Contacts of the helix formed by residues 172 - 191 (chain A) in PDB entry 3QXY
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY 3.3 4.4 + - - -
171A THR* 1.3 77.9 - - - +
173A VAL* 1.3 62.3 + - - +
174A PRO* 3.6 2.0 - - - +
175A GLU* 3.6 18.2 + - - +
176A ALA* 3.3 23.6 + - - +
291A TRP* 3.7 15.0 - - - -
314A GLN* 6.3 1.6 - - - -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PRO* 4.0 15.3 - - + -
164A ARG* 5.2 0.7 - - + -
168A LEU* 3.8 24.2 - - + -
171A THR* 3.2 14.8 - - - +
172A GLY* 1.3 75.2 - - - +
174A PRO* 1.4 73.1 - - + +
176A ALA* 3.2 3.3 + - - +
177A VAL* 2.9 38.7 + - + +
291A TRP* 3.7 37.0 - - + +
294A ILE* 3.8 13.5 - - + -
295A HIS* 4.4 7.6 - - + -
457A VAL* 4.9 0.2 - - + -
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Residues in contact with PRO 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 3.8 30.3 + - + +
165A ARG* 4.4 9.4 - - - -
168A LEU* 3.2 35.0 - - + +
169A GLN* 4.2 6.7 - - - +
170A GLY 5.1 0.4 - - - +
171A THR* 3.7 0.4 - - - +
172A GLY 3.7 1.3 - - - +
173A VAL* 1.4 92.0 - - + +
175A GLU* 1.3 66.4 + - - +
177A VAL* 3.5 1.9 + - - +
178A GLU* 3.0 28.9 + - - +
484A EDO 3.8 27.3 - - - +
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLY* 4.9 9.1 + - - -
172A GLY* 3.6 19.3 + - - +
174A PRO* 1.3 90.0 - - - +
176A ALA* 1.3 66.2 + - - +
178A GLU* 3.5 18.4 - - - +
179A LYS* 3.2 23.2 + - - +
484A EDO 4.5 12.3 + - - -
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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 GLY 3.3 16.5 + - - +
173A VAL* 3.2 5.5 + - - +
175A GLU* 1.3 80.4 - - - +
177A VAL* 1.3 58.3 + - - +
179A LYS* 3.4 9.4 + - - +
180A ASP* 2.9 30.7 + - - +
291A TRP* 4.3 10.5 - - + -
295A HIS* 3.8 29.8 - - + +
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PRO* 4.5 1.8 - - + -
157A MET* 3.7 31.9 - - + +
164A ARG* 3.5 40.2 - - - +
173A VAL* 2.9 36.4 + - + +
174A PRO 3.9 1.1 - - - +
176A ALA* 1.3 74.2 - - - +
178A GLU* 1.3 60.1 + - - +
180A ASP* 3.1 8.4 + - - +
181A LEU* 2.8 36.1 + - + +
295A HIS* 4.0 15.9 - - + -
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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
----------------------------------------------------------
164A ARG* 5.9 2.9 - - - +
174A PRO 3.0 16.0 + - - +
175A GLU* 3.5 19.4 - - - +
177A VAL* 1.3 78.1 - - - +
179A LYS* 1.3 59.9 + - + +
181A LEU* 3.3 9.6 + - + +
182A ALA* 2.9 31.1 + - - +
484A EDO 3.2 34.1 + - - +
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.3 19.6 + - - +
175A GLU 3.2 14.4 + - - +
176A ALA* 3.4 11.9 - - - +
178A GLU* 1.3 78.8 - - + +
180A ASP* 1.3 64.5 + - - +
182A ALA* 3.3 6.5 + - - +
183A ASN* 3.0 34.8 + - - +
351A GLU* 5.9 1.4 + - - -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A MET* 5.4 7.3 - - + +
176A ALA 2.9 16.2 + - - +
177A VAL* 3.4 10.8 - - + +
179A LYS* 1.3 78.3 - - - +
181A LEU* 1.3 59.3 + - + +
183A ASN* 3.8 7.1 + - - +
184A ILE* 2.9 41.1 + - + +
217A VAL* 6.3 1.8 - - + -
221A MET* 4.1 15.9 - - + +
295A HIS* 2.6 35.1 + - - -
475A EDO 4.6 6.7 + - - -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A MET* 3.9 37.5 - - + +
164A ARG* 3.9 20.0 - - - +
177A VAL* 2.8 40.5 + - + +
178A GLU* 3.3 7.4 + - + +
180A ASP* 1.3 73.7 - - + +
182A ALA* 1.3 63.5 + - - +
184A ILE* 3.3 4.8 + - + +
185A ARG* 3.0 24.8 + - - +
214A HIS* 3.9 21.1 + - + +
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Residues in contact with ALA 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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178A GLU 2.9 17.1 + - - +
