Contacts of the helix formed by residues 158 - 181 (chain A) in PDB entry 4U0J
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 TYR 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A MET* 3.7 10.8 - - + +
149A PHE* 3.4 37.1 - + + +
155A MET* 3.7 18.2 - - + -
156A PRO 2.8 8.9 + - - -
157A ALA* 1.3 72.2 - - - +
159A ASN* 1.3 67.2 + - - +
160A TRP 3.1 0.7 + - - -
161A MET* 2.9 47.3 + - + +
162A THR* 3.0 43.7 - - + +
165A LYS* 3.4 14.3 - - + +
401A 566 2.7 75.5 + + + -
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Residues in contact with ASN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY 3.2 14.0 + - - +
103A MET* 4.1 5.3 - - - +
104A GLY 3.4 20.8 + - - -
106A ASN 3.5 16.8 + - - -
108A PHE* 3.9 37.1 - - + +
155A MET 4.2 8.5 + - - +
157A ALA 3.3 25.1 + - - +
158A TYR* 1.3 73.7 - - - +
160A TRP* 1.3 65.2 + - + +
162A THR* 2.8 26.7 + - - -
163A VAL* 3.5 5.7 + - - +
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Residues in contact with TRP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A MET* 3.4 25.9 - - + +
101A THR 4.9 0.2 - - - -
102A GLY* 2.9 16.8 + - - +
108A PHE* 2.8 62.6 + + - -
109A PHE* 5.8 1.6 - + - -
111A ALA* 3.5 24.8 - - + +
113A TYR* 6.3 1.3 - + - -
116A VAL* 3.6 35.7 - - + -
120A ILE* 5.4 0.7 - - + +
159A ASN* 1.3 79.1 - - + +
161A MET* 1.3 64.5 + - - +
163A VAL* 3.2 38.4 + - + +
164A ALA 2.9 18.2 + - - -
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Residues in contact with MET 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY* 4.4 1.3 - - - -
97A PHE 4.0 10.1 - - - +
98A MET* 3.9 22.6 - - + +
102A GLY 4.0 2.4 + - - -
103A MET* 4.0 12.6 - - + -
123A SER* 3.3 34.1 - - - +
158A TYR* 2.9 40.6 + - + +
160A TRP* 1.3 79.8 - - - +
162A THR* 1.3 56.4 + - - +
164A ALA* 3.2 7.7 + - + +
165A LYS* 2.9 57.0 + - + +
400A NAD 4.0 9.6 - - - +
401A 566 4.1 13.7 - - + +
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Residues in contact with THR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 3.4 36.6 - - + +
153A ARG 4.0 11.9 - - - +
154A ALA* 4.9 6.5 - - - -
155A MET* 4.6 7.3 + - + +
158A TYR* 3.0 36.7 - - + +
159A ASN* 2.8 17.7 + - - -
161A MET* 1.3 77.7 - - - +
163A VAL* 1.3 60.0 + - - +
165A LYS 3.1 1.7 + - - -
166A SER* 2.9 31.3 + - - +
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.4 11.2 - - + -
120A ILE* 4.6 14.6 - - + -
159A ASN 4.0 10.1 - - - +
160A TRP* 3.2 43.4 + - + +
162A THR* 1.3 77.0 - - - +
164A ALA* 1.3 56.3 + - - +
166A SER* 3.2 9.6 + - - -
167A ALA* 2.9 27.9 + - + +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A MET* 4.0 14.6 - - + -
119A GLY 4.4 0.2 - - - +
120A ILE* 4.2 20.1 - - + +
123A SER* 4.0 25.1 - - - +
124A ALA* 3.7 4.8 - - + +
160A TRP 2.9 13.1 + - - +
161A MET* 3.4 11.9 - - - +
163A VAL* 1.3 76.8 - - - +
165A LYS* 1.3 58.2 + - - +
167A ALA* 3.2 6.1 + - - +
168A LEU* 2.9 26.9 + - - +
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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
----------------------------------------------------------
95A ILE 4.7 3.2 + - - -
123A SER 5.0 3.4 + - - +
147A MET 2.8 25.2 + - - -
148A ASP* 3.6 18.6 - - - +
149A PHE* 3.7 25.4 - - - +
151A PRO* 3.8 6.3 - - + -
