Contacts of the helix formed by residues 178 - 195 (chain A) in PDB entry 3QPV
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 ASN 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A CYS* 1.3 74.0 - - - +
179A SER* 1.3 67.9 + - - +
180A ALA* 2.7 34.6 + - - +
181A GLU* 2.5 49.4 + - - +
182A ALA* 2.9 24.3 + - - +
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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
----------------------------------------------------------
165A MET* 4.7 12.2 - - - +
169A ILE* 4.1 24.8 - - - +
178A ASN* 1.3 74.2 - - - +
180A ALA* 1.3 54.9 + - - -
182A ALA* 3.4 4.7 + - - +
183A MET* 2.7 38.5 + - - +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASN* 2.7 17.0 + - - +
179A SER* 1.3 75.7 - - - +
181A GLU* 1.3 56.8 + - + +
183A MET* 4.0 7.9 - - - +
184A ASP* 3.1 25.3 + - - +
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Residues in contact with GLU 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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176A ASP 4.9 0.3 - - - +
177A CYS* 3.4 20.8 - - - -
178A ASN* 2.5 47.5 + - - +
180A ALA* 1.3 77.9 - - + +
182A ALA* 1.3 60.8 + - - +
184A ASP* 3.7 6.2 - - + +
185A ASP* 2.7 36.8 + - - +
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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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169A ILE* 3.7 22.7 - - + +
174A TYR* 3.7 42.1 - - + -
177A CYS* 4.1 2.7 - - - +
178A ASN 2.9 19.3 + - - +
179A SER 3.6 2.9 - - - +
181A GLU* 1.3 78.7 - - - +
183A MET* 1.3 62.3 + - - +
185A ASP* 3.6 1.7 - - - +
186A PHE* 2.9 25.9 + - - +
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Residues in contact with MET 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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161A ALA* 3.7 35.9 - - + +
164A ILE* 3.8 28.0 - - + -
165A MET* 3.8 24.5 - - + -
169A ILE* 3.8 11.0 - - + +
179A SER 2.7 22.6 + - - +
180A ALA* 4.0 7.6 - - - +
182A ALA* 1.3 72.9 - - - +
184A ASP* 1.3 63.7 + - - +
186A PHE* 3.5 1.4 + - - +
187A MET* 3.1 36.2 + - + +
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Residues in contact with ASP 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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180A ALA 3.1 20.6 + - - +
181A GLU* 3.7 7.7 - - - +
182A ALA 3.3 0.4 - - - -
183A MET* 1.3 78.4 - - - +
185A ASP* 1.3 65.3 + - - +
187A MET* 3.2 9.0 + - - +
188A LYS* 2.8 56.6 + - - +
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Residues in contact with ASP 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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81A TYR* 2.7 16.3 + - - -
82A SER 5.5 0.7 - - - -
83A SER* 3.4 11.0 - - - -
84A TYR* 2.8 40.0 + - + +
174A TYR* 2.4 36.6 + - + -
181A GLU 2.7 21.6 + - - +
182A ALA 3.6 3.4 - - - +
184A ASP* 1.3 76.4 + - - +
186A PHE* 1.3 56.9 + - - +
188A LYS* 3.1 5.7 + - - +
189A ARG* 2.8 23.9 + - - +
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Residues in contact with PHE 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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43A PRO* 3.8 29.2 - - + -
44A ALA* 4.0 4.7 - - + -
164A ILE* 3.8 26.5 - - + -
168A LYS* 3.4 46.0 - - + -
169A ILE* 6.0 0.2 - - + -
174A TYR* 3.4 28.5 - + + +
182A ALA 2.9 16.4 + - - +
183A MET 4.1 3.1 - - - +
185A ASP* 1.3 73.6 - - - +
187A MET* 1.3 60.4 + - - +
189A ARG* 3.3 35.1 + - - +
190A ILE* 2.9 37.5 + - + +
524A FDP 4.1 4.3 - - - -
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Residues in contact with MET 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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160A VAL* 4.4 10.1 - - + -
161A ALA* 6.0 1.8 - - - -
164A ILE* 3.9 20.2 - - + -
183A MET* 3.1 31.9 + - + +
184A ASP* 3.2 10.5 + - - +
186A PHE* 1.3 77.7 - - - +
188A LYS* 1.3 61.3 + - + +
190A ILE* 3.3 17.2 + - + +
