Contacts of the helix formed by residues 175 - 189 (chain A) in PDB entry 1DQU
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLY* 1.3 71.6 - - - -
176A LEU* 1.3 71.1 + - - -
177A THR* 3.2 4.5 - - - -
178A ALA* 3.2 8.0 + - - +
179A VAL* 3.0 25.6 + - - +
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Residues in contact with LEU 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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175A GLY* 1.3 76.4 - - - +
177A THR* 1.3 64.6 + - + +
179A VAL* 3.6 14.4 - - + +
180A MET* 3.4 27.9 + - + +
219A GLU* 4.9 3.1 - - + +
222A ASN* 4.1 45.1 - - + +
223A ARG* 4.7 7.2 - - + -
226A ALA* 4.1 12.1 - - + +
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Residues in contact with THR 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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175A GLY* 4.9 1.6 - - - -
176A LEU* 1.3 78.7 + - + +
178A ALA* 1.3 69.5 + - - +
180A MET* 2.9 30.0 + - + +
181A LYS* 3.0 22.4 + - - +
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Residues in contact with ALA 178 (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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120A MET* 4.1 9.5 - - - +
172A GLY 3.8 2.9 - - - +
173A HIS 3.5 25.1 - - - +
174A GLY* 3.8 1.6 - - - -
175A GLY 3.2 19.1 + - - +
177A THR* 1.3 83.5 + - - +
179A VAL* 1.3 51.6 + - - +
181A LYS* 3.0 10.6 + - - +
182A LEU* 2.8 35.2 + - - +
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Residues in contact with VAL 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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171A THR 4.7 0.4 - - - +
172A GLY* 3.5 29.4 + - - +
174A GLY 4.4 3.4 - - - +
175A GLY 3.0 20.9 + - - +
176A LEU* 3.6 11.7 - - + +
178A ALA* 1.3 75.5 - - - +
180A MET* 1.3 57.2 + - - +
182A LEU* 3.5 5.1 + - - +
183A THR* 2.8 31.5 + - - +
196A ILE* 4.9 1.6 - - + -
223A ARG* 4.4 23.8 - - + +
226A ALA* 4.1 15.0 - - + -
227A ILE* 3.8 28.0 - - + +
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Residues in contact with MET 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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176A LEU* 3.4 23.1 + - + +
177A THR* 2.9 22.4 + - + +
179A VAL* 1.3 74.4 - - - +
181A LYS* 1.3 70.7 + - + +
183A THR* 3.1 2.3 + - - -
184A LYS* 3.0 17.5 + - - +
226A ALA* 3.5 35.2 - - + +
229A ALA* 4.7 10.5 - - - -
230A GLN* 3.3 34.9 - - + +
233A ILE* 6.3 2.7 - - - -
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Residues in contact with LYS 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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120A MET* 4.2 9.0 - - + -
177A THR* 3.0 18.3 + - - +
178A ALA* 3.5 10.5 - - - +
180A MET* 1.3 76.5 - - + +
182A LEU* 1.3 65.5 + - - +
183A THR 2.7 1.9 + - - -
184A LYS* 2.8 19.7 + - + +
185A LEU* 3.0 18.7 + - + +
230A GLN* 5.6 0.7 - - - +
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Residues in contact with LEU 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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120A MET* 3.0 45.8 - - + +
124A PRO* 3.8 7.9 - - + -
169A ALA* 3.5 29.2 - - + +
172A GLY* 4.0 20.6 - - - +
173A HIS* 4.0 11.0 - - + -
178A ALA 2.8 17.6 + - - +
179A VAL* 3.6 6.5 - - - +
181A LYS* 1.3 72.0 - - - +
183A THR* 1.3 60.9 + - - +
185A LEU* 3.6 2.8 + - + +
186A PHE* 3.1 54.4 + - + -
194A ILE* 6.1 0.7 - - + -
