Contacts of the helix formed by residues 156 - 177 (chain A) in PDB entry 4UPG
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 PHE 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ILE 5.3 0.2 - - - -
64A ALA* 4.3 9.6 - - + -
67A TYR* 3.4 43.5 - + + -
68A LYS 5.8 0.2 - - - +
70A PHE* 3.6 25.1 - + - -
102A LEU 5.6 0.2 - - - -
106A ARG* 4.0 36.3 - - + -
109A PHE* 3.7 43.0 - + + -
118A GLY* 3.0 14.3 + - - +
155A THR* 1.3 73.2 - - - +
157A ASP* 1.3 69.4 + - - +
159A TYR* 3.3 2.4 + - - +
160A ILE* 2.9 55.1 + - + +
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Residues in contact with ASP 157 (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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68A LYS* 2.6 61.8 - - - +
69A PRO 3.5 5.3 - - - +
70A PHE* 3.8 17.7 - - + -
71A ASN* 5.2 4.1 + - - +
74A THR* 4.6 9.5 + - - +
155A THR* 3.2 8.1 + - - +
156A PHE* 1.3 88.6 - - - +
158A ASP* 1.3 60.2 + - - +
160A ILE* 3.4 3.1 + - - +
161A ALA* 3.0 26.0 + - - +
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Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 3.8 46.2 - - + +
154A ILE* 4.1 7.0 - - + -
155A THR* 3.2 25.3 + - - +
157A ASP* 1.3 75.1 - - - +
159A TYR* 1.3 61.8 + - - +
161A ALA* 3.7 7.1 - - - +
162A CYS* 2.8 31.4 + - - +
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Residues in contact with TYR 159 (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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105A TRP* 3.1 30.4 + - + +
108A HIS* 3.9 3.5 + - - +
109A PHE* 3.3 44.1 + + + -
120A VAL* 5.6 1.1 - - + -
125A LEU* 3.9 21.1 - - + -
128A ALA* 4.4 12.1 - - + -
129A LEU* 4.8 0.4 - - + -
132A MET* 3.0 39.3 - - + +
154A ILE* 3.8 13.0 - - + +
155A THR 2.9 17.9 + - - +
156A PHE* 3.4 6.1 - + - +
158A ASP* 1.3 77.7 - - - +
160A ILE* 1.3 83.6 + - + +
162A CYS* 3.2 6.2 + - - +
163A CYS* 2.9 33.5 + - - -
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Residues in contact with ILE 160 (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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70A PHE* 3.6 33.9 - - + -
74A THR* 4.7 0.4 - - + -
78A MET* 3.8 22.9 - - + -
102A LEU* 3.8 17.0 - - + +
105A TRP* 3.8 23.3 - - + -
106A ARG 4.6 2.0 - - - +
156A PHE* 2.9 41.0 + - + +
157A ASP 3.8 1.6 - - - +
158A ASP 3.3 0.2 - - - -
159A TYR* 1.3 94.6 - - + +
161A ALA* 1.3 59.3 - - - +
163A CYS* 3.1 5.2 + - - +
164A VAL* 2.8 35.5 + - + +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 4.1 24.0 - - - +
77A LEU* 4.1 18.5 - - + +
148A TYR* 4.4 11.7 - - + +
157A ASP 3.0 17.6 + - - +
158A ASP* 3.7 11.9 - - - +
160A ILE* 1.3 75.9 - - - +
162A CYS* 1.3 63.4 + - - +
164A VAL* 3.4 4.4 + - - +
165A LYS* 3.0 26.0 + - - +
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Residues in contact with CYS 162 (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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125A LEU* 5.2 4.7 - - + -
129A LEU* 4.5 10.3 - - - -
144A ILE* 3.4 34.5 - - - -
148A TYR* 3.6 25.0 + - + -
154A ILE* 6.3 0.4 - - + -
158A ASP 2.8 22.1 + - - +
159A TYR* 3.3 8.5 - - - +
161A ALA* 1.3 72.5 - - - +
163A CYS* 1.3 57.7 + - - +
165A LYS* 3.4 1.6 + - - +
166A LEU* 2.9 48.6 + - - +
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Residues in contact with CYS 163 (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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105A TRP* 3.5 35.4 - - + -
