
196A LYS* 3.4 15.5 + - - +
197A ALA* 3.0 28.6 + - + +
232A THR* 4.2 9.9 + - - +
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Residues in contact with GLU 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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132A TYR* 2.7 38.4 + - - -
135A HIS* 3.3 19.8 + - - -
138A VAL* 3.7 19.9 - - + +
190A GLU* 3.1 15.8 + - + +
191A VAL 3.9 4.0 - - - +
193A THR* 1.3 75.7 - - + +
195A LEU* 1.3 61.6 + - - +
197A ALA* 3.1 7.7 + - - +
198A ALA* 2.8 32.1 + - - +
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Residues in contact with LEU 195 (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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137A ALA* 4.3 6.1 - - + +
138A VAL* 3.4 40.6 - - + +
141A TYR* 4.8 4.3 - - + -
153A PRO* 4.0 26.5 - - + -
155A LEU* 4.8 3.1 - - + -
191A VAL* 3.0 42.8 + - + +
192A ILE* 3.6 10.5 - - + +
194A GLU* 1.3 77.9 - - - +
196A LYS* 1.3 61.9 + - + +
198A ALA* 3.3 6.4 + - - +
199A GLY 3.3 4.9 + - - -
200A ALA* 3.0 33.6 + - + +
203A ILE* 4.1 21.3 - - + -
236A LEU* 6.0 1.3 - - + -
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Residues in contact with LYS 196 (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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192A ILE 3.0 22.9 + - - +
193A THR* 3.8 17.0 + - - +
195A LEU* 1.3 73.2 - - - +
197A ALA* 1.3 68.0 + - - +
199A GLY* 3.0 15.6 + - - -
200A ALA 3.9 9.1 - - - +
231A SER 4.8 2.6 + - - -
232A THR* 2.9 28.7 + - - +
234A SER* 3.6 18.9 + - - +
235A GLY 4.5 4.0 - - - +
236A LEU* 3.5 37.0 - - + -
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Residues in contact with ALA 197 (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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193A THR* 3.0 19.3 + - + +
194A GLU* 3.4 8.7 - - - +
196A LYS* 1.3 78.0 - - - +
198A ALA* 1.3 60.9 + - - +
199A GLY* 3.3 1.0 + - - -
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Residues in contact with ALA 198 (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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138A VAL* 4.5 4.0 - - + -
141A TYR* 3.4 31.6 - - + -
142A LYS* 3.7 32.4 - - + +
145A LYS* 3.9 11.6 - - - +
194A GLU 2.8 16.1 + - - +
195A LEU* 3.7 5.4 - - - +
196A LYS 3.2 0.2 - - - -
197A ALA* 1.3 76.7 - - - +
199A GLY* 1.3 58.4 + - - +
200A ALA 3.7 0.4 - - - -
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Residues in contact with GLY 199 (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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141A TYR* 2.9 11.3 + - - -
145A LYS* 4.0 10.2 + - - -
150A ASP* 4.8 1.9 - - - +
196A LYS 3.0 11.5 + - - -
197A ALA 3.2 1.9 - - - -
198A ALA* 1.3 79.8 - - - +
200A ALA* 1.3 66.8 + - - +
201A THR* 3.3 14.8 + - - +
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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