Contacts of the helix formed by residues 172 - 187 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G LEU* 3.7 12.9 - - - +
147G PHE* 3.6 24.0 - - - -
170G ALA 3.8 1.8 + - - -
171G TYR* 1.3 73.4 - - - +
173G ARG* 1.3 66.3 + - - +
174G ASP* 3.1 3.8 - - - -
175G ILE* 3.0 27.5 + - - +
176G VAL* 3.5 3.8 + - - +
202G TRP* 4.2 3.1 - - - -
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Residues in contact with ARG 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LYS* 5.7 0.4 - - - +
29F MET* 4.2 20.6 - - - +
42F CYS* 4.7 6.6 - - - -
227F ARG* 3.5 37.9 - - - +
230F GLU* 2.7 42.7 + - - +
164G GLY 3.1 25.7 + - - -
165G VAL* 3.8 9.5 - - - +
170G ALA* 3.5 9.5 + - + +
171G TYR 3.7 1.6 - - - -
172G GLY* 1.3 75.1 - - - +
174G ASP* 1.3 56.4 + - - +
176G VAL* 2.9 8.6 + - + +
177G GLU* 2.7 51.3 + - + +
195G ALA* 5.9 0.4 - - - +
202G TRP* 3.8 29.5 - - + -
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Residues in contact with ASP 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ASN 4.7 5.5 + - - +
11F LYS* 2.7 43.6 + - - +
14F LYS* 3.3 35.0 + - + +
231F ASP* 4.6 1.4 - - - +
172G GLY* 3.0 0.9 + - - -
173G ARG* 1.3 79.3 - - - +
175G ILE* 1.3 67.4 + - + +
177G GLU* 3.3 2.1 + - - +
178G ALA* 2.9 26.9 + - - +
232G PHE* 3.7 27.0 - - + -
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Residues in contact with ILE 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G TYR* 4.7 2.2 - - - +
139G LEU* 3.9 14.6 - - + -
147G PHE* 5.1 7.9 - - + -
172G GLY* 3.0 25.8 + - - +
174G ASP* 1.3 77.5 - - + +
176G VAL* 1.3 56.2 + - - +
178G ALA* 3.6 1.2 - - - +
179G HIS* 2.8 37.2 + - - +
225G LEU* 3.8 16.4 - - + -
228G VAL* 3.8 5.6 - - + +
229G CYS* 3.7 24.7 - - - -
232G PHE* 3.9 38.6 - - + -
234G VAL* 3.9 25.1 - - + -
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Residues in contact with VAL 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ARG* 6.0 0.2 - - - +
137G TYR* 3.7 16.4 - - - +
139G LEU* 5.3 0.4 - - + -
172G GLY 3.9 7.6 - - - +
173G ARG* 2.9 11.8 + - + +
175G ILE* 1.3 78.1 - - + +
177G GLU* 1.3 63.5 + - - +
179G HIS* 3.6 4.7 + - - +
180G TYR* 2.9 29.5 + - + +
193G THR* 4.0 32.5 - - + +
202G TRP* 3.3 54.7 - - + -
203G GLU 5.2 1.3 - - - +
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Residues in contact with GLU 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LYS* 3.8 26.9 - - - +
18F MET* 4.3 13.1 - - - +
27F GLN* 4.9 3.3 + - - -
29F MET* 4.6 3.1 - - - +
89F PHE 5.5 0.2 - - - +
90F ARG* 2.7 54.1 + - - +
227F ARG* 4.8 6.3 + - - -
173G ARG* 2.7 48.0 + - + +
174G ASP 3.7 2.9 - - - +
176G VAL* 1.3 77.2 - - - +
178G ALA* 1.3 63.2 + - - +
180G TYR* 3.3 7.8 + - - +
181G ARG* 3.1 23.7 + - - +
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Residues in contact with ALA 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LYS* 5.0 4.2 - - - +
17F TYR* 3.7 40.5 - - + -
18F MET* 4.9 2.2 - - - -
174G ASP 2.9 17.9 + - - +
175G ILE 3.6 3.4 - - - +
177G GLU* 1.3 76.7 - - - +
179G HIS* 1.3 51.3 + - - +
181G ARG* 3.2 3.8 + - - +
182G ALA* 2.8 36.6 + - - +
228G VAL* 3.8 14.4 - - + -
232G PHE* 4.0 8.1 - - + -
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Residues in contact with HIS 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G TYR* 5.5 1.0 + - - -
175G ILE 2.8 20.7 + - - +
176G VAL* 3.6 6.5 + - - +
178G ALA* 1.3 72.0 - - - +
180G TYR* 1.3 67.8 + - - +
182G ALA* 3.5 6.0 - - - +
183G CYS* 2.9 51.0 + - - -
190G ILE* 4.3 6.9 - - + +
193G THR* 5.9 1.2 - - - +
204G PHE* 3.7 43.0 - + - +
221G ALA 2.8 22.7 + - - -
224G ILE* 3.6 11.2 - - + -
225G LEU* 3.4 41.7 + - + +
228G VAL* 4.2 6.6 - - + +