129A LEU* 4.0 11.0 - - - -
132A MET* 3.7 23.6 - - - -
134A PHE* 4.0 5.1 - - + -
159A TYR* 2.9 48.3 + - - +
160A ILE 3.6 3.8 - - - +
162A CYS* 1.3 72.1 - - - +
164A VAL* 1.3 65.1 + - - +
166A LEU* 3.8 6.6 - - - +
167A ARG* 2.9 20.3 + - - +
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Residues in contact with VAL 164 (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 THR 5.3 0.9 - - - +
77A LEU* 3.5 41.7 - - + +
78A MET* 3.8 22.7 - - + +
81A MET* 3.6 25.8 - - + +
102A LEU* 4.6 1.8 - - + -
105A TRP* 3.6 14.8 - - + -
160A ILE* 2.8 33.5 + - + +
161A ALA* 3.7 7.2 - - - +
163A CYS* 1.3 72.8 - - - +
165A LYS* 1.3 60.9 + - - +
167A ARG 3.4 0.2 + - - -
168A ALA* 2.9 27.6 + - + +
198A VAL* 6.3 0.2 - - + -
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Residues in contact with LYS 165 (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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77A LEU* 4.7 6.5 - - + -
147A ARG* 4.9 6.7 - - - +
148A TYR* 3.9 18.0 + - - +
161A ALA 3.0 17.2 + - - +
162A CYS 3.9 3.4 - - - +
164A VAL* 1.3 79.1 - - - +
166A LEU* 1.3 57.8 + - - +
168A ALA* 3.3 4.9 + - - +
169A LEU* 2.9 57.0 + - + +
195A VAL* 5.9 5.7 - - - +
198A VAL* 3.4 29.2 - - + +
1200A SO4 2.9 36.5 + - - +
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Residues in contact with LEU 166 (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 LEU* 3.9 35.2 - - + -
134A PHE* 3.8 28.3 - - + -
136A LEU* 4.3 18.2 - - + -
144A ILE* 4.1 18.4 - - + -
162A CYS* 2.9 31.7 + - - +
163A CYS 3.8 3.8 - - - +
164A VAL 3.3 0.2 - - - -
165A LYS* 1.3 77.5 - - - +
167A ARG* 1.3 54.9 + - - +
169A LEU* 4.1 7.2 - - + +
170A THR* 2.6 40.8 + - - +
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Residues in contact with ARG 167 (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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81A MET* 4.0 17.5 - - + -
101A VAL* 5.1 5.6 - - - +
105A TRP* 3.6 30.0 - - + +
132A MET 4.0 16.0 + - - -
133A GLY 5.2 2.8 + - - -
134A PHE* 3.3 34.9 - - + -
163A CYS 2.9 18.2 + - - +
164A VAL 3.9 2.7 - - - +
166A LEU* 1.3 73.7 - - - +
168A ALA* 1.3 61.1 + - - +
170A THR* 3.9 3.6 - - - +
171A ASP* 2.8 54.7 + - - +
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Residues in contact with ALA 168 (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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80A SER 5.2 0.7 - - - -
81A MET* 3.9 27.3 - - + +
84A ARG* 5.7 0.2 + - - -
164A VAL* 2.9 18.3 + - + +
165A LYS* 3.8 2.9 - - - +
167A ARG* 1.3 77.2 - - - +
169A LEU* 1.3 58.6 + - - +
171A ASP* 3.3 7.8 + - - +
172A SER* 2.9 32.2 + - - -
198A VAL* 3.7 28.9 - - + -
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Residues in contact with LEU 169 (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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165A LYS* 2.9 45.9 + - + +
166A LEU* 4.1 7.0 - - + +
168A ALA* 1.3 74.1 - - - +
170A THR* 1.3 61.7 + - - +
172A SER* 3.6 4.6 - - - +
173A PHE* 2.9 29.5 + - - +
194A CYS* 4.7 11.0 - - - +
195A VAL* 4.5 26.7 - - + -
198A VAL* 3.5 25.4 - - + -
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Residues in contact with THR 170 (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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134A PHE* 4.5 15.0 - - + -
166A LEU* 2.6 29.0 + - - +
