Contacts of the helix formed by residues 194 - 206 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192E GLY 3.7 0.6 + - - -
193E LYS* 1.3 71.7 - - - +
195E HIS* 1.3 67.8 + - - -
196E GLY 3.2 0.7 - - - -
197E VAL* 3.2 6.2 + - - +
198E TRP* 3.0 22.5 + - - +
190W ARG* 3.4 35.3 - - - +
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Residues in contact with HIS 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E LYS 3.7 2.4 + - - -
194E GLY* 1.3 71.4 - - - -
196E GLY* 1.3 62.2 + - - +
198E TRP* 3.3 12.7 + + - +
199E HIS* 2.9 20.9 + - + +
195L HIS* 3.6 23.5 + + + +
190W ARG 3.7 3.8 + - - -
191W VAL* 3.7 24.1 + - + +
195W HIS* 3.8 37.7 + + - +
196W GLY* 3.8 21.8 + - - -
199W HIS* 2.8 35.6 + - - +
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Residues in contact with GLY 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E VAL* 3.4 33.6 + - - +
192E GLY 3.6 10.3 + - - -
193E LYS 4.3 1.6 + - - -
194E GLY 3.2 0.8 - - - -
195E HIS* 1.3 79.1 - - - +
197E VAL* 1.3 56.6 + - - +
199E HIS* 3.2 3.5 + - - +
200E PHE* 2.9 24.4 + - - +
195L HIS* 3.8 18.1 + - - -
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Residues in contact with VAL 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E LEU* 4.2 9.4 - - + -
80E LEU* 5.2 1.3 - - + -
126E LYS 6.0 0.7 - - - +
127E GLY* 6.5 0.2 - - - -
129E ALA* 3.7 26.9 - - + -
130E LEU* 5.6 2.9 - - + +
188E LEU* 3.8 20.2 - - + +
191E VAL* 4.2 4.5 - - + -
192E GLY 3.1 18.3 + - - +
193E LYS* 3.9 15.3 - - + -
194E GLY 3.2 10.3 + - - +
196E GLY* 1.3 72.1 - - - +
198E TRP* 1.3 61.9 + - - +
200E PHE* 3.3 5.8 + - - +
201E ASP* 2.9 26.7 + - - +
190W ARG* 3.8 21.5 - - - +
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Residues in contact with TRP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ALA 5.1 1.1 - - - -
77E LEU* 4.5 7.4 - - + -
194E GLY 3.0 16.7 + - - +
195E HIS* 3.7 9.2 - + - +
197E VAL* 1.3 78.4