Contacts of the helix formed by residues 174 - 195 (chain A) in PDB entry 1UZF
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 LYS 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A SER* 3.2 5.8 + - - +
173A ARG* 1.3 81.8 - - + +
175A TYR* 1.3 67.6 + - - +
176A GLU* 3.1 4.0 - - + +
177A ASP* 2.8 48.9 + - - +
178A LEU* 3.0 14.2 + - - +
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Residues in contact with TYR 175 (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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173A ARG 3.9 4.0 + - - -
174A LYS* 1.3 70.1 - - - +
176A GLU* 1.3 75.8 + - + +
178A LEU* 3.5 4.2 + - - -
179A LEU* 3.0 34.6 + - + +
259A TYR* 4.0 26.1 - + + -
263A HIS* 4.2 38.0 + + + +
271A PRO* 4.0 12.5 - - + +
273A HIS* 3.3 38.8 - + - -
274A LEU* 4.0 20.0 - - + -
498A PRO* 4.3 12.2 + - + +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 3.1 4.3 - - + +
175A TYR* 1.3 93.2 - - + +
177A ASP* 1.3 67.9 + - - +
179A LEU* 3.5 20.1 + - - +
180A TRP* 3.1 26.2 + - - +
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.1 8.5 - - + +
172A SER* 3.6 19.3 + - - +
174A LYS* 2.8 42.9 + - - +
176A GLU* 1.3 75.9 - - - +
178A LEU* 1.3 67.4 + - - +
180A TRP* 3.3 9.6 + - - +
181A ALA* 3.3 21.3 + - - +
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Residues in contact with LEU 178 (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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168A VAL* 3.7 20.9 - - + +
169A MET* 3.9 26.4 - - - +
172A SER* 3.5 27.4 - - - +
174A LYS 3.0 15.8 + - - +
175A TYR 3.7 2.7 - - - +
177A ASP* 1.3 78.7 - - - +
179A LEU* 1.3 61.1 + - - +
181A ALA* 3.4 1.4 + - - -
182A TRP* 2.9 25.5 + - - +
259A TYR* 3.5 26.2 - - + +
273A HIS* 3.6 33.7 - - + +
274A LEU* 3.9 15.9 - - + +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.0 26.7 + - + +
176A GLU* 3.7 26.0 - - - +
178A LEU* 1.3 77.4 - - - +
180A TRP* 1.3 53.5 + - - +
182A TRP* 4.3 6.1 - - + -
183A GLU* 2.8 42.7 + - + +
273A HIS* 3.5 7.8 - - + +
498A PRO* 3.6 30.1 - - + +
499A VAL* 3.4 35.7 - - + -
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Residues in contact with TRP 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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151A VAL* 3.6 33.5 - - + +
152A CYS 3.3 25.9 + - - -
153A HIS* 3.3 46.3 + + - +
154A PRO* 5.7 2.0 - - - +
159A LEU* 3.9 13.7 - - + -
165A LEU* 4.1 19.7 - - + -
168A VAL* 5.6 4.3 - - + -
176A GLU 3.1 14.1 + - - +
177A ASP* 3.5 13.2 - - - +
178A LEU 3.3 0.2 - - - -
179A LEU* 1.3 77.9 - - - +
181A ALA* 1.3 73.2 + - + +
183A GLU* 5.0 1.8 - - - -
184A GLY* 2.9 28.5 + - - -
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Residues in contact with ALA 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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151A VAL* 5.1 0.6 - - - +
165A LEU* 4.0 21.0 - - + +
168A VAL* 4.0 16.8 - - + -
169A MET* 3.9 21.5 - - + -
177A ASP 3.3 9.5 + - - +
178A LEU 3.9 2.2 - - - +
180A TRP* 1.3 88.4 - - + +
182A TRP* 1.3 66.2 + - - +
185A TRP* 3.0 27.1 + - - +
278A MET* 3.6 4.9 - - + +
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Residues in contact with TRP 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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169A MET* 4.1 7.4 - - + -
