Contacts of the helix formed by residues 194 - 207 (chain Q) in PDB entry 3A9Q
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 194 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190K ARG* 3.3 38.1 - - - +
193Q LYS* 1.3 72.9 - - - +
195Q HIS* 1.3 66.6 + - - -
196Q GLY 3.2 1.7 + - - -
197Q VAL* 3.3 6.6 + - - +
198Q TRP* 3.1 18.2 + - - +
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Residues in contact with HIS 195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K ARG 3.7 3.6 + - - -
191K VAL* 3.7 23.4 + - + +
195K HIS* 3.7 41.9 + + - +
196K GLY* 3.8 21.5 + - - -
199K HIS* 2.8 33.8 + + - +
193Q LYS 3.7 2.0 + - - -
194Q GLY* 1.3 71.0 - - - -
196Q GLY* 1.3 58.3 + - - +
198Q TRP* 3.3 13.2 + + - +
199Q HIS* 2.9 25.4 + - + +
195X HIS* 3.6 20.8 + + + +
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Residues in contact with GLY 196 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q VAL* 3.5 40.9 + - - +
192Q GLY 3.7 2.0 + - - -
193Q LYS 4.2 2.2 + - - -
194Q GLY 3.2 0.8 - - - -
195Q HIS* 1.3 79.3 - - - +
197Q VAL* 1.3 57.2 + - - +
199Q HIS* 3.1 3.3 + - - +
200Q PHE 2.8 26.0 + - - -
195X HIS* 3.8 16.8 + - - -
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Residues in contact with VAL 197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K ARG* 3.9 21.3 - - - +
77Q LEU* 4.3 9.2 - - + -
80Q LEU* 6.1 0.2 - - + -
127Q GLY* 6.5 0.2 - - - -
129Q ALA* 3.7 27.4 - - + -
130Q LEU* 5.7 2.2 - - + +
188Q LEU* 3.9 22.0 - - + +
191Q VAL* 4.3 4.5 - - + -
192Q GLY 3.1 19.8 + - - +
193Q LYS* 3.7 17.7 - - + -
194Q GLY 3.3 10.4 + - - +
196Q GLY* 1.3 74.0 - - - +
198Q TRP* 1.3 59.2 + - - +
200Q PHE* 3.3 3.3 + - - +
201Q ASP* 2.9 27.6 + - + +
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Residues in contact with TRP 198 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K GLN* 2.8 46.9 + - + +
190K ARG* 4.0 16.1 - - - +
191K VAL* 3.5 28.9 - - + -
199K HIS* 3.6 37.9 - + + -
200K PHE* 3.8 20.9 - + - -
203K MET* 3.8 28.7 - - + -
76Q ALA 5.0 1.3 - - - -
77Q LEU* 4.5 7.6 - - + -
194Q GLY 3.1 10.3 + - - +
195Q HIS* 3.6 13.0 - + - +
197Q VAL* 1.3 76.6 - - - +
199Q HIS* 1.3 64.3 + - - +
201Q ASP* 3.3 9.6 + - - +
202Q GLN* 3.0 57.3 + - + +
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Residues in contact with HIS 199 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K HIS* 3.5 33.0 + + + -
195Q HIS* 2.9 17.3 + - + +
196Q GLY 3.4 4.0 - - - +
198Q TRP* 1.3 82.2 - - + +
200Q PHE* 1.3 66.7 + - - +
202Q GLN* 3.1 9.5 + - + +
203Q MET* 3.0 20.5 + - + +
195X HIS* 3.0 24.5 + - + +
198X TRP* 3.5 20.7 - + + -
199X HIS* 3.6 42.4 + + - -
202X GLN* 5.7 1.4 - - - +
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Residues in contact with PHE 200 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Q LEU* 4.3 8.1 - - + -
133Q MET* 4.6 2.2 - - + -
184Q TYR* 3.6 39.3 - + + -
187Q GLN* 3.8 32.8 - - + -
188Q LEU* 3.6 36.1 - - + -
191Q VAL* 4.4 7.6 - - + -
196Q GLY 2.8 16.6 + - - +