158A TYR* 3.4 24.9 - - + +
161A MET* 2.9 24.7 + - + +
162A THR* 3.1 7.6 + - - +
164A ALA* 1.3 72.6 - - - +
166A SER* 1.3 67.0 + - - +
168A LEU* 3.1 17.0 + - + +
169A GLU* 3.0 27.7 + - - +
400A NAD 2.8 37.4 + - - -
401A 566 4.0 0.4 - - - -
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 3.4 27.3 + - - +
162A THR* 2.9 16.0 + - - +
163A VAL* 3.5 12.6 - - - -
165A LYS* 1.3 75.7 - - - +
167A ALA* 1.3 62.9 + - - +
169A GLU* 3.4 7.2 + - - +
170A SER* 3.3 20.1 + - - -
173A ARG* 5.3 0.9 + - - -
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Residues in contact with ALA 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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120A ILE* 4.7 13.0 - - + -
124A ALA* 3.9 12.3 - - + -
163A VAL* 2.9 13.8 + - + +
164A ALA* 3.4 11.4 - - - +
165A LYS 3.2 0.2 - - - -
166A SER* 1.3 75.7 - - - +
168A LEU* 1.3 57.9 + - - +
170A SER* 3.1 9.3 + - - -
171A VAL* 2.8 34.4 + - + +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS* 5.1 4.9 - - + -
123A SER 3.8 23.8 - - - +
124A ALA* 3.7 8.0 - - - +
127A TYR* 3.5 41.5 - - + -
146A GLY 5.4 0.2 - - - -
147A MET 3.4 27.1 - - - +
148A ASP* 4.6 1.3 - - - +
164A ALA 2.9 14.2 + - - +
165A LYS* 3.1 22.6 + - + +
167A ALA* 1.3 75.2 - - - +
169A GLU* 1.3 59.2 + - - +
171A VAL* 3.2 3.6 + - + +
172A ASN* 2.8 28.8 + - - +
188A LEU* 4.0 21.8 - - + -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP* 2.5 30.0 - - - +
150A ASP* 4.5 2.9 - - - +
151A PRO* 3.0 32.2 - - - +
152A SER* 5.0 5.5 + - - -
165A LYS 3.0 14.9 + - - +
166A SER* 3.7 8.7 - - - +
167A ALA 3.3 0.2 - - - -
168A LEU* 1.3 75.8 - - - +
170A SER* 1.3 63.2 + - - +
172A ASN* 3.4 4.9 + - - +
173A ARG* 3.3 40.3 + - - +
188A LEU* 3.7 11.7 - - + -
257A ILE* 3.4 25.7 - - + +
259A TYR* 4.8 2.3 + - - -
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER 3.3 9.0 + - - -
167A ALA* 3.1 12.2 + - - -
169A GLU* 1.3 76.6 - - - +
171A VAL* 1.3 65.8 + - - +
173A ARG* 3.1 34.6 + - - +
174A PHE* 3.4 29.8 + - - -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA* 3.9 27.8 - - + +
125A TYR* 5.0 3.6 - - - +
127A TYR* 4.2 5.8 - - + -
128A ALA* 3.9 19.1 - - + +
167A ALA* 2.8 22.1 + - + +
168A LEU* 3.5 9.4 - - - +
170A SER* 1.3 75.5 - - - +
172A ASN* 1.3 58.1 + - - +
174A PHE* 3.0 10.1 + - + +
175A VAL* 2.8 42.5 + - + +
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Residues in contact with ASN 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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127A TYR* 3.6 18.3 + - + -
168A LEU 2.8 20.0 + - - +
169A GLU 3.5 6.7 + - - +
170A SER 3.2 0.2 - - - -
171A VAL* 1.3 72.4 - - - +
173A ARG* 1.3 57.7 + - - +
175A VAL* 3.3 0.5 + - - +
176A ALA* 2.9 27.7 + - - +
186A SER* 2.7 37.6 + - - -
187A ASN* 3.4 2.6 + - - -
188A LEU* 3.8 23.4 - - + +
255A GLY 3.4 20.4 + - - -
256A ASP 3.1 27.3 + - - +
257A ILE* 4.8 1.8 - - - +
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Residues in contact with ARG 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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166A SER 5.3 0.6 + - - -
169A GLU* 3.3 30.2 + - - +
170A SER* 3.1 35.0 + - - +
172A ASN* 1.3 77.4 - - - +
