Contacts of the helix formed by residues 175 - 193 (chain A) in PDB entry 4U1D
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 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 5.0 3.6 - - - -
86A LEU* 3.4 36.1 - - + +
87A VAL* 5.5 0.4 - - - -
89A VAL* 4.0 17.3 - - + -
90A GLY* 3.9 20.0 - - - +
168A LEU 4.6 4.5 - - - +
169A LEU* 4.1 27.8 - - + +
172A ASN* 3.1 41.0 + - + +
174A LEU* 1.3 82.0 - - - +
176A GLU* 1.3 58.7 + - - +
177A ILE 3.2 3.3 + - - -
178A THR* 3.3 8.7 + - - +
179A TYR* 2.9 30.2 + - - +
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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
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172A ASN 3.1 17.7 + - - +
173A ALA* 3.3 21.9 - - - +
174A LEU 3.4 2.2 - - - -
175A LEU* 1.3 77.7 - - - +
177A ILE* 1.3 60.2 + - + +
179A TYR* 3.5 10.8 + - - +
180A SER* 2.9 29.3 + - - -
225A VAL* 3.4 32.8 - - + +
226A ASP 4.1 1.4 + - - -
232A THR* 2.7 36.6 + - - +
235A ARG* 2.9 24.7 + - - +
236A TYR* 4.8 8.6 - - + +
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Residues in contact with ILE 177 (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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174A LEU 5.0 3.7 + - - +
175A LEU 3.2 0.8 - - - -
176A GLU* 1.3 77.5 - - + +
178A THR* 1.3 63.6 + - - +
180A SER* 3.4 4.2 + - - -
181A GLY* 3.2 17.2 + - - -
235A ARG* 3.7 36.1 - - - +
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLY* 3.6 30.6 - - - +
93A ALA* 4.8 0.4 - - + -
94A ARG* 3.7 39.5 + - + +
169A LEU* 3.7 17.9 - - + -
174A LEU 5.3 1.2 + - - -
175A LEU* 3.3 13.6 + - - +
177A ILE* 1.3 76.4 - - - +
179A TYR* 1.3 65.6 + - - +
181A GLY* 3.1 3.7 + - - -
182A VAL* 3.1 24.4 + - + +
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Residues in contact with TYR 179 (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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166A LEU* 3.7 34.8 - - + -
169A LEU* 3.5 40.7 - - + +
170A ARG* 4.2 5.8 - - - -
171A ASN 5.6 1.8 - - - -
175A LEU 2.9 18.0 + - - +
176A GLU* 3.5 10.5 - - - +
178A THR* 1.3 77.6 - - - +
180A SER* 1.3 61.1 + - - +
182A VAL* 3.0 5.9 + - - +
183A VAL* 2.9 46.2 + - + +
206A LEU* 3.3 15.8 - - - +
209A HIS* 2.7 35.4 + + + +
236A TYR* 4.3 25.6 - + - -
239A GLN* 4.3 9.2 - - - -
240A ARG* 5.7 2.1 + - - -
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLU 2.9 17.6 + - - -
177A ILE 3.7 6.1 - - - -
178A THR 3.3 0.2 - - - -
179A TYR* 1.3 76.6 - - - +
181A GLY* 1.3 61.8 + - - +
183A VAL* 3.6 2.0 + - - +
184A LYS* 3.3 39.5 + - - +
235A ARG* 4.0 24.7 - - - +
239A GLN* 3.0 30.2 + - - +
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Residues in contact with GLY 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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177A ILE 3.2 9.3 + - - -
178A THR* 3.1 8.3 + - - -
179A TYR 3.1 1.2 - - - -
180A SER* 1.3 78.8 - - - +
182A VAL* 1.3 60.0 + - - +
184A LYS* 3.4 6.3 + - - +
185A LYS* 3.1 29.2 + - - +
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Residues in contact with VAL 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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93A ALA* 5.9 1.3 - - + +
94A ARG* 6.1 2.0 - - + -
97A ILE* 4.3 14.8 - - + -
162A TYR* 3.9 18.6 - - + +
165A VAL* 3.8 28.9 - - + -
166A LEU* 3.6 22.2 - - + -
169A LEU* 4.0 7.9 - - + -
178A THR* 3.1 17.9 + - + +
179A TYR 3.0 5.7 + - - +
181A GLY* 1.3 72.8 - - - +
183A VAL* 1.3 55.6 + - - +
185A LYS* 3.1 8.9 + - + +
186A THR* 2.6 47.9 + - - +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.7 17.9 - - + -
179A TYR* 2.9 43.7 + - + +
180A SER 3.8 6.1 - - - +
182A VAL* 1.3 76.7 - - - +
184A LYS* 1.3 57.6 + - - +
186A THR* 3.2 7.0 + - - -
187A MET* 2.9 54.3 + - + +
202A LEU* 5.5 2.0 - - + -
206A LEU* 3.9 18.6 - - + -
239A GLN* 4.0 22.9 - - + +
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Residues in contact with LYS 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 SER* 3.3 27.7 + - - +
181A GLY* 3.8 8.3 - - - +
182A VAL 3.3 0.2 - - - -
183A VAL* 1.3 78.2 - - + +
185A LYS* 1.3 57.9 + - + +