191A SER* 3.0 20.1 + - - -
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Residues in contact with LYS 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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84A TYR* 3.7 47.3 - - + +
184A ASP* 2.8 47.3 + - - +
185A ASP* 3.1 6.6 + - - +
187A MET* 1.3 75.7 - - + +
189A ARG* 1.3 66.0 + - - +
191A SER* 2.9 26.5 + - - +
192A CYS* 2.9 12.7 + - - -
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Residues in contact with ARG 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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43A PRO* 5.3 2.0 - - + -
74A ARG* 3.4 0.6 - - - +
81A TYR* 3.3 31.5 + - - -
84A TYR* 3.7 8.8 - - + +
87A PHE* 3.4 39.3 - - + -
173A ASP* 3.3 28.2 + - - -
174A TYR* 3.4 15.9 + - - -
185A ASP 2.8 16.1 + - - +
186A PHE* 3.4 30.7 - - + +
188A LYS* 1.3 70.4 - - - +
190A ILE* 1.3 63.9 + - + +
192A CYS* 3.2 23.0 + - - +
193A TYR* 3.4 19.9 - - + -
524A FDP 3.3 45.7 + - - +
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Residues in contact with ILE 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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42A LEU* 4.5 5.6 - - + -
43A PRO* 3.8 44.0 - - + +
44A ALA* 4.4 0.4 - - + -
45A ARG* 4.0 19.7 - - - +
160A VAL* 4.1 7.0 - - + -
164A ILE* 4.0 16.6 - - + -
186A PHE* 2.9 37.8 + - + +
187A MET* 3.6 16.6 - - + +
188A LYS 3.2 0.2 - - - -
189A ARG* 1.3 77.0 - - - +
191A SER* 1.3 63.2 + - - +
193A TYR* 3.0 15.1 + - - +
194A GLU* 3.2 28.1 + - - +
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Residues in contact with SER 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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187A MET 3.0 10.0 + - - -
188A LYS* 2.9 29.8 + - - +
190A ILE* 1.3 74.4 - - - +
192A CYS* 1.3 65.1 + - - +
193A TYR 3.1 1.0 + - - -
194A GLU* 3.1 32.8 + - - +
195A ALA* 3.9 4.2 + - - +
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Residues in contact with CYS 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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84A TYR* 4.1 22.9 - - - -
87A PHE* 3.4 38.4 - - + +
88A ARG* 3.9 11.9 - - - -
89A PRO* 4.0 25.1 - - + +
188A LYS 2.9 20.1 + - - -
189A ARG* 3.3 10.3 - - - +
190A ILE 3.1 0.4 - - - -
191A SER* 1.3 77.8 + - - +
193A TYR* 1.3 60.4 + - + +
195A ALA* 4.1 7.8 + - - +
196A SER* 5.0 2.3 + - - -
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Residues in contact with TYR 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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42A LEU* 3.8 16.6 - - + -
43A PRO* 3.8 26.0 - - + -
87A PHE* 3.4 30.5 - + + -
98A ARG* 3.2 25.2 + - - -
126A THR* 3.3 33.2 - - + -
128A THR* 3.8 11.0 + - - +
189A ARG* 3.4 25.1 - - + -
190A ILE 3.0 7.4 + - - +
192A CYS* 1.3 76.8 - - + +
194A GLU* 1.3 65.9 + - - +
195A ALA 3.3 1.4 + - - -
196A SER* 3.5 4.4 + - - -
197A TYR* 3.4 21.3 + - - +
524A FDP 2.7 31.0 + - - -
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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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42A LEU* 3.9 26.8 - - + +
45A ARG* 5.1 3.3 + - - -
190A ILE* 3.2 23.4 + - - +
191A SER* 3.1 29.2 + - - +
193A TYR* 1.3 77.3 - - - +
195A ALA* 1.3 64.8 + - - +
196A SER 3.3 0.5 + - - -
197A TYR* 3.4 13.1 + - + +
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Residues in contact with ALA 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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89A PRO* 5.6 7.0 - - + -
191A SER 3.9 5.3 + - - +
192A CYS 4.1 7.3 + - - +
193A TYR 3.3 1.8 - - - -
194A GLU* 1.3 79.6 - - - +
196A SER* 1.3 62.0 + - - +
197A TYR 3.6 1.4 + - - +
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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
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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