Contacts of the helix formed by residues 177 - 195 (chain A) in PDB entry 1QNB
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 MET 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ILE* 6.2 2.2 - - + -
118A ILE* 3.8 4.0 - - - -
175A ALA* 3.6 5.2 - - - +
176A LYS* 1.3 94.2 - - - +
178A ARG* 1.3 66.5 + - - +
179A ASP* 4.3 8.3 - - + +
180A GLU* 3.0 38.9 + - + +
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Residues in contact with ARG 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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25A LEU* 3.5 26.3 - - + +
86A SER* 4.5 10.1 - - - -
87A GLU* 2.7 44.6 + - - +
118A ILE* 3.5 13.2 - - + +
177A MET* 1.3 72.2 - - - +
179A ASP* 1.3 70.7 + - - +
181A THR* 3.1 12.4 + - - -
182A TYR* 3.1 59.1 + - + -
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Residues in contact with ASP 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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16A LYS* 3.4 28.3 + - - -
177A MET* 3.1 8.6 + - + +
178A ARG* 1.3 83.9 - - - +
180A GLU* 1.3 56.8 + - + +
182A TYR* 3.5 12.9 - - + +
183A LYS* 2.8 31.1 + - - +
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Residues in contact with GLU 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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158A PRO* 3.6 25.2 - - + +
160A ILE* 3.9 11.3 - - + +
175A ALA* 3.4 9.8 - - + -
176A LYS* 2.8 35.2 + - - +
177A MET* 3.0 25.7 + - + +
179A ASP* 1.3 74.9 - - + +
181A THR* 1.3 59.7 + - - +
183A LYS* 4.3 2.0 - - - -
184A ALA* 2.8 31.5 + - - +
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Residues in contact with THR 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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23A PRO* 4.2 18.3 - - + +
25A LEU* 4.5 9.6 - - + -
118A ILE* 4.0 9.9 + - - +
120A GLY* 4.4 13.9 - - - +
160A ILE* 5.2 0.2 - - - -
172A ILE* 3.7 35.1 - - + +
175A ALA* 3.1 23.1 - - - +
178A ARG* 3.1 17.1 + - - -
180A GLU* 1.3 79.4 - - - +
182A TYR* 1.3 64.0 + - + +
184A ALA* 3.8 1.0 - - - +
185A PHE* 3.2 22.7 + - - +
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Residues in contact with TYR 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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16A LYS* 3.6 19.1 - - - +
17A HIS* 3.5 25.5 + + + +
22A VAL* 4.0 17.1 - - + +
23A PRO* 3.7 41.8 + - + -
25A LEU* 4.5 13.9 - - + +
178A ARG* 3.1 53.9 + - + -
179A ASP* 3.5 24.5 - - - +
181A THR* 1.3 79.2 - - - +
183A LYS* 1.3 56.8 + - - +
185A PHE* 3.5 3.8 + - - +
186A GLU* 3.1 34.1 + - + +
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Residues in contact with LYS 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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157A VAL* 6.4 1.8 - - - -
158A PRO* 3.9 17.7 - - + -
179A ASP 2.8 19.3 + - - +
180A GLU* 3.8 6.5 - - - +
182A TYR* 1.3 74.7 - - - +
184A ALA* 1.3 59.9 + - - +
186A GLU* 3.2 10.1 + - + +
187A ASN* 2.8 56.6 + - - +
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Residues in contact with ALA 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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155A MET* 3.4 26.5 - - - +
158A PRO* 4.3 2.6 - - + +
160A ILE* 3.5 34.8 - - + -
162A LEU* 4.0 5.8 - - + +
172A ILE* 4.0 5.2 - - + -
180A GLU 2.8 19.8 + - - +
181A THR 3.8 5.2 - - - +
183A LYS* 1.3 74.6 - - - +
185A PHE* 1.3 63.0 + - - +
187A ASN 3.3 0.3 + - - -
188A ILE* 3.0 20.4 + - - +
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Residues in contact with PHE 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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19A SER* 3.2 27.8 - - - -
21A ILE* 3.7 27.4 - - + -
23A PRO* 3.8 18.6 - - + -
122A CYS* 3.3 28.3 - - - -
124A VAL* 3.8 26.5 - - + -
170A ILE* 4.8 3.8 - - + -
172A ILE* 3.6 21.9 - - + +
181A THR 3.2 5.3 + - - +
182A TYR 3.6 7.4 - - - +
183A LYS 3.2 0.4 - - - -
184A ALA* 1.3 77.4 - - - +
186A GLU* 1.3 69.6 + - - +
188A ILE* 3.0 19.5 - - + +
189A TYR* 2.9 41.5 + + - +
192A LEU* 4.7 1.3 - - + -
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Residues in contact with GLU 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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16A LYS 4.5 7.0 - - - +
17A HIS* 3.5 16.3 + - - +
18A PRO* 3.2 35.5 - - + +
19A SER* 2.7 34.1 + - - -
21A ILE 3.9 3.1 - - - +
182A TYR* 3.1 20.0 + - + +
183A LYS* 3.7 12.3 - - + +
185A PHE* 1.3 85.2 - - + +
187A ASN* 1.3 64.2 + - - +
189A TYR* 3.6 3.6 + - - +
190A PRO* 3.1 21.1 - - - +
14B LEU* 3.8 13.4 - - + +