174A PHE* 1.3 67.6 + - + +
176A ALA* 3.6 4.7 - - - +
177A ARG* 3.5 23.2 + - - +
255A GLY* 3.4 27.7 + - - +
257A ILE* 4.9 8.7 - - - +
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Residues in contact with PHE 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 SER* 3.4 24.7 - - - -
171A VAL* 3.0 9.9 + - + +
173A ARG* 1.3 79.4 - - + +
175A VAL* 1.3 65.3 + - + +
176A ALA 3.1 1.6 - - - -
177A ARG* 3.0 36.0 + - - +
178A GLU* 3.3 16.0 + - - +
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Residues in contact with VAL 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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127A TYR* 3.9 15.7 - - + -
128A ALA* 3.9 19.1 - - + -
131A ALA* 3.6 24.0 - - + -
135A LEU* 5.3 1.3 - - + -
144A ILE* 4.5 7.4 - - + -
171A VAL* 2.8 38.9 + - + +
172A ASN 3.3 4.5 + - - +
174A PHE* 1.3 73.2 - - + +
176A ALA* 1.3 58.3 + - - +
178A GLU* 3.1 9.0 + - + +
179A ALA* 2.8 28.2 + - + +
186A SER* 3.5 19.7 - - - +
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Residues in contact with ALA 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 2.9 8.1 + - - +
173A ARG 3.6 9.0 - - - +
174A PHE 3.1 0.2 - - - -
175A VAL* 1.3 75.7 - - - +
177A ARG* 1.3 61.9 + - + +
179A ALA* 4.4 1.6 - - - -
180A GLY* 3.0 22.3 + - - -
184A VAL 4.7 1.0 - - - +
186A SER* 3.9 10.5 - - - -
254A THR* 3.6 18.1 + - + +
255A GLY* 3.4 38.4 - - - +
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Residues in contact with ARG 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 ARG 3.5 15.5 + - - +
174A PHE* 3.0 34.0 + - - +
176A ALA* 1.3 78.9 - - + +
178A GLU* 1.3 69.9 + - - +
180A GLY* 3.7 5.8 + - - -
181A LYS* 3.8 16.7 + - - +
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Residues in contact with GLU 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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135A LEU* 4.3 13.0 - - + -
174A PHE 3.8 11.4 - - - +
175A VAL* 3.1 9.5 + - + +
177A ARG* 1.3 80.3 + - - +
179A ALA* 1.3 64.8 + - - +
181A LYS* 2.9 56.0 + - - +
182A TYR* 3.5 10.0 - - + -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.8 27.8 - - + +
144A ILE* 4.5 7.6 - - + -
175A VAL 2.8 21.7 + - - +
176A ALA* 4.0 4.9 - - - +
178A GLU* 1.3 73.1 - - - +
180A GLY* 1.3 57.6 + - - +
182A TYR* 2.9 21.1 + - - +
184A VAL* 3.0 39.3 + - + +
186A SER* 4.6 5.8 - - - -
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Residues in contact with GLY 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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176A ALA 3.0 16.6 + - - -
177A ARG 3.7 3.3 + - - -
178A GLU 3.2 0.6 - - - -
179A ALA* 1.3 76.2 - - - +
181A LYS* 1.3 61.7 + - - +
183A GLY* 3.0 14.5 + - - -
184A VAL 3.4 8.9 + - - -
254A THR* 6.6 0.4 - - - -
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG 3.8 13.6 + - - +
178A GLU* 2.9 45.8 + - - +
179A ALA 3.1 0.6 - - - -
180A GLY* 1.3 76.7 - - - +
182A TYR* 1.3 68.8 + - + +
183A GLY 3.4 0.4 + - - -
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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
------------------------------------------------------------
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