187A MET* 3.3 0.7 + - - -
188A HIS* 2.9 30.0 + - - +
235A ARG* 5.8 0.4 - - - +
238A ASP* 3.4 48.4 + - - +
239A GLN* 4.1 9.4 - - + +
242A GLN* 3.2 33.8 + - - +
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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
----------------------------------------------------------
97A ILE* 3.7 15.0 - - + -
98A ASP* 4.2 14.1 + - - -
101A GLU* 3.1 37.7 + - - +
162A TYR* 3.7 16.5 + - + +
181A GLY 3.1 20.1 + - - +
182A VAL* 3.1 10.9 + - + +
184A LYS* 1.3 75.9 - - + +
186A THR* 1.3 62.5 + - - +
188A HIS* 3.4 6.4 + - - +
189A PHE* 3.1 23.4 + - - +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 3.7 26.0 - - + -
162A TYR* 3.4 35.0 - - + +
166A LEU* 3.7 9.5 - - + +
182A VAL* 2.6 32.2 + - - +
183A VAL 3.5 5.4 - - - -
185A LYS* 1.3 74.7 - - - +
187A MET* 1.3 60.3 + - - +
189A PHE* 3.3 3.6 + - - +
190A CYS* 3.2 22.6 + - - -
202A LEU* 3.5 27.6 - - + -
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Residues in contact with MET 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 VAL* 2.9 26.0 + - + +
185A LYS 3.3 0.2 - - - -
186A THR* 1.3 75.4 - - - +
188A HIS* 1.3 65.6 + - - +
190A CYS* 3.3 6.0 + - - +
191A LEU* 3.2 22.3 + - - +
199A PHE* 4.3 8.1 - - + -
202A LEU* 3.7 17.9 - - + -
203A ALA* 6.0 0.2 - - - -
206A LEU* 3.5 32.5 - - + -
239A GLN* 3.6 18.6 - - - +
242A GLN* 3.5 29.2 - - - +
243A GLN* 3.6 39.5 - - + +
246A VAL* 4.0 11.7 - - + +
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Residues in contact with HIS 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 LYS 2.9 17.7 + - - +
185A LYS* 3.8 6.7 - - - +
186A THR 3.3 0.2 - - - -
187A MET* 1.3 76.9 - - - +
189A PHE* 1.3 62.3 + - - +
191A LEU* 3.5 13.1 + - + +
192A LYS* 3.1 43.2 + - + +
242A GLN* 4.2 6.7 - - - +
246A VAL* 5.6 0.7 - - - -
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Residues in contact with PHE 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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104A ILE* 5.2 3.6 - - + -
155A LEU* 3.6 21.5 - - + -
158A THR* 3.6 24.9 - - - -
159A TRP* 4.0 15.7 - + + -
162A TYR* 3.7 28.3 - + + +
185A LYS 3.1 16.6 + - - +
186A THR 3.5 6.1 - - - +
187A MET 3.1 0.2 - - - -
188A HIS* 1.3 77.6 - - - +
190A CYS* 1.3 72.2 + - - +
192A LYS* 3.2 2.7 + - - -
193A TYR* 3.1 58.4 + + - +
195A ARG* 4.0 20.0 - - + -
198A GLU* 4.0 19.5 - - - -
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Residues in contact with CYS 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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159A TRP* 4.3 19.5 - - - -
186A THR* 3.2 18.2 + - - -
187A MET 3.3 7.4 + - - +
189A PHE* 1.3 84.7 - - - +
191A LEU* 1.3 58.7 + - - +
194A GLN* 3.0 9.4 + - - -
195A ARG* 2.9 38.1 + - - +
198A GLU 4.4 0.4 - - - -
199A PHE* 3.7 52.0 - - + -
202A LEU* 4.6 1.3 - - - -
250A LEU* 4.0 5.6 - - + +
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Residues in contact with LEU 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 MET 3.2 13.1 + - - +
188A HIS* 3.8 13.9 - - + +
189A PHE 3.2 0.4 - - - -
190A CYS* 1.3 78.7 - - - +
192A LYS* 1.3 62.6 + - - +
193A TYR 3.3 0.3 + - - -
194A GLN* 3.0 30.1 + - - +
246A VAL* 4.1 20.1 - - + +
249A LYS* 3.6 51.6 - - + +
250A LEU* 3.6 22.7 - - + -
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Residues in contact with LYS 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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104A ILE* 5.9 0.2 - - - +
108A GLN* 6.1 0.2 - - - +
188A HIS* 3.1 39.1 + - + +
189A PHE* 3.2 0.6 + - - -
191A LEU* 1.3 77.4 - - - +
193A TYR* 1.3 100.8 + - + +
194A GLN* 3.6 3.2 + - - +
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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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104A ILE* 3.1 23.6 - - + +
108A GLN* 3.6 22.3 + - - -
155A LEU* 3.5 36.1 - - + +
189A PHE* 3.1 40.0 + + + -
192A LYS* 1.3 120.7 + - + +
194A GLN* 1.3 69.8 + - - +
195A ARG* 2.9 32.3 + - + -
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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