Contacts of the helix formed by residues 172 - 187 (chain E) in PDB entry 2QC8
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 GLY 172 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LEU* 3.7 17.0 - - - +
147E PHE* 3.7 19.5 - - - -
170E ALA 3.8 2.4 + - - -
171E TYR* 1.3 73.8 - - - +
173E ARG* 1.3 66.7 + - - +
174E ASP* 3.1 4.7 - - - -
175E ILE* 2.9 27.5 + - - +
176E VAL* 3.7 3.1 + - - +
202E TRP* 4.3 3.8 - - - -
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Residues in contact with ARG 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS* 6.2 0.2 - - - +
29D MET* 4.2 18.0 - - - +
42D CYS* 4.4 8.8 - - - -
227D ARG* 3.6 33.2 - - - +
230D GLU* 2.7 47.4 + - - +
704D CL 4.5 6.3 - - - +
164E GLY 3.1 24.0 + - - -
165E VAL* 3.8 11.3 - - - +
170E ALA* 3.6 5.1 + - + +
171E TYR 3.8 1.2 - - - -
172E GLY* 1.3 75.7 - - - +
174E ASP* 1.3 64.8 + - - +
176E VAL* 3.1 6.7 + - + +
177E GLU* 2.9 41.7 + - + +
195E ALA* 5.7 0.6 - - - +
202E TRP* 3.8 34.9 - - + -
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Residues in contact with ASP 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN* 4.3 12.6 + - - -
11D LYS* 2.9 47.8 + - - +
14D LYS* 3.5 29.4 + - + +
231D ASP* 4.8 0.9 - - - +
172E GLY* 2.9 1.9 + - - -
173E ARG* 1.3 77.8 - - - +
175E ILE* 1.3 66.9 + - + +
177E GLU* 3.5 2.5 + - - +
178E ALA* 3.0 25.3 + - - +
232E PHE* 3.6 23.6 - - + -
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Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E TYR* 4.5 3.1 - - - +
139E LEU* 4.1 17.5 - - + -
147E PHE* 5.5 5.4 - - + -
172E GLY* 2.9 20.0 + - - +
174E ASP* 1.3 77.3 - - + +
176E VAL* 1.3 55.4 + - - +
178E ALA* 3.6 1.4 - - - +
179E HIS* 2.7 33.6 + - - +
225E LEU* 3.8 17.5 - - + -
228E VAL* 3.9 6.8 - - + +
229E CYS* 3.8 24.2 - - - -
232E PHE* 3.7 43.7 - - + -
234E VAL* 4.0 25.6 - - + -
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Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ARG* 6.0 0.7 - - - +
137E TYR* 3.6 18.4 - - - +
139E LEU* 5.4 0.2 - - + -
172E GLY 4.0 7.0 - - - +
173E ARG* 3.1 11.4 + - + +
175E ILE* 1.3 77.4 - - + +
177E GLU* 1.3 61.1 + - - +
179E HIS* 3.7 4.8 + - - +
180E TYR* 2.8 33.9 + - + +
193E THR* 4.0 33.5 - - + +
202E TRP* 3.3 51.4 - - + -
203E GLU 5.2 1.8 - - - +
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Residues in contact with GLU 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS* 3.9 27.4 - - - +
18D MET* 4.2 13.1 - - - +
27D GLN* 4.8 4.0 + - - -
29D MET* 4.7 2.8 - - - +
90D ARG* 2.9 51.1 + - - +
227D ARG* 4.5 8.6 + - - +
173E ARG* 2.9 45.4 + - + +
174E ASP 3.8 3.4 - - - +
176E VAL* 1.3 79.9 - - - +
178E ALA* 1.3 62.9 + - - +
180E TYR* 3.4 6.2 + - - +
181E ARG* 3.2 23.7 + - - +
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Residues in contact with ALA 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS* 4.9 5.3 - - + +
17D TYR* 3.6 43.0 - - + -
18D MET* 4.8 2.9 - - - -
174E ASP 3.0 15.7 + - - +
175E ILE 3.6 3.1 - - - +
177E GLU* 1.3 79.0 - - - +
179E HIS* 1.3 58.4 + - - +
181E ARG* 3.2 4.4 + - - +
182E ALA* 2.8 29.3 + - - +
228E VAL* 4.1 3.6 - - + -
232E PHE* 4.0 14.6 - - + -
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Residues in contact with HIS 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E TYR* 5.6 0.8 + - - +
175E ILE 2.7 22.9 + - - +
176E VAL* 3.7 6.6 + - - +
178E ALA* 1.3 72.9 - - - +
180E TYR* 1.3 58.6 + - - +
182E ALA* 3.3 1.4 + - - +
183E CYS* 2.9 52.1 + - - -
190E ILE* 4.0 6.3 - - + +
193E THR* 5.8 1.0 - - - +
204E PHE* 3.5 42.0 - + - +
221E ALA 2.9 22.1 + - - -
224E ILE* 3.5 11.9 - - + -
225E LEU* 3.3 42.1 + - + +
228E VAL* 4.1 12.0 - - + +