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Residues in contact with TYR 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLN* 3.3 28.3 - - + +
44F THR* 3.5 22.7 - - + +
45F ARG 3.4 7.3 + - - -
46F THR* 2.6 42.2 + - - -
90F ARG* 4.7 4.9 - - - -
176G VAL* 2.9 17.2 + - + +
177G GLU* 3.3 8.5 + - - +
179G HIS* 1.3 76.3 + - - +
181G ARG* 1.3 63.3 + - - +
183G CYS* 3.3 1.6 + - - +
184G LEU* 3.1 31.3 + - + +
190G ILE* 3.5 29.8 - - + -
192G GLY* 3.5 11.0 - - - -
193G THR* 3.2 35.2 - - + -
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Residues in contact with ARG 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR 3.3 24.0 - - - +
18F MET* 2.9 52.6 + - - +
20F LEU* 3.0 23.9 + - + +
22F GLN* 3.6 37.7 + - - +
27F GLN* 3.8 14.8 + - - +
90F ARG* 3.1 29.1 + - - +
91F LYS* 5.9 0.6 - - - +
94F ASN* 4.2 1.8 - - - +
177G GLU 3.1 15.2 + - - +
178G ALA 3.7 3.6 - - - +
180G TYR* 1.3 77.0 - - + +
182G ALA* 1.3 65.0 + - - +
184G LEU* 3.4 9.2 + - - +
185G TYR* 3.0 26.2 + - - +
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Residues in contact with ALA 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR* 4.2 5.8 - - + -
20F LEU* 4.4 4.8 - - - +
88G PRO* 3.5 28.1 - - + +
178G ALA 2.8 20.8 + - - +
179G HIS* 3.5 4.5 - - - +
181G ARG* 1.3 73.3 - - - +
183G CYS* 1.3 56.8 + - - +
186G ALA* 2.9 29.3 + - - +
224G ILE* 3.4 26.9 - - + -
228G VAL* 4.1 8.3 - - + -
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Residues in contact with CYS 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G HIS* 2.9 56.8 + - - +
180G TYR 3.7 3.4 - - - +
181G ARG 3.2 0.2 - - - -
182G ALA* 1.3 75.3 - - - +
184G LEU* 1.3 65.7 + - - +
186G ALA* 3.2 3.6 + - - +
187G GLY 3.0 20.3 + - - -
188G VAL* 3.0 39.1 + - + -
190G ILE* 4.0 17.5 - - + -
206G ILE* 5.5 0.2 - - - -
221G ALA* 4.4 4.0 - - - -
224G ILE* 4.1 12.8 - - - -
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Residues in contact with LEU 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLN* 3.9 30.1 - - + +
25F LYS* 3.6 36.1 - - + -
27F GLN* 4.2 19.5 - - + +
46F THR* 4.3 8.3 - - + -
86G ARG* 5.0 1.0 + - - -
180G TYR* 3.1 41.6 + - + +
181G ARG* 3.8 12.6 - - - +
183G CYS* 1.3 77.1 - - - +
185G TYR* 1.3 63.9 + - - +
187G GLY* 3.4 8.7 + - - -
188G VAL 4.5 4.5 - - - +
190G ILE* 3.9 18.2 - - + +
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Residues in contact with TYR 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 3.9 25.4 - - + -
21F PRO* 3.4 45.0 + - + +
22F GLN* 4.7 1.3 + - - -
86G ARG* 3.0 66.0 + - + +
87G ASP 3.8 18.4 - - - -
88G PRO* 3.8 17.9 - - + -
91G LYS* 3.5 14.7 - - + +
92G ASP* 2.8 35.1 + - - +
181G ARG 3.0 17.7 + - - +
182G ALA 3.8 2.7 - - - +
184G LEU* 1.3 79.1 - - - +
186G ALA* 1.3 62.9 + - - +
187G GLY* 3.3 0.7 + - - -
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Residues in contact with ALA 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G PHE* 3.4 16.2 - - + +
86G ARG* 2.9 51.4 + - - +
88G PRO* 4.3 2.5 - - + -
96G LEU* 5.3 0.4 - - + -
182G ALA 2.9 18.1 + - - +
183G CYS 3.2 5.1 + - - +
185G TYR* 1.3 78.2 - - - +
187G GLY* 1.3 57.4 + - - +
188G VAL* 4.3 4.3 - - + +
224G ILE* 3.9 21.5 - - + -
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Residues in contact with GLY 187 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G PHE* 3.8 7.5 - - - -
86G ARG* 5.8 0.9 - - - -
183G CYS 3.0 4.0 + - - -
184G LEU 3.4 6.8 + - - -
185G TYR 3.3 4.2 - - - -
186G ALA* 1.3 77.5 - - - +
188G VAL* 1.3 64.5 + - - +
189G LYS* 3.5 1.0 + - - +
217G HIS* 3.4 14.9 - - - -
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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