Contacts of the helix formed by residues 178 - 185 (chain A) in PDB entry 4QNW
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 TYR 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A TYR* 3.9 14.2 + - - -
108A TRP* 3.6 34.2 - + + -
109A ALA 3.5 8.7 - - - +
110A THR* 4.0 8.5 - - - -
113A ALA* 3.7 29.4 - - + -
173A HIS* 3.5 31.2 - - + +
175A ALA 3.2 13.5 + - - +
176A ASN* 3.1 20.6 - - + -
177A GLY* 1.3 79.0 - - - +
179A LEU* 1.3 69.8 + - - +
180A ILE 3.3 2.2 - - - -
181A ASP 3.0 4.6 + - - -
182A GLN* 2.8 23.3 + - - +
232A TYR* 2.9 29.7 + + - -
233A LEU* 5.0 3.4 - - + +
401A FMN 6.1 2.0 - + - -
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Residues in contact with LEU 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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109A ALA* 2.8 47.2 + - + +
111A GLY* 3.9 4.5 - - - +
126A ILE* 3.9 31.0 - - + -
127A SER* 4.0 8.3 - - - -
128A SER 4.6 0.2 - - - +
143A LEU* 4.5 4.0 - - + -
151A CYS* 4.0 23.3 - - - -
155A PHE* 5.3 1.3 - - + -
173A HIS 5.5 0.2 + - - -
178A TYR* 1.3 71.5 - - - +
180A ILE* 1.3 66.1 + - + +
182A GLN* 3.2 33.2 + - - +
183A PHE* 3.2 28.3 + - + -
205A PHE* 4.0 14.4 - - + -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.9 23.1 - - + -
172A ILE* 3.3 33.9 - - + -
173A HIS 3.6 15.9 + - - +
174A GLY* 3.9 19.3 - - - +
178A TYR 3.3 0.8 - - - -
179A LEU* 1.3 76.2 - - - +
181A ASP* 1.3 58.5 + - - +
183A PHE* 3.0 18.9 + - - +
184A THR* 3.0 14.7 + - - +
205A PHE* 3.6 24.0 - - + -
206A ALA* 3.6 33.7 - - + +
209A VAL* 4.1 10.1 - - + -
226A LEU* 5.9 0.9 - - + -
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Residues in contact with ASP 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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174A GLY 3.7 20.1 + - - +
175A ALA* 3.9 5.6 - - - +
176A ASN 3.4 6.9 + - - -
177A GLY* 2.8 29.9 + - - +
178A TYR 3.0 8.0 + - - +
180A ILE* 1.3 80.0 - - - +
182A GLN* 1.3 57.6 - - - +
184A THR* 4.1 5.8 - - - -
185A GLN* 2.9 65.4 + - - +
227A SER* 4.1 5.1 + - - -
235A MET* 3.5 9.9 - - - +
245A PHE* 3.6 14.6 - - - -
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Residues in contact with GLN 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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110A THR 2.9 25.9 + - - -
111A GLY* 3.6 3.6 - - - -
112A ARG* 2.8 33.3 + - - +
113A ALA 4.0 0.8 - - - +
127A SER* 2.6 35.9 + - - +
128A SER* 2.8 21.3 + - - +
177A GLY 2.9 26.1 + - - +
178A TYR 2.8 17.8 + - - +
179A LEU* 3.2 12.0 + - + +
181A ASP* 1.3 75.9 - - - +
183A PHE* 1.3 58.6 + - - +
185A GLN 3.8 0.9 - - - +
188A CYS* 3.5 22.6 - - - +
189A ASN* 3.5 9.2 + - - +
235A MET* 4.5 4.0 - - + -
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Residues in contact with PHE 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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128A SER* 3.6 25.4 - - - -
143A LEU* 3.8 29.8 - - + -
148A ILE* 3.8 28.7 - - + -
179A LEU* 3.2 27.0 + - + -
180A ILE 3.0 9.5 + - - +
182A GLN* 1.3 75.1 - - - +
184A THR* 1.4 65.1 + - - +
185A GLN 3.3 0.9 + - - -
189A ASN* 2.8 32.7 + - - +
191A ARG* 3.8 19.1 - - - -
195A TRP* 4.0 10.8 - - + -
202A ARG* 3.2 12.2 - - - +
205A PHE* 3.4 45.1 - + + -
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Residues in contact with THR 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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174A GLY 5.4 0.9 + - - -
180A ILE* 3.0 15.0 + - - +
181A ASP* 3.3 16.9 + - - -
183A PHE* 1.4 75.0 - - - +
185A GLN* 1.3 58.7 + - - +
202A ARG* 3.4 29.8 + - - +
203A ALA* 5.1 1.3 - - - -
206A ALA* 4.3 10.0 - - - +
244A GLN* 3.4 28.4 - - + +
245A PHE* 3.7 26.2 - - + -
248A LEU* 3.8 27.6 - - + +
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Residues in contact with GLN 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 ASP* 2.9 47.3 + - - +
182A GLN 3.8 2.1 - - - +
183A PHE 3.3 1.0 - - - -
184A THR* 1.3 80.9 - - - +
186A LYS* 1.3 60.6 + - - +
187A SER* 3.1 7.9 + - - +
188A CYS* 3.1 7.1 + - - +
189A ASN* 2.9 23.2 + - - +
202A ARG* 3.9 2.5 - - - -
227A SER 4.8 4.4 + - - -
228A PRO 4.7 3.4 + - - -
230A SER 5.1 0.2 + - - -
235A MET* 3.5 23.3 - - - +
236A GLY 2.8 25.6 + - - +
237A THR 4.5 1.0 + - - -
238A MET* 3.9 9.5 - - + +
241A LEU* 3.5 10.3 - - - +
245A PHE* 3.5 27.8 - - + -
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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