179A LYS* 3.6 7.6 - - + +
181A LEU* 1.3 75.5 - - - +
183A ASN* 1.3 63.2 + - - +
185A ARG* 3.1 16.6 + - - +
186A SER* 3.1 14.6 + - - -
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Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.7 44.4 + - - +
179A LYS* 3.0 31.5 + - - +
180A ASP* 3.8 5.3 + - - +
182A ALA* 1.3 80.8 - - - +
184A ILE* 1.3 64.0 + - - +
186A SER* 3.0 20.6 + - - -
187A GLU* 3.0 20.5 + - - +
475A EDO 3.5 19.6 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A MET* 3.5 31.9 - - + -
180A ASP* 2.9 26.0 + - + +
181A LEU* 3.6 6.3 - - + +
183A ASN* 1.3 76.4 - - - +
185A ARG* 1.3 65.3 + - - +
187A GLU* 3.6 4.6 + - - +
188A TYR* 3.0 23.2 + - - +
210A LEU* 4.9 1.1 - - + -
213A TYR* 4.0 18.2 - - + -
214A HIS* 3.6 35.4 - - + +
217A VAL* 4.0 24.9 - - + -
475A EDO 3.8 20.4 - - - -
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Residues in contact with ARG 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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181A LEU 3.0 13.2 + - - +
182A ALA* 3.1 11.6 + - - +
184A ILE* 1.3 77.4 - - - +
186A SER* 1.3 65.8 + - - +
188A TYR* 3.3 3.2 + - - +
189A GLN* 2.7 66.4 + - - +
210A LEU* 4.7 26.3 - - - +
214A HIS* 5.4 4.8 + - - -
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA 3.1 9.2 + - - -
183A ASN* 3.0 21.3 + - - -
185A ARG* 1.3 79.0 - - - +
187A GLU* 1.3 64.3 + - - +
189A GLN* 4.0 4.6 - - - +
190A SER* 2.9 35.0 + - - -
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 2.8 39.9 + - - -
119A GLN* 4.2 1.6 + - - +
120A SER* 3.2 5.9 + - - -
123A VAL* 4.0 10.3 - - + +
183A ASN* 3.0 21.0 + - + +
184A ILE* 3.9 2.4 - - - +
186A SER* 1.3 77.5 + - - +
188A TYR* 1.3 60.5 + - - +
190A SER* 4.4 1.3 - - - -
191A ILE* 2.8 36.5 + - + +
192A VAL* 2.8 11.6 + - + -
213A TYR* 3.1 21.2 + - - +
475A EDO 2.8 42.6 + - - -
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Residues in contact with TYR 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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184A ILE 3.0 19.0 + - - +
185A ARG* 3.7 4.9 - - - +
186A SER 3.2 0.4 - - - -
187A GLU* 1.3 77.8 - - - +
189A GLN* 1.3 70.7 + - + +
192A VAL* 3.5 12.5 + - + -
193A LEU* 2.8 64.7 + - + +
196A MET* 4.4 15.9 - - + -
208A ARG 3.7 7.4 + - - -
209A SER 3.5 13.3 + - - -
210A LEU* 3.3 47.7 + - + -
213A TYR* 3.8 38.1 - + + -
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Residues in contact with GLN 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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185A ARG* 2.7 62.0 + - - +
186A SER* 4.2 3.0 - - - +
188A TYR* 1.3 89.7 - - + +
190A SER* 1.3 60.3 + - - +
193A LEU* 4.8 4.8 - - - +
194A PRO* 3.4 17.3 - - - +
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER* 2.9 23.9 + - - -
189A GLN* 1.3 78.4 - - - +
191A ILE* 1.3 75.5 + - - +
194A PRO* 3.6 9.9 - - - +
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Residues in contact with ILE 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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115A ALA 3.8 20.9 - - - +
116A LEU* 4.1 12.3 - - + +
117A GLN 3.2 27.4 - - - +
118A SER* 4.6 8.1 - - - -
123A VAL* 4.0 24.2 - - + -
187A GLU* 2.8 22.9 + - + +
189A GLN 3.5 0.6 - - - -
190A SER* 1.3 96.6 - - - +
192A VAL* 1.3 65.7 + - + +
194A PRO* 3.2 12.5 - - - +
195A PHE* 3.3 15.1 + - - +
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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
------------------------------------------------------------
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