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Residues in contact with ASN 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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155A MET* 3.6 17.2 - - + -
157A VAL* 3.0 27.7 + - - +
158A PRO* 4.0 5.7 - - - +
183A LYS* 2.8 48.3 + - - +
184A ALA 3.5 5.8 - - - +
185A PHE 3.1 0.2 - - - -
186A GLU* 1.3 78.7 - - - +
188A ILE* 1.3 59.3 + - - +
190A PRO* 3.6 10.4 - - - +
191A VAL* 3.8 11.3 - - - +
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Residues in contact with ILE 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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153A TYR* 3.8 45.1 - - + -
155A MET* 4.0 5.8 - - + +
162A LEU* 3.8 17.5 - - + -
164A ILE* 4.1 12.6 - - + -
170A ILE* 5.2 2.5 - - + -
184A ALA 3.0 15.0 + - - +
185A PHE* 3.0 27.1 - - + +
187A ASN* 1.3 77.9 - - - +
189A TYR* 1.3 66.3 + - - +
191A VAL* 2.7 30.5 + - + +
192A LEU* 2.9 41.2 + - + +
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Residues in contact with TYR 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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19A SER* 3.7 21.8 + - - -
21A ILE* 4.2 13.6 - - + +
124A VAL* 4.0 29.0 + - + -
126A PHE* 3.8 18.7 - + - -
185A PHE* 2.9 33.7 + + + +
186A GLU 3.9 4.0 - - - +
188A ILE* 1.3 77.8 - - - +
190A PRO* 1.3 68.9 - - + +
192A LEU* 3.0 8.5 + - + +
193A SER* 3.0 30.6 + - - -
14B LEU* 3.5 45.5 + - + -
15B SER* 5.9 0.3 - - - -
18B PRO* 3.8 22.6 - - + +
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Residues in contact with PRO 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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186A GLU 3.1 17.0 - - - +
187A ASN 3.6 7.6 - - - +
188A ILE 3.6 2.7 - - - -
189A TYR* 1.3 91.6 - - + +
191A VAL* 1.3 57.9 + - + +
193A SER* 3.6 2.3 + - - -
194A GLU* 3.1 27.6 + - - +
14B LEU* 3.8 27.1 - - + -
18B PRO 3.3 11.4 - - - +
19B SER 3.6 20.4 - - - +
20B GLY* 4.7 2.2 - - - -
189B TYR* 4.5 1.2 + - - -
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Residues in contact with VAL 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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133A LEU* 3.7 23.7 - - + +
137A HIS* 3.3 38.1 - - + +
153A TYR* 5.2 2.7 - - + +
187A ASN 3.8 14.8 - - - +
188A ILE* 2.7 33.5 + - + +
190A PRO* 1.3 72.3 - - + +
192A LEU* 1.3 61.7 + - - +
194A GLU* 3.4 8.9 + - - +
195A PHE* 3.3 26.5 + - + +
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Residues in contact with LEU 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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124A VAL* 3.7 30.7 - - + -
126A PHE* 3.3 14.2 - - + -
128A ILE* 3.8 16.4 - - + +
133A LEU* 4.1 11.4 - - + -
164A ILE* 4.1 30.3 - - + -
170A ILE* 3.8 16.2 - - + -
185A PHE* 4.7 0.7 - - + -
188A ILE* 2.9 49.9 + - + +
189A TYR* 3.5 9.6 - - - +
191A VAL* 1.3 76.6 - - - +
193A SER* 1.3 63.3 + - - +
195A PHE 3.2 4.7 + - - +
196A ARG 3.1 17.2 + - - -
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Residues in contact with SER 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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126A PHE* 3.8 18.5 - - - -
189A TYR* 3.0 14.2 + - - -
190A PRO 3.7 2.7 - - - -
192A LEU* 1.3 74.3 - - - +
194A GLU* 1.3 64.6 + - - +
195A PHE 3.0 2.7 + - - -
196A ARG* 3.2 18.4 + - - +
18B PRO* 3.0 50.3 + - - +
19B SER* 3.9 4.7 - - - -
186B GLU* 5.4 0.7 - - - -
189B TYR* 4.5 2.2 - - - -
190B PRO* 3.9 11.6 - - - +
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Residues in contact with GLU 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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137A HIS* 4.9 5.2 + - - -
190A PRO 3.1 13.3 + - - +
191A VAL* 3.6 12.0 - - - +
193A SER* 1.3 79.8 - - - +
195A PHE* 1.3 75.3 + - + +
126B PHE* 3.6 23.4 - - - -
189B TYR* 3.2 42.1 + - + +
190B PRO* 3.6 9.2 - - - +
193B SER* 2.6 41.7 + - - -
196B ARG* 6.2 0.2 - - - -
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Residues in contact with PHE 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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128A ILE* 3.5 6.5 - - + -
129A ARG* 2.8 66.2 + - + +
132A GLY* 3.3 17.0 - - - -
133A LEU* 3.6 26.9 - - + -
136A SER* 2.8 33.2 - - - -
137A HIS* 4.1 9.9 - - - -
191A VAL* 3.3 24.1 + - + +
192A LEU 3.2 8.0 + - - +
193A SER 3.0 0.6 - - - -
194A GLU* 1.3 106.9 - - + +
196A ARG* 1.3 58.4 + - - +
193B SER* 4.0 16.2 - - - -
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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