178A LEU 2.9 17.5 + - - +
179A LEU* 3.7 4.5 - - + +
181A ALA* 1.3 79.6 - - - +
183A GLU* 1.3 97.2 + - + +
186A ARG* 2.8 78.0 + - - +
272A ALA* 3.7 14.2 + - + +
273A HIS* 3.7 26.7 - - + -
278A MET* 3.7 17.0 + - - -
486A TRP* 3.7 31.9 - + - -
489A ARG* 4.8 0.8 - - - +
497A PRO* 4.0 6.1 - - + -
498A PRO* 3.7 36.8 - - + -
499A VAL 4.7 2.2 - - - -
501A ARG* 3.8 13.5 - - - -
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Residues in contact with GLU 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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179A LEU* 2.8 27.7 + - + +
180A TRP* 4.3 2.2 - - - +
182A TRP* 1.3 84.4 - - + +
184A GLY* 1.3 60.4 + - - +
186A ARG* 3.2 3.6 + - - +
187A ASP* 2.5 66.3 + - - +
191A ARG* 4.3 6.1 + - - -
499A VAL* 3.6 18.8 - - + +
501A ARG* 2.9 36.4 + - - -
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Residues in contact with GLY 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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151A VAL* 3.7 20.9 - - - -
180A TRP* 2.9 19.9 + - - -
183A GLU* 1.3 78.3 - - - +
185A TRP* 1.3 61.6 + - - +
187A ASP* 3.2 9.5 + - - +
188A LYS* 2.9 30.4 + - - +
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Residues in contact with TRP 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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146A TYR* 3.7 33.9 - + - -
149A ALA* 3.6 31.0 - - + -
150A THR 4.7 0.2 - - - -
151A VAL* 3.7 8.7 - - + +
161A LEU* 3.6 43.1 - - + +
165A LEU* 3.7 19.5 - - + -
181A ALA 3.0 18.8 + - - +
182A TRP 4.0 1.3 - - - +
184A GLY* 1.3 75.0 - - - +
186A ARG* 1.3 58.6 + - - +
188A LYS* 5.4 0.2 - - + -
189A ALA* 2.8 48.4 + - + +
278A MET* 3.5 35.0 - - + -
279A TRP* 4.2 2.6 - - - -
510A ALA* 2.9 36.3 + - + +
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Residues in contact with ARG 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 TRP* 2.8 77.0 + - - +
183A GLU 3.2 8.3 + - - +
185A TRP* 1.3 75.3 - - - +
187A ASP* 1.3 61.5 + - - +
190A GLY* 3.1 8.7 + - - +
191A ARG* 3.0 29.7 + - - +
278A MET* 2.8 39.3 + - - +
279A TRP* 4.0 14.6 - - - +
489A ARG* 4.5 0.4 - - - +
501A ARG* 4.0 7.4 - - - +
505A ASP* 5.7 0.2 - - - -
506A PHE 5.6 0.5 + - - -
507A ASP* 3.3 29.9 - - - +
510A ALA* 3.8 18.1 - - + +
703A CL 3.1 30.3 - - - +
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Residues in contact with ASP 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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183A GLU* 2.5 58.8 + - - +
184A GLY* 3.6 8.6 - - - +
186A ARG* 1.3 76.9 - - - +
188A LYS* 1.3 66.6 + - + +
191A ARG* 3.2 58.4 + - - +
192A ALA 4.7 0.2 + - - -
501A ARG* 4.6 0.3 + - - -
505A ASP* 4.3 1.6 - - - +
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Residues in contact with LYS 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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149A ALA* 4.6 11.0 - - + +
150A THR* 2.9 44.6 + - - +
151A VAL* 4.2 13.3 - - + +
152A CYS* 5.2 7.7 - - - +
184A GLY* 2.9 20.2 + - - +
185A TRP* 4.2 0.9 - - + +
187A ASP* 1.3 86.1 - - + +
189A ALA* 1.3 59.8 + - - +
192A ALA* 3.2 24.1 - - - +
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Residues in contact with ALA 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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145A THR* 5.4 2.2 - - - -
