Contacts of the helix formed by residues 176 - 189 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PRO* 3.8 45.8 - - + -
81B LEU* 5.2 6.3 - - + -
82B LEU* 4.1 24.2 - - + -
85B PRO* 4.0 17.9 - - + -
86B GLN 2.8 26.2 + - - +
87B PHE* 4.3 3.8 - - - -
131B PHE* 4.4 11.4 - + + -
158B LEU* 4.5 4.0 - - + -
165B LEU* 4.3 25.8 - - + -
169B HIS* 6.3 0.2 - - + -
170B SER* 6.3 2.0 - - - -
173B GLY 5.2 4.3 - - - -
174B ASN* 5.2 0.7 - - - -
175B GLU* 1.3 74.2 - - - +
177B TRP* 1.3 67.0 + - - +
178B SER 3.2 2.5 - - - -
179B ALA* 2.8 19.2 + - + +
180B LEU* 3.1 17.1 + - + +
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Residues in contact with TRP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PHE* 2.8 65.7 + - + +
88B ILE* 3.5 24.3 - - + +
90B ASP* 5.0 2.0 - - - -
111B ILE* 4.0 31.9 - - + -
114B LEU* 5.1 5.8 - - + -
115B THR* 4.0 21.5 - - - -
121B LEU* 4.1 23.8 - - + -
125B VAL* 3.9 20.9 - - + -
141B PHE* 4.0 2.1 - - - -
175B GLU* 3.0 34.5 + - + +
176B PHE* 1.3 73.3 - - - +
178B SER* 1.3 78.1 + - - +
180B LEU 3.6 0.7 + - - -
181B LEU* 2.9 42.3 + - + +
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 4.8 8.8 - - - +
111B ILE* 3.9 25.4 - - - +
168B VAL* 4.0 17.6 - - - +
170B SER* 4.1 19.1 + - - -
175B GLU* 4.2 9.8 + - - +
176B PHE 3.0 0.8 + - - -
177B TRP* 1.3 101.3 - - - +
179B ALA* 1.4 66.8 + - - +
181B LEU* 3.9 1.5 - - - -
182B GLU* 3.0 25.8 + - - +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B LEU* 3.6 30.4 - - + +
165B LEU* 4.8 5.2 - - + -
168B VAL 3.6 23.6 - - - +
169B HIS* 4.7 5.2 - - + -
176B PHE* 2.8 16.0 + - + +
178B SER* 1.4 84.3 + - - +
180B LEU* 1.4 57.4 + - - +
182B GLU* 2.9 28.9 + - - +
183B LYS* 3.1 6.2 + - - +
192B TYR* 5.0 0.7 + - - -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PRO* 5.4 0.4 - - + -
87B PHE* 3.3 32.8 - - + -
131B PHE* 4.7 5.6 - - + -
139B PHE* 3.9 20.9 - - + -
141B PHE* 3.6 22.9 - - + -
154B VAL* 4.4 9.1 - - + +
155B ASP 4.1 7.6 - - - +
156B ASP* 3.7 31.0 - - + -
158B LEU* 3.9 24.0 - - + -
176B PHE* 3.1 14.1 + - + +
179B ALA* 1.4 71.6 - - - +
181B LEU* 1.4 67.6 + - - +
183B LYS* 2.8 17.5 + - + +
184B ALA 2.9 10.2 + - - -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 4.2 16.4 - - + -
114B LEU* 4.7 5.8 - - + -
124B VAL* 3.8 23.8 - - + -
125B VAL* 4.8 2.2 - - + -
141B PHE* 3.4 32.0 - - + -
143B LEU* 4.3 10.1 - - + -
177B TRP* 2.9 38.9 + - + +
178B SER* 4.0 2.2 - - - +
179B ALA 3.3 0.2 - - - -
180B LEU* 1.4 73.1 - - - +
182B GLU* 1.3 63.4 + - - +
183B LYS 3.2 0.3 + - - -
184B ALA* 3.3 2.9 + - - +
185B TYR* 3.3 16.7 + - - +
207B PHE* 3.9 34.8 - - + -
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.2 22.1 - - + +
111B ILE* 5.1 0.6 - - - +
167B PHE* 3.4 22.6 - - - +
168B VAL* 2.7 54.0 + - + +
178B SER 3.0 11.7 + - - +
179B ALA 2.9 12.5 + - - +
181B LEU* 1.3 76.8 - - - +
183B LYS* 1.3 55.0 + - - +
185B TYR* 3.3 7.5 + - + +