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Residues in contact with THR 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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179A VAL* 2.8 21.3 + - - +
180A MET 3.6 5.4 - - - -
181A LYS 2.7 5.3 + - - -
182A LEU* 1.3 72.8 - - - +
184A LYS* 1.3 54.5 + - - -
186A PHE* 3.0 9.6 + - - +
187A VAL* 2.5 48.7 + - + +
194A ILE* 4.2 6.6 - - + +
227A ILE* 3.8 32.9 - - + +
230A GLN* 3.9 22.4 - - + -
231A ALA 4.5 2.2 - - - +
238A LEU* 4.0 17.9 - - + -
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Residues in contact with LYS 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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50A TYR* 4.4 13.2 + - - -
180A MET 3.0 11.3 + - - +
181A LYS* 2.8 12.2 + - + +
183A THR* 1.3 76.0 - - - +
185A LEU* 1.3 65.8 + - + +
187A VAL* 2.9 2.9 + - - +
188A GLU* 2.8 49.6 + - + +
230A GLN* 4.3 13.6 + - - +
233A ILE* 6.3 0.6 - - - +
234A MET* 3.4 31.1 - - - +
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Residues in contact with LEU 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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120A MET* 3.9 25.8 - - + -
121A ASN* 4.0 31.0 - - + +
124A PRO* 4.0 12.6 - - + -
181A LYS* 3.0 18.1 + - + +
182A LEU 3.7 5.8 - - - +
184A LYS* 1.3 76.9 - - + +
186A PHE* 1.3 58.6 + - - +
188A GLU* 2.9 28.0 + - - +
189A ARG* 3.0 39.6 + - - +
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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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123A VAL* 4.1 2.5 - - + -
124A PRO* 3.9 26.7 - - + +
127A VAL* 3.9 11.0 - - + -
167A ALA* 3.2 24.9 - - + -
168A ASP 3.6 22.0 - - - -
169A ALA* 4.0 15.5 - - + -
182A LEU* 3.1 44.7 + - + -
183A THR* 3.0 11.3 + - - +
185A LEU* 1.3 79.4 - - - +
187A VAL* 1.3 61.0 + - + +
188A GLU 3.1 1.2 + - - -
189A ARG* 3.7 5.9 + - - +
191A ALA* 3.0 40.3 + - + +
194A ILE* 3.5 30.7 - - + -
238A LEU* 5.4 1.1 - - + -
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Residues in contact with VAL 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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50A TYR* 3.8 13.9 - - + +
51A PRO* 5.9 0.2 - - - +
52A SER* 3.2 33.0 + - - +
183A THR* 2.5 53.8 + - + +
184A LYS 2.9 0.6 + - - +
186A PHE* 1.3 74.0 - - - +
188A GLU* 1.3 61.7 + - - +
190A GLY 4.3 0.8 + - - -
191A ALA 4.9 2.5 - - - +
231A ALA* 5.6 0.7 - - - -
234A MET* 2.7 37.0 - - + -
236A THR* 3.6 26.2 - - + +
238A LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 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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50A TYR* 3.7 28.3 + - + -
51A PRO* 6.0 2.3 - - - +
128A ASN* 4.7 1.7 - - - +
131A TRP* 5.1 2.9 + - - -
184A LYS* 2.8 40.2 + - + +
185A LEU* 2.9 19.8 + - - +
187A VAL* 1.3 81.8 - - - +
189A ARG* 1.3 80.6 + - - +
190A GLY 3.4 3.2 + - - -
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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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121A ASN* 5.6 2.1 - - - +
124A PRO* 3.5 34.5 - - + +
125A ASN* 2.5 33.3 + - - +
127A VAL* 3.4 14.7 - - + +
128A ASN* 3.5 30.3 - - + +
131A TRP* 3.5 18.5 - - - +
185A LEU* 3.0 38.2 + - - +
186A PHE* 3.7 3.0 + - - +
187A VAL 3.5 0.4 - - - -
188A GLU* 1.3 96.8 + - - +
190A GLY* 1.3 60.1 + - - -
191A ALA 3.6 1.8 - - - -
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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