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Residues in contact with TYR 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLN* 3.1 33.4 - - + +
44D THR* 3.6 13.2 - - + +
45D ARG 3.5 4.5 - - - -
46D THR* 2.7 37.2 + - - -
90D ARG* 4.6 5.6 - - - -
176E VAL* 2.8 22.2 + - + +
177E GLU* 3.5 8.3 - - - +
178E ALA 3.3 0.2 - - - -
179E HIS* 1.3 74.5 + - - +
181E ARG* 1.3 57.9 + - - +
183E CYS* 3.5 1.9 + - - +
184E LEU* 3.1 35.4 + - + +
190E ILE* 3.8 33.7 - - + -
192E GLY* 3.4 12.2 - - - -
193E THR* 3.2 39.9 - - + -
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Residues in contact with ARG 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR 3.4 24.2 - - - +
18D MET* 3.3 46.4 + - - +
20D LEU* 3.0 28.5 + - + +
21D PRO 5.6 0.2 - - - +
22D GLN* 3.6 39.6 + - - +
27D GLN* 4.1 11.7 + - - +
90D ARG* 3.0 31.7 + - - +
94D ASN* 4.3 0.2 - - - +
177E GLU 3.2 14.6 + - - +
178E ALA 3.7 3.8 - - - +
180E TYR* 1.3 76.8 - - - +
182E ALA* 1.3 66.6 + - - +
184E LEU* 3.4 7.5 + - - +
185E TYR* 3.0 24.4 + - - +
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Residues in contact with ALA 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR* 4.1 15.5 - - + -
20D LEU* 4.3 4.6 - - - +
88E PRO* 3.5 27.3 - - + +
178E ALA 2.8 17.6 + - - +
179E HIS* 3.6 2.5 - - - +
181E ARG* 1.3 76.4 - - - +
183E CYS* 1.3 51.1 + - - +
185E TYR 3.3 0.9 + - - -
186E ALA* 2.7 37.4 + - - +
224E ILE* 3.6 25.4 - - + -
228E VAL* 4.4 0.2 - - + -
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Residues in contact with CYS 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E HIS* 2.9 55.8 + - - +
180E TYR 3.7 4.5 - - - +
182E ALA* 1.3 74.3 - - - +
184E LEU* 1.3 65.4 + - - +
186E ALA* 3.3 4.1 + - - +
187E GLY 3.0 4.5 + - - -
188E VAL* 2.9 52.4 + - + +
190E ILE* 3.9 20.2 - - + -
221E ALA* 4.5 5.8 - - - -
224E ILE* 4.3 11.0 - - - -
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Residues in contact with LEU 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLN* 3.7 40.7 - - + +
25D LYS* 4.0 31.0 - - + +
27D GLN* 4.2 18.8 - - + -
46D THR* 4.4 9.4 - - + -
86E ARG* 5.0 1.0 + - - -
180E TYR* 3.1 40.6 + - + +
181E ARG* 3.4 7.8 + - - +
183E CYS* 1.3 74.1 - - - +
185E TYR* 1.3 63.6 + - - +
187E GLY* 3.1 12.5 + - - -
188E VAL 4.5 4.7 - - - +
190E ILE* 3.4 23.3 - - + +
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Residues in contact with TYR 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 3.9 27.6 - - + -
21D PRO* 3.3 44.8 + - + +
22D GLN* 4.6 1.1 + - - +
86E ARG* 2.9 63.6 + - + +
87E ASP 3.5 21.1 - - - -
88E PRO* 3.6 19.1 - - + -
91E LYS* 3.5 11.9 - - + +
92E ASP* 2.8 35.3 + - - +
181E ARG 3.0 18.6 + - - +
182E ALA 3.6 3.1 - - - +
184E LEU* 1.3 76.7 - - - +
186E ALA* 1.3 62.3 + - - +
187E GLY 3.1 1.4 + - - -
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE* 3.4 19.1 - - + -
86E ARG* 3.2 45.4 + - - +
88E PRO* 4.4 2.5 - - + -
182E ALA 2.7 21.2 + - - +
183E CYS 3.3 5.1 + - - +
185E TYR* 1.3 74.1 - - - +
187E GLY* 1.3 56.9 + - - +
188E VAL* 4.2 5.6 - - + +
224E ILE* 3.8 24.5 - - + -
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Residues in contact with GLY 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE* 3.7 8.2 - - - -
86E ARG* 5.8 1.6 - - - -
183E CYS 3.0 4.3 + - - -
184E LEU 3.1 6.8 + - - -
185E TYR 3.1 5.9 + - - -
186E ALA* 1.3 79.0 - - - +
188E VAL* 1.3 61.9 + - - +
189E LYS* 3.7 0.3 + - - -
217E HIS* 3.4 16.3 - - - -
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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
------------------------------------------------------------
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