186B ALA* 3.0 23.9 + - - +
192B TYR* 4.1 16.8 + - + +
195B LEU* 4.8 12.4 - - + +
207B PHE* 6.4 0.4 - - - -
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 4.5 2.2 - - - -
51B PHE* 3.8 33.1 + - + -
53B PRO* 5.9 2.0 - - - +
75B TRP* 4.3 9.7 - - - -
154B VAL* 3.9 15.0 - - + -
155B ASP* 2.6 49.0 + - - +
157B LEU* 2.7 29.6 + - - +
158B LEU* 4.2 9.9 - - + -
179B ALA 3.1 6.3 + - - +
180B LEU* 2.8 17.8 + - + +
182B GLU* 1.3 72.0 - - - +
184B ALA* 1.3 65.0 + - - +
186B ALA* 3.1 1.7 + - - +
187B LYS* 2.8 24.3 + - - +
192B TYR* 3.5 26.4 + - + +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 4.0 24.7 - - + -
143B LEU* 4.4 9.2 - - + -
152B VAL* 3.9 25.7 - - + +
154B VAL* 4.4 7.8 - - + +
180B LEU 2.9 10.4 + - - +
181B LEU 3.6 8.7 - - - +
183B LYS* 1.3 77.0 - - - +
185B TYR* 1.3 64.7 + - - +
187B LYS* 3.1 6.3 + - - +
188B VAL* 3.0 25.5 + - - +
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TRP* 4.2 4.1 - + - -
107B LEU* 3.4 32.1 - - + -
143B LEU* 4.0 20.5 - - + +
145B GLN* 4.6 3.8 - - - -
181B LEU 3.3 9.3 + - - +
182B GLU* 3.6 10.3 - - - +
183B LYS 3.2 0.6 - - - -
184B ALA* 1.3 79.6 - - - +
186B ALA* 1.2 61.1 + - - +
188B VAL* 4.5 4.9 - - + +
189B ASN* 2.9 54.1 + - - -
195B LEU* 3.5 22.1 - - + +
202B GLU* 3.3 24.9 + - - +
203B ALA* 3.7 8.9 + - + +
206B ASP* 3.8 26.2 + - + -
207B PHE* 4.1 15.0 - + + -
470B ARG* 4.9 1.2 + - - -
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 3.7 13.9 - - + -
182B GLU 3.0 11.7 + - - +
183B LYS 3.5 6.3 - - - +
185B TYR* 1.2 77.9 - - - +
187B LYS* 1.3 71.8 + - - +
188B VAL 2.9 2.7 + - - -
189B ASN 3.0 9.9 + - - -
190B GLY 3.2 8.0 + - - -
191B SER 3.4 26.2 + - - +
192B TYR* 3.9 22.7 - - + +
195B LEU* 4.2 8.4 - - + +
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 3.5 32.6 + - + -
28B LEU* 3.5 7.4 - - + +
30B GLN* 3.3 23.6 - - - +
48B ASP* 3.3 22.2 - - - +
50B ALA* 3.7 10.3 - - - +
51B PHE* 3.1 41.2 - - + +
152B VAL* 4.1 10.3 - - + -
153B VAL 3.2 27.4 - - - +
154B VAL* 4.3 3.1 - - + -
183B LYS 2.8 16.6 + - - +
184B ALA 3.5 7.9 - - - +
186B ALA* 1.3 78.4 - - - +
188B VAL* 1.3 61.6 + - - +
190B GLY* 3.1 11.1 + - - -
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.4 32.7 + - + -
143B LEU* 4.5 7.6 - - + -
145B GLN* 3.0 49.1 - - + +
150B VAL* 5.5 0.4 - - + -
152B VAL* 3.8 28.0 - - + -
184B ALA 3.0 16.1 + - - +
185B TYR* 4.3 8.1 - - + +
186B ALA 2.9 1.8 + - - -
187B LYS* 1.3 73.5 - - - +
189B ASN* 1.3 69.8 + - - +
190B GLY 3.0 6.1 + - - -
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN* 5.3 2.4 + - - +
146B PHE* 6.0 2.1 - - - -
185B TYR* 2.9 52.1 + - - +
186B ALA 3.0 3.4 + - - +
188B VAL* 1.3 85.1 - - - +
190B GLY* 1.4 52.9 + - - -
191B SER 3.3 4.7 - - - -
194B ALA* 3.1 26.2 - - - +
195B LEU* 3.6 28.4 - - + +
417B HIS* 5.6 5.2 + - - -
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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