197Q VAL 3.6 6.3 - - - +
199Q HIS* 1.3 72.8 - - - +
201Q ASP* 1.3 63.1 + - - +
203Q MET* 3.0 31.8 + - + +
204Q LEU* 2.9 45.9 + - + +
198X TRP* 3.8 16.1 - + + -
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Residues in contact with ASP 201 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q ALA 5.0 0.3 - - - +
77Q LEU* 3.3 28.1 - - + +
78Q ARG* 3.1 9.5 + - - +
79Q GLY* 2.8 20.6 + - - -
80Q LEU* 2.7 39.3 + - + +
197Q VAL 2.9 14.0 + - - +
198Q TRP* 3.4 11.8 - - + +
199Q HIS 3.1 0.2 - - - -
200Q PHE* 1.3 84.2 - - - +
202Q GLN* 1.3 63.5 + - - +
204Q LEU* 3.3 4.1 + - - -
205Q LEU* 2.8 27.5 + - - +
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Residues in contact with GLN 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K HIS* 5.6 1.6 - - - +
203K MET* 3.4 22.4 - - - +
78Q ARG* 3.2 23.8 + - - +
198Q TRP* 3.0 55.2 + - + +
199Q HIS* 3.1 13.9 + - + +
201Q ASP* 1.3 81.4 - - - +
203Q MET* 1.3 63.1 + - - +
205Q LEU* 3.3 11.4 + - - +
206Q HIS* 3.0 51.3 + - + -
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Residues in contact with MET 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184Q TYR* 4.7 2.7 - - + -
187Q GLN* 3.8 13.9 - - - +
199Q HIS* 3.0 13.2 + - + +
200Q PHE* 3.1 46.7 - - + +
202Q GLN* 1.3 75.6 - - - +
204Q LEU* 1.3 66.2 + - + +
206Q HIS* 3.1 6.0 + - - +
207Q GLU* 2.9 53.7 + - - +
78X ARG* 3.8 11.0 - - - +
198X TRP* 3.8 10.3 - - + -
202X GLN* 3.3 31.6 - - - +
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Residues in contact with LEU 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q GLY* 3.7 20.9 - - - +
80Q LEU* 3.8 23.8 - - + -
82Q LYS* 5.1 5.0 - - - +
83Q PHE* 3.9 22.2 - - + -
133Q MET* 4.0 15.0 - - + -
180Q ARG* 5.0 1.1 - - - +
184Q TYR* 3.4 39.3 - - + +
200Q PHE* 2.9 18.4 + - + +
201Q ASP 3.7 7.6 - - - +
203Q MET* 1.3 82.1 - - + +
205Q LEU* 1.3 63.2 + - - +
207Q GLU* 3.2 26.9 + - + +
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Residues in contact with LEU 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Q ARG* 3.9 54.7 - - + +
79Q GLY* 3.6 9.1 - - - +
82Q LYS* 3.9 30.7 - - + -
201Q ASP* 2.8 18.7 + - - +
202Q GLN* 3.4 21.1 - - - +
203Q MET 3.2 0.2 - - - -
204Q LEU* 1.3 77.8 - - - +
206Q HIS* 1.3 81.5 + - + +
207Q GLU 3.9 0.3 + - - +
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Residues in contact with HIS 206 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202Q GLN* 3.0 43.8 + - + +
203Q MET* 3.1 6.8 + - - +
205Q LEU* 1.3 95.2 + - + +
207Q GLU* 1.3 68.7 + - - +
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Residues in contact with GLU 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Q LYS* 5.7 3.5 - - - -
180Q ARG* 4.3 6.4 + - - -
184Q TYR* 2.7 37.4 + - - -
203Q MET* 2.9 31.8 + - - +
204Q LEU* 3.2 20.2 + - + +
205Q LEU 5.0 0.7 - - - +
206Q HIS* 1.3 83.2 - - - +
78X ARG* 3.3 26.7 + - - +
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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