Contacts of the helix formed by residues 183 - 190 (chain B) in PDB entry 1QAG
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 LEU 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B GLN* 3.1 39.5 - - + +
170B VAL* 3.7 11.0 - - + -
181B ASP* 3.1 19.5 + - - +
182B GLY* 1.3 76.2 - - - +
184B ALA* 1.3 67.4 + - - +
186B ASN* 3.0 8.9 + - - +
187B ALA* 3.0 20.8 + - - +
199B TRP* 3.9 14.1 - - + -
202B VAL* 3.9 15.0 - - + -
203B VAL* 4.3 13.2 - - + -
210B ARG* 2.9 45.5 - - - +
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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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164B THR* 4.3 0.6 - - + +
170B VAL* 3.8 18.9 - - + +
172B VAL* 3.8 20.6 - - + -
178B SER 3.7 20.0 - - - +
179B TRP* 3.7 23.1 - - + -
181B ASP* 4.8 1.8 + - - -
182B GLY 3.5 0.2 - - - -
183B LEU* 1.3 79.8 - - - +
185B PHE* 1.3 61.1 + - - +
187B ALA* 3.5 2.0 + - - +
188B VAL* 3.1 28.4 + - - +
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B TRP* 3.3 36.7 - + + -
182B GLY* 3.8 10.8 + - - +
183B LEU 3.1 0.8 + - - -
184B ALA* 1.3 79.4 - - - +
186B ASN* 1.3 63.2 + - - +
188B VAL* 3.6 10.3 + - - +
189B LEU* 3.6 13.7 + - - +
211B LEU* 3.6 14.6 - - + -
214B ALA* 4.3 14.9 - - + +
215B PHE* 3.6 22.9 - + - -
228B LEU* 3.6 34.1 - - + -
233B VAL* 4.0 13.5 - - + -
243B ILE* 4.4 15.9 - - + -
246B TYR* 4.3 15.0 - + - -
247B LEU* 4.4 16.2 - - + -
250B LEU* 4.8 11.3 - - + +
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Residues in contact with ASN 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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182B GLY 2.7 21.4 + - - -
183B LEU 3.0 5.5 + - - +
185B PHE* 1.3 73.2 - - - +
187B ALA* 1.3 66.4 + - - +
188B VAL 3.1 1.6 - - - -
189B LEU* 2.9 9.7 + - - +
190B HIS* 2.8 24.6 + - - +
197B PHE* 4.0 11.1 - - + -
199B TRP* 4.0 13.9 - - + -
202B VAL* 4.1 11.7 - - + +
210B ARG* 2.7 30.8 + - - +
213B HIS* 3.1 23.3 + - - -
214B ALA* 3.0 23.4 - - - +
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Residues in contact with ALA 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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164B THR* 3.6 26.7 - - + -
167B TYR* 3.9 16.3 - - + -
170B VAL* 4.0 7.6 - - + -
183B LEU 3.0 12.9 + - - +
184B ALA 3.7 6.1 - - - +
186B ASN* 1.3 74.8 - - - +
188B VAL* 1.3 63.2 + - - +
190B HIS* 4.4 1.1 - - - -
191B ARG* 3.0 27.5 + - - +
199B TRP* 3.7 23.1 - - + -
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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
----------------------------------------------------------
159B TRP* 4.2 27.1 - - + -
160B VAL* 4.5 5.8 - - + -
163B THR* 4.2 8.6 - - + +
164B THR* 3.8 17.0 - - + +
179B TRP* 4.1 22.4 - - + -
184B ALA 3.1 16.4 - - - +
185B PHE 3.6 8.1 - - - +
186B ASN 3.1 0.6 - - - -
187B ALA* 1.3 78.1 - - - +
189B LEU* 1.3 66.7 + - + +
191B ARG* 3.8 8.8 + - - +
192B HIS* 4.2 2.4 + - - -
247B LEU* 4.7 11.7 - - + -
250B LEU* 5.1 11.2 - - + -
251B PHE 6.2 0.2 - - - +
254B LEU* 4.1 18.1 - - + +
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Residues in contact with LEU 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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185B PHE 3.6 8.9 + - - +
186B ASN 2.9 9.7 + - - +
188B VAL* 1.3 82.9 - - + +
190B HIS* 1.3 67.9 + - - +
192B HIS* 3.1 15.4 + - - +
193B LYS* 4.1 3.6 + - - +
196B LEU* 5.6 8.7 - - + -
197B PHE* 4.4 14.6 - - + -
214B ALA* 3.8 15.9 - - + +
217B LYS* 3.7 15.7 - - + -
218B ALA* 3.7 26.0 - - + +
222B LEU* 3.6 30.7 - - + -
250B LEU* 3.9 18.8 - - + -
254B LEU* 4.3 11.9 - - + +
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Residues in contact with HIS 190 (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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167B TYR* 2.6 34.8 + + + +
186B ASN 2.8 15.3 + - - +
187B ALA 3.8 2.0 - - - +
189B LEU* 1.3 76.0 - - - +
191B ARG* 1.3 53.1 + - - +
192B HIS 2.5 15.6 + - - -
193B LYS 2.7 23.9 + - - -
194B PRO* 3.3 35.4 + - + +
197B PHE* 3.2 57.2 + + + -
199B TRP* 3.8 26.4 + + + -
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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