146A TYR* 4.4 12.8 - - + -
149A ALA* 4.0 10.3 - - + -
185A TRP* 2.8 57.1 + - + +
188A LYS* 1.3 73.1 - - - +
190A GLY* 1.3 68.3 + - - +
192A ALA* 3.2 9.6 + - - +
193A ILE* 3.2 21.4 + - - +
509A GLY 4.4 0.7 - - - -
510A ALA* 4.5 1.6 - - - -
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Residues in contact with GLY 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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185A TRP 3.6 2.2 + - - -
186A ARG* 3.1 12.8 + - - +
189A ALA* 1.3 78.4 - - - +
191A ARG* 1.3 62.1 + - - +
193A ILE* 3.0 14.6 + - - +
194A LEU 3.5 7.3 + - - -
506A PHE* 3.3 32.2 - - - +
509A GLY 3.9 0.9 - - - -
510A ALA* 3.8 18.4 - - - +
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Residues in contact with ARG 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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183A GLU* 4.3 4.0 + - - -
186A ARG 3.0 13.4 + - - +
187A ASP* 3.2 49.2 + - - +
189A ALA 3.4 0.2 - - - -
190A GLY* 1.3 72.9 - - - +
192A ALA* 1.3 62.1 + - - +
193A ILE 3.3 0.9 + - - -
194A LEU* 3.4 17.2 + - - +
195A GLN* 4.4 2.1 + - - +
502A THR* 3.9 15.0 + - - +
503A GLN 5.7 1.1 + - - -
504A GLY* 3.4 26.8 + - - +
505A ASP* 2.7 30.3 + - - +
506A PHE 4.6 1.9 - - - +
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Residues in contact with ALA 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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145A THR* 3.5 24.0 - - + +
187A ASP 4.7 0.2 + - - -
188A LYS 3.2 21.9 + - - +
189A ALA 3.2 2.6 + - - +
190A GLY 3.2 1.2 - - - -
191A ARG* 1.3 77.9 - - - +
193A ILE* 1.3 60.9 + - - +
195A GLN* 3.7 10.3 - - - +
196A PHE* 3.5 21.3 - - - -
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Residues in contact with ILE 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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142A MET* 3.5 44.9 - - + +
145A THR* 3.8 20.2 - - + -
146A TYR* 4.4 5.4 - - + +
189A ALA* 3.2 15.3 - - - +
190A GLY 3.0 8.5 + - - +
192A ALA* 1.3 76.7 - - - +
194A LEU* 1.3 66.8 + - - +
195A GLN 3.3 1.3 - - - -
196A PHE* 2.9 17.1 + - + +
197A TYR* 3.3 10.7 + - + +
506A PHE* 3.9 16.4 - - + -
509A GLY* 3.7 20.9 - - - +
515A PRO* 3.9 23.6 - - + -
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Residues in contact with LEU 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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190A GLY 3.5 3.0 + - - -
191A ARG 3.4 14.6 + - - +
193A ILE* 1.3 78.5 - - - +
195A GLN* 1.3 63.3 + - - +
196A PHE 3.0 1.2 + - - -
197A TYR 3.4 0.3 + - - -
198A PRO* 3.2 25.4 - - + +
478A LYS* 5.5 3.4 - - + +
481A TYR* 3.8 32.1 - - + -
503A GLN* 5.7 2.9 - - - +
504A GLY* 3.5 35.9 - - - +
505A ASP 4.3 5.6 - - - +
506A PHE* 3.9 24.8 - - + -
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Residues in contact with GLN 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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191A ARG 4.4 2.2 + - - +
192A ALA* 3.7 10.3 + - - +
194A LEU* 1.3 78.0 - - - +
196A PHE* 1.3 97.9 + - + +
198A PRO* 4.5 4.7 - - - +
199A LYS* 5.4 3.6 + - - +
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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