Contacts of the helix formed by residues 176 - 190 (chain A) in PDB entry 1QXP
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 PHE 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A PRO* 3.4 42.2 - - + -
81A LEU* 4.4 12.6 - - + -
82A LEU* 4.2 20.0 - - + -
85A PRO* 4.5 0.7 - - + -
86A GLN 3.3 22.4 - - - +
87A PHE* 3.1 8.4 + - - +
131A PHE* 4.5 12.6 - + + -
158A LEU* 4.4 8.3 - - + -
165A LEU* 5.0 10.3 - - + -
174A ASN* 3.8 28.9 - - + -
175A GLU* 1.4 86.3 - - - +
177A TRP* 1.4 55.1 + - - +
178A SER* 3.3 3.4 - - - -
179A ALA* 2.7 43.1 + - + +
180A LEU* 3.3 9.7 + - + +
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Residues in contact with TRP 177 (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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87A PHE* 2.6 42.3 + - + +
88A ILE* 3.9 19.1 - - + +
90A ASP* 5.1 4.4 + - - -
111A ILE* 4.0 20.9 - - + -
114A LEU* 4.2 2.2 - - + -
115A THR* 3.5 27.3 - - + +
121A LEU* 3.6 33.6 - - + +
125A VAL* 4.1 18.2 - - + -
141A PHE* 3.7 4.3 - - - -
175A GLU* 3.7 27.5 + - + -
176A PHE* 1.4 64.8 - - - +
178A SER* 1.3 92.6 + - - +
179A ALA 2.8 4.7 + - - -
180A LEU* 2.9 6.1 + - - +
181A LEU* 2.8 44.6 + - + -
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.1 10.0 - - - +
111A ILE* 3.9 24.8 - - - +
168A VAL* 3.6 22.4 - - - +
169A HIS* 4.2 8.1 + - - -
175A GLU 5.7 0.9 + - - -
176A PHE* 5.0 0.7 - - - -
177A TRP* 1.3 108.4 - - - +
179A ALA* 1.3 67.5 + - - +
180A LEU 3.1 1.2 + - - -
181A LEU* 3.8 5.6 - - - +
182A GLU* 3.4 21.8 + - - +
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Residues in contact with ALA 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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158A LEU* 3.6 21.4 - - + +
165A LEU* 4.8 11.5 - - + +
168A VAL* 3.7 22.6 - - - +
169A HIS* 4.8 5.8 - - + -
175A GLU 5.0 0.4 - - - +
176A PHE* 2.7 38.3 + - + +
178A SER* 1.3 86.0 + - - +
180A LEU* 1.4 57.4 + - + +
182A GLU* 4.5 5.5 + - - +
183A LYS* 4.4 5.9 + - - +
192A TYR* 5.3 2.3 + - - -
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Residues in contact with LEU 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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78A PRO* 5.9 0.2 - - + -
87A PHE* 3.3 35.0 - - + -
131A PHE* 4.5 7.6 - - + -
139A PHE* 3.4 20.9 - - + -
141A PHE* 3.4 22.6 - - + -
154A VAL* 4.3 9.0 - - + +
155A ASP 4.2 7.4 - - - +
156A ASP* 3.9 25.6 - - + -
157A LEU 4.9 0.2 - - - +
158A LEU* 4.3 17.5 - - + -
176A PHE* 3.8 9.0 - - + +
177A TRP 2.9 1.9 + - - +
179A ALA* 1.4 77.8 - - + +
181A LEU* 1.3 66.7 + - - +
182A GLU 3.2 0.7 - - - -
183A LYS* 3.0 17.2 + - + +
184A ALA* 3.3 8.7 + - - +
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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
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111A ILE* 4.5 13.9 - - + -
114A LEU* 4.2 10.1 - - + -
124A VAL* 3.8 32.3 - - + -
125A VAL* 4.2 4.7 - - + -
141A PHE* 3.1 24.9 - - + -
143A LEU* 4.0 18.2 - - + -
177A TRP* 2.8 40.3 + - + +
178A SER* 3.9 8.3 - - - +
180A LEU* 1.3 73.5 - - - +
182A GLU* 1.3 64.2 + - - +
184A ALA* 3.2 2.5 + - + +
185A TYR* 3.1 14.5 + - + +
207A PHE* 4.3 16.4 - - + -
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Residues in contact with GLU 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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103A GLY* 5.7 0.2 - - - -
107A LEU* 4.2 19.3 - - + +
111A ILE* 4.6 10.7 - - + +
167A PHE* 3.6 20.3 - - - +
168A VAL* 2.9 43.4 + - - +
178A SER 3.4 11.5 + - - +
179A ALA 4.8 4.4 - - - +
180A LEU 3.2 1.0 - - - -
181A LEU* 1.3 78.5 - - - +
183A LYS* 1.3 51.9 + - - +
185A TYR* 2.6 8.6 + - - +
186A ALA* 2.5 35.2 + - - +
192A TYR* 4.0 23.2 - - + +
195A LEU* 4.8 10.5 - - + +
207A PHE* 6.4 0.2 - - - -
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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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48A ASP* 4.6 5.3 - - - +
