Contacts of the helix formed by residues 163 - 188 (chain A) in PDB entry 5DHG
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 THR 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA* 4.6 6.3 - - - +
161A VAL* 4.1 11.4 + - + -
162A ARG* 1.3 82.0 - - - +
164A SER* 1.3 67.1 + - - +
165A SER* 4.2 9.0 + - - -
166A LYS* 3.2 41.3 + - - +
167A ALA* 3.2 11.8 + - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 3.2 35.4 + - - +
84A THR* 5.6 0.2 - - - +
85A ALA 4.8 4.5 - - - +
88A ILE* 3.8 20.3 - - - +
163A THR* 1.3 72.8 - - - +
165A SER* 1.3 62.0 + - - +
167A ALA* 3.3 4.5 + - - +
168A GLN* 2.8 41.6 + - - +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 3.1 9.3 - - - -
164A SER* 1.3 84.3 + - - +
166A LYS* 1.3 58.3 + - - +
168A GLN* 3.3 14.6 + - - +
169A ALA* 3.0 25.6 + - - +
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Residues in contact with LYS 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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89A TYR* 4.9 0.2 - - - -
161A VAL* 3.4 37.0 + - - +
162A ARG* 5.2 0.9 - - - -
163A THR* 3.2 25.5 + - - +
165A SER* 1.3 75.0 - - - +
167A ALA* 1.3 61.4 + - - +
169A ALA* 3.1 10.8 + - - +
170A VAL* 2.9 31.5 + - + +
1203A OLA 5.1 8.5 - - - +
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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
----------------------------------------------------------
85A ALA* 3.9 19.5 - - + +
88A ILE* 4.0 10.8 - - + -
89A TYR* 3.5 39.1 - - + +
163A THR 3.2 10.1 + - - +
164A SER 3.7 6.5 - - - +
166A LYS* 1.3 77.4 - - - +
168A GLN* 1.3 58.4 + - - +
170A VAL* 3.2 3.5 + - - +
171A ASN* 2.9 31.7 + - - -
1203A OLA 5.4 0.6 + - - +
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Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 6.1 1.9 - - - +
88A ILE* 3.9 23.3 - - + +
164A SER* 2.8 34.0 + - - +
165A SER* 3.4 13.0 + - - +
167A ALA* 1.3 76.4 - - - +
169A ALA* 1.3 61.6 + - - +
171A ASN* 3.2 8.3 + - - +
172A VAL* 3.1 25.8 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A SER 3.0 13.9 + - - +
166A LYS* 3.1 13.0 + - - +
168A GLN* 1.3 74.3 - - - +
170A VAL* 1.3 64.5 + - + +
172A VAL* 3.1 13.0 + - - +
173A ALA* 3.0 20.3 + - - +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.6 28.7 - - + +
143A ALA* 3.9 18.2 - - + -
166A LYS* 2.9 19.2 + - + +
167A ALA 3.2 7.6 + - - +
169A ALA* 1.3 76.6 - - + +
171A ASN* 1.3 63.6 + - - +
173A ALA* 3.0 9.4 + - + +
174A ILE* 2.8 35.7 + - + +
1203A OLA 3.8 35.2 - - + +
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Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.1 44.5 + - - +
89A TYR* 3.4 20.0 - - - -
91A PHE* 5.6 2.0 - - - +
92A ASN* 3.0 38.7 + - - +
167A ALA 2.9 10.8 + - - -
168A GLN* 3.2 10.5 + - - +
170A VAL* 1.3 74.5 - - - +
172A VAL* 1.3 64.2 + - + +
174A ILE* 3.1 5.9 + - - +
175A TRP* 3.0 31.0 + - + -
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Residues in contact with VAL 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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168A GLN 3.1 15.5 + - - +
169A ALA* 3.1 13.4 + - - +
171A ASN* 1.3 77.0 - - + +
173A ALA* 1.3 64.9 + - - +
175A TRP* 3.1 9.7 + - - +
176A ALA* 3.0 21.7 + - + +
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Residues in contact with ALA 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 ALA 3.0 10.2 + - - +
170A VAL* 3.0 12.3 + - + +
172A VAL* 1.3 77.5 - - - +
174A ILE* 1.3 62.7 + - + +
176A ALA* 3.2 8.7 + - - +
177A LEU* 3.1 29.9 + - + +
1203A OLA 5.9 6.1 - - + -
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Residues in contact with ILE 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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89A TYR* 5.2 0.2 - - + -
92A ASN* 4.0 12.1 - - - +
136A THR* 3.8 23.3 - - + -
139A PHE* 3.8 32.1 - - + +
140A THR* 3.5 37.9 - - - +
143A ALA* 4.3 2.7 - - + -
170A VAL* 2.8 35.8 + - + +
171A ASN* 3.3 11.7 - - - +
172A VAL 3.1 0.2 - - - -
173A ALA* 1.3 77.8 - - - +
175A TRP* 1.3 56.8 + - + +
177A LEU* 3.5 6.1 + - - +
178A ALA* 3.0 27.2 + - - +
1203A OLA 4.5 9.6 - - + -
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Residues in contact with TRP 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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92A ASN* 2.8 30.6 + - - +
95A LEU* 4.1 26.8 - - + +
96A ALA* 4.6 14.4 - - + -
99A LEU* 4.3 23.3 - - + -
132A TYR* 3.5 45.8 - + + -
136A THR* 3.8 23.6 - - + -
171A ASN* 3.0 28.0 + - + -
172A VAL* 3.1 8.0 + - - +
174A ILE* 1.3 77.1 - - - +
176A ALA* 1.3 52.8 + - - +
178A ALA* 3.7 4.0 - - - +
179A SER* 2.7 37.7 + - - +
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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
----------------------------------------------------------
172A VAL* 3.0 13.9 + - + +
