Contacts of the helix formed by residues 184 - 192 (chain A) in PDB entry 4QQI
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 THR 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A HIS* 3.8 2.5 - - - -
175A ILE 5.0 0.4 - - - -
176A ASN* 3.9 15.9 - - - +
177A HIS 3.7 2.2 - - - -
178A THR* 4.0 9.0 - - + -
182A GLY 4.7 0.4 - - - +
183A PHE* 1.3 74.6 - - - +
185A PRO* 1.4 75.2 - - - +
186A LEU* 3.7 9.3 + - - +
187A MET* 3.1 40.3 + - + +
188A TRP* 3.2 12.6 + - - -
207A ASP 5.3 3.1 + - - +
210A LEU* 3.7 38.1 - - + -
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Residues in contact with PRO 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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153A VAL* 3.8 28.3 - - + +
154A HIS* 3.9 12.3 - - + -
157A ALA* 3.3 26.6 - - + +
174A VAL 4.0 5.6 - - - +
175A ILE* 3.4 25.4 - - - +
177A HIS 3.2 16.4 - - - +
184A THR* 1.4 89.8 - - - +
186A LEU* 1.3 56.4 + - - +
188A TRP* 3.3 2.7 + - + -
189A ALA* 2.9 24.8 + - - +
201A LEU* 3.9 13.9 - - + -
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Residues in contact with LEU 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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175A ILE 5.1 1.0 + - - +
184A THR* 3.2 9.3 + - - +
185A PRO* 1.3 77.1 - - - +
187A MET* 1.3 61.0 + - - +
189A ALA* 3.7 1.3 - - - +
190A ALA* 2.9 31.1 + - + +
198A VAL* 4.0 33.2 - - + +
201A LEU* 3.7 29.5 - - + +
202A LEU* 4.0 13.5 - - + -
206A ALA* 4.4 11.7 - - + -
207A ASP 4.0 7.2 - - - +
208A PRO* 3.5 40.2 - - + -
218A ALA* 4.2 11.4 - - + -
234A LEU* 4.4 6.5 - - + -
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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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182A GLY 4.1 2.0 - - - +
183A PHE* 3.7 26.2 - - + -
184A THR* 3.1 39.9 + - + +
186A LEU* 1.3 76.4 - - - +
188A TRP* 1.3 57.4 + - - +
190A ALA* 3.8 0.5 - - - +
191A ALA* 3.0 31.9 + - - +
210A LEU* 3.0 42.4 - - + +
211A LEU 3.6 1.8 - - - +
212A GLY* 3.5 18.8 - - - +
216A GLU 3.7 6.7 - - - +
217A SER* 4.5 0.7 - - - -
218A ALA* 3.9 22.7 - - + +
221A LEU* 3.8 17.8 - - + +
90X MET* 4.2 1.8 - - + -
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Residues in contact with TRP 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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154A HIS* 3.6 39.2 - + + +
155A GLN* 3.5 18.8 - - - -
158A ALA* 3.6 22.2 - - + +
179A ASP* 2.9 28.7 + - - -
183A PHE* 3.5 11.9 - + + +
184A THR 3.2 21.8 + - - -
185A PRO 3.6 7.4 - - - +
187A MET* 1.3 79.4 - - - +
189A ALA* 1.3 65.0 + - - +
191A ALA* 4.6 0.7 - - - -
192A HIS* 3.2 40.1 + + - +
88X VAL 3.3 20.9 - - - -
89X HIS* 3.6 3.6 - - - -
90X MET* 3.4 51.1 - - + -
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Residues in contact with ALA 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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157A ALA* 3.9 14.3 - - + +
158A ALA* 4.6 0.4 - - - +
185A PRO 2.9 18.0 + - - +
186A LEU 3.7 4.5 - - - +
188A TRP* 1.3 78.7 - - - +
190A ALA* 1.3 62.7 + - - +
192A HIS* 3.2 1.4 + - - -
193A GLY 3.1 17.5 + - - -
194A GLN* 3.1 11.8 + - + +
197A VAL* 3.5 32.3 - - + -
198A VAL* 3.9 15.0 - - + -
201A LEU* 4.3 2.9 - - + -
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Residues in contact with ALA 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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186A LEU* 2.9 21.3 + - + +
187A MET 3.8 3.1 - - - +
189A ALA* 1.3 73.8 - - - +
191A ALA* 1.3 61.0 + - - +
193A GLY* 3.2 10.6 + - - -
198A VAL* 3.7 11.3 - - + +
218A ALA* 3.7 32.8 - - + +
221A LEU* 4.9 0.4 - - + -
222A ALA* 4.2 5.8 - - + +
227A TYR* 3.3 16.6 - - - -
230A ILE* 4.1 20.0 - - + +
234A LEU* 4.9 0.7 - - + -
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Residues in contact with ALA 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 19.9 + - - +
188A TRP 3.9 2.7 - - - +
190A ALA* 1.3 76.0 - - - +
192A HIS* 1.3 58.7 + - - +
193A GLY 3.5 0.2 - - - -
221A LEU* 4.0 24.4 - - + +
225A LYS* 4.0 8.2 - - - +
227A TYR* 3.7 12.5 + - - -
90X MET* 3.4 27.8 - - - -
91X PRO* 3.8 24.0 - - + +
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Residues in contact with HIS 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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158A ALA* 3.6 33.5 + - + +
188A TRP* 3.2 36.3 + + - +
189A ALA 4.0 1.8 - - - +
190A ALA 3.1 0.6 - - - -
191A ALA* 1.3 80.1 + - + +
193A GLY* 1.3 62.6 + - - +
194A GLN* 3.3 9.6 + - + +
227A TYR* 3.9 8.9 + - - -
88X VAL* 3.7 22.4 - - + +
89X HIS 2.8 30.2 + - - -
91X PRO* 3.5 17.7 - - + +
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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