167A ARG* 3.9 6.7 - - - +
169A LEU* 1.3 73.6 - - - +
171A ASP* 1.3 66.6 + - - +
173A PHE* 3.3 5.6 + - + +
174A ARG* 2.9 51.5 + - + +
1202A SO4 4.4 14.4 - - - +
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Residues in contact with ASP 171 (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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81A MET* 4.8 5.9 - - - +
84A ARG* 3.3 37.4 + - - +
167A ARG* 2.8 50.6 + - - +
168A ALA* 3.6 7.4 - - - +
170A THR* 1.3 76.6 - - - +
172A SER* 1.3 56.5 - - - +
174A ARG* 3.9 7.7 - - - +
175A ARG* 2.9 30.5 + - - +
1199A SO4 4.9 1.6 + - - +
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Residues in contact with SER 172 (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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84A ARG* 5.2 1.0 + - - -
168A ALA* 2.9 20.1 + - - +
169A LEU* 3.6 8.8 - - - +
171A ASP* 1.3 75.3 - - - +
173A PHE* 1.3 64.9 + - - +
175A ARG* 3.5 1.7 - - - +
176A ARG* 3.0 30.8 + - - +
186A PHE* 5.4 1.1 - - - -
194A CYS* 3.5 31.6 - - - -
1201A SO4 3.0 27.4 + - - -
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Residues in contact with PHE 173 (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 LEU 2.9 17.4 + - - +
170A THR* 3.7 6.7 - - + +
172A SER* 1.3 77.2 - - - +
174A ARG* 1.3 65.4 + - + +
176A ARG* 3.0 4.3 + - - -
177A ASP* 2.9 18.4 + - - -
182A GLY 3.4 32.3 - - - -
183A VAL* 3.9 0.4 - - - -
184A VAL* 3.4 46.7 - - + +
186A PHE* 4.3 17.2 - + + -
1202A SO4 4.1 13.7 - - - -
1205A PEG 3.7 20.2 - - - -
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Residues in contact with ARG 174 (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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170A THR* 2.9 35.0 + - + +
171A ASP* 4.0 7.9 - - - +
173A PHE* 1.3 76.8 - - + +
175A ARG* 1.3 63.9 + - - +
177A ASP* 3.0 18.5 + - - +
1202A SO4 3.0 29.8 + - - +
1204A PEG 3.3 47.8 - - - -
1205A PEG 3.2 42.5 + - - +
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Residues in contact with ARG 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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84A ARG* 2.7 45.2 + - - +
171A ASP 2.9 14.5 + - - +
172A SER* 3.5 7.2 - - - +
174A ARG* 1.3 77.0 - - - +
176A ARG* 1.3 67.3 + - + +
177A ASP 4.8 0.2 - - - -
178A THR* 4.1 13.9 - - - +
1199A SO4 2.1 57.7 + - - +
1201A SO4 4.0 17.8 + - - +
1204A PEG 3.9 14.6 + - - -
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Residues in contact with ARG 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 SER* 3.0 26.2 + - - +
173A PHE 3.0 8.9 + - - +
175A ARG* 1.3 82.9 - - + +
177A ASP* 1.3 57.9 + - - +
178A THR* 2.9 19.1 + - - +
184A VAL* 3.7 20.1 - - + +
186A PHE* 3.6 25.8 - - - -
190A ASP* 2.8 39.5 + - - -
193A GLN* 6.3 0.2 - - - +
194A CYS* 4.0 10.6 - - - +
1201A SO4 3.0 48.3 + - - -
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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
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173A PHE* 2.9 11.6 + - - +
174A ARG 3.0 11.4 + - - +
176A ARG* 1.3 75.5 - - - +
178A THR* 1.3 56.8 + - - +
179A ALA* 4.1 2.3 + - - +
180A GLN* 3.0 25.2 + - - +
181A GLN* 3.0 22.6 + - - +
182A GLY* 2.9 24.1 + - - -
183A VAL 3.3 16.9 - - - +
184A VAL* 3.7 10.8 - - + -
1205A PEG 2.2 36.4 + - - +
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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