173A ALA* 3.2 13.9 + - - +
175A TRP* 1.3 74.5 - - - +
177A LEU* 1.3 64.0 + - - +
179A SER* 3.1 21.5 + - - -
180A VAL* 3.2 11.3 + - - +
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Residues in contact with LEU 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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135A PHE* 5.5 0.7 - - - -
139A PHE* 4.0 30.0 - - + -
173A ALA* 3.1 19.0 + - + +
174A ILE* 3.9 4.3 - - - +
176A ALA* 1.3 72.7 - - + +
178A ALA* 1.3 69.2 + - - +
180A VAL* 2.8 35.7 + - + +
181A VAL* 3.7 4.5 + - - +
1203A OLA 5.5 10.1 - - + -
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Residues in contact with ALA 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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131A TYR 6.0 0.2 - - - -
132A TYR* 3.6 16.6 - - + +
135A PHE* 4.1 25.3 - - + +
136A THR* 3.6 27.6 - - + +
139A PHE* 4.5 2.7 - - + -
174A ILE 3.0 19.1 + - - +
175A TRP 3.7 3.6 - - - +
177A LEU* 1.3 74.3 - - - +
179A SER* 1.3 51.4 + - - +
181A VAL* 3.0 6.8 + - - +
182A GLY* 2.7 32.1 + - - -
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Residues in contact with SER 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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132A TYR* 2.7 28.7 + - - -
175A TRP 2.7 19.9 + - - -
176A ALA* 3.2 15.2 - - - -
177A LEU 3.1 0.4 - - - -
178A ALA* 1.3 75.8 - - - +
180A VAL* 1.3 62.9 + - - +
181A VAL 3.0 1.0 + - - -
183A VAL* 3.0 31.1 + - - +
184A PRO* 3.4 3.6 - - - +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA 3.2 11.5 + - - +
177A LEU* 2.8 31.4 + - + +
179A SER* 1.3 75.1 - - - +
181A VAL* 1.3 63.6 + - + +
184A PRO* 3.1 21.1 - - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 4.4 5.4 - - + -
135A PHE* 3.7 49.4 - - + -
177A LEU 3.7 2.7 + - - +
178A ALA 3.0 5.8 + - - +
179A SER 3.0 0.2 - - - -
180A VAL* 1.3 87.7 - - + +
182A GLY* 1.3 67.0 + - - +
183A VAL 3.4 0.9 - - - -
184A PRO* 3.4 4.0 - - - +
185A VAL* 3.1 36.5 + - + +
219A ILE* 3.9 18.4 - - + -
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Residues in contact with GLY 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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128A ALA* 4.1 7.8 - - - +
131A TYR* 4.8 13.0 - - - +
132A TYR* 3.7 27.6 - - - -
135A PHE* 6.0 0.2 - - - -
178A ALA 2.7 19.7 + - - -
179A SER 3.1 0.6 + - - -
181A VAL* 1.3 75.0 - - - +
183A VAL* 1.3 61.1 + - - +
185A VAL* 3.9 2.6 - - - +
186A ALA* 3.2 21.7 + - - +
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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
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132A TYR* 3.6 17.5 - - + +
179A SER* 3.0 18.4 + - - +
182A GLY* 1.3 72.9 - - - +
184A PRO* 1.3 72.4 - - + +
186A ALA* 3.1 17.2 + - + +
187A ILE* 3.1 25.3 + - + +
1202A OLA 6.1 4.7 - - + -
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Residues in contact with PRO 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A SER 3.4 2.9 - - - +
180A VAL* 3.1 28.3 - - - +
181A VAL* 3.4 7.9 - - - +
183A VAL* 1.3 94.7 - - + +
185A VAL* 1.3 57.5 + - + +
187A ILE* 3.1 12.4 + - + +
188A MET* 2.8 40.4 + - + +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.4 30.8 - - + +
128A ALA* 5.5 0.4 - - - -
131A TYR* 3.8 28.9 - - + -
181A VAL* 3.1 32.9 + - + +
182A GLY* 3.9 3.8 - - - +
183A VAL 3.3 0.8 - - - -
184A PRO* 1.3 76.5 - - + +
186A ALA* 1.3 53.8 + - - +
188A MET* 4.2 19.3 - - + -
189A GLY* 2.6 34.8 + - - -
202A VAL* 3.9 12.8 - - + -
219A ILE* 6.2 0.7 - - + -
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Residues in contact with ALA 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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124A LYS* 3.3 46.0 + - + +
127A ILE* 5.6 0.9 - - - -
128A ALA* 4.0 19.3 - - + +
182A GLY 3.2 13.7 + - - +
183A VAL* 3.1 13.5 + - + +
185A VAL* 1.3 78.3 - - - +
187A ILE* 1.3 60.9 + - - +
189A GLY* 3.4 2.0 - - - +
1202A OLA 4.3 14.4 - - + -
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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
----------------------------------------------------------
124A LYS* 3.2 14.7 + - - -
183A VAL* 3.1 24.8 + - + +
184A PRO* 3.1 11.4 + - + +
186A ALA* 1.3 75.9 - - - +
188A MET* 1.3 68.0 + - + +
190A SER* 5.7 0.2 - - - -
1202A OLA 3.9 29.6 - - + +
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Residues in contact with MET 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PRO* 2.8 22.8 + - + +
185A VAL* 3.7 22.4 - - + +
187A ILE* 1.3 82.7 - - + +
189A GLY* 1.3 62.1 + - - +
190A SER* 3.7 2.8 + - - -
202A VAL* 4.1 21.5 - - + -
203A GLU* 3.6 43.0 + - - +
205A PRO* 4.9 4.5 - - - -
215A PHE* 4.5 27.4 - - + -
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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