51A PHE* 3.5 31.9 + - + -
53A PRO* 6.0 1.4 - - - +
75A TRP* 4.6 11.7 - - + -
154A VAL* 3.2 19.5 - - + +
155A ASP* 2.5 60.4 + - - +
157A LEU* 3.5 20.0 + - - +
158A LEU* 4.8 3.4 - - + -
179A ALA 4.4 4.5 + - - +
180A LEU* 3.0 20.8 + - + +
182A GLU* 1.3 76.3 - - - +
184A ALA* 1.3 63.3 + - - +
186A ALA* 3.9 5.1 - - - +
187A LYS* 2.9 23.7 + - - +
192A TYR* 4.2 21.1 + - + +
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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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141A PHE* 3.8 30.3 - - + -
143A LEU* 4.1 5.1 - - + +
152A VAL* 3.9 22.1 - - + +
154A VAL* 4.5 10.5 - - + -
180A LEU 3.3 2.0 + - - +
181A LEU 3.2 8.5 + - - +
182A GLU 3.1 0.4 - - - -
183A LYS* 1.3 83.4 - - - +
185A TYR* 1.4 60.2 + - - +
187A LYS* 3.2 6.4 - - - +
188A VAL* 3.0 33.4 + - - +
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Residues in contact with TYR 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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106A TRP* 4.6 11.4 - + - -
107A LEU* 4.2 26.9 - - + -
143A LEU* 4.2 19.1 - - + -
145A GLN* 4.5 7.9 - - - -
181A LEU* 3.1 11.6 + - + +
182A GLU* 2.6 12.6 + - - +
184A ALA* 1.4 75.2 - - - +
186A ALA* 1.4 55.7 - - - +
187A LYS 2.9 11.3 + - - -
188A VAL* 3.2 16.9 - - + +
189A ASN* 3.1 30.2 + - - +
195A LEU* 4.3 17.3 - - + -
202A GLU* 4.3 1.4 - - - +
203A ALA* 3.9 16.0 + - + -
206A ASP* 2.1 52.5 + - + +
207A PHE* 4.2 19.5 - + + -
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Residues in contact with ALA 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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51A PHE* 4.1 2.5 - - + -
182A GLU* 2.5 15.2 + - + +
183A LYS 4.0 4.7 - - - +
185A TYR* 1.4 75.6 - - - +
187A LYS* 1.4 56.9 + - - +
189A ASN* 4.0 1.5 + - - -
190A GLY 3.2 4.9 + - - +
191A SER* 2.6 43.9 + - - +
192A TYR* 3.9 34.8 - - + -
195A LEU* 3.8 18.5 - - + +
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Residues in contact with LYS 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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27A TYR* 4.3 7.7 + - + -
28A LEU* 4.6 4.7 - - + +
30A GLN* 2.5 37.0 - - - +
48A ASP* 2.7 34.2 + - - +
50A ALA* 4.4 4.3 - - - -
51A PHE* 3.2 46.4 - - + +
152A VAL* 4.2 8.6 - - + +
153A VAL* 2.9 20.9 + - - +
154A VAL* 4.6 4.0 - - + -
183A LYS 2.9 19.6 + - - +
184A ALA 3.2 5.6 - - - +
185A TYR 2.9 1.0 - - - -
186A ALA* 1.4 76.4 - - - +
188A VAL* 1.3 70.5 + - - +
189A ASN 3.0 2.3 + - - -
190A GLY* 3.0 15.9 + - - +
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Residues in contact with VAL 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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27A TYR* 3.1 40.6 + - + -
143A LEU* 3.8 13.9 - - + -
145A GLN* 3.6 27.0 - - + +
150A VAL* 5.7 0.4 - - + -
152A VAL* 3.6 31.9 - - + -
184A ALA 3.0 9.8 + - - +
185A TYR* 3.2 16.2 - - + +
187A LYS* 1.3 75.3 - - - +
189A ASN* 1.4 68.9 + - - +
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Residues in contact with ASN 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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145A GLN* 4.6 6.7 + - - -
146A PHE* 6.3 0.6 - - - -
185A TYR* 3.1 23.2 + - - +
186A ALA 4.4 0.9 - - - +
187A LYS 3.0 2.4 + - - -
188A VAL* 1.4 85.9 + - - +
190A GLY* 1.4 54.9 + - - +
191A SER 4.1 0.2 - - - -
194A ALA* 3.7 26.7 - - + +
195A LEU* 2.7 29.3 - - + +
206A ASP* 5.9 0.6 + - - -
470A ARG* 6.1 0.8 - - - +
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Residues in contact with GLY 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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51A PHE* 3.1 26.0 - - - -
57A SER* 5.0 0.9 - - - -
186A ALA 3.2 3.7 + - - +
187A LYS 3.0 9.6 + - - +
189A ASN* 1.4 77.2 - - - +
191A SER* 1.3 60.8 + - - +
194A ALA* 4.5 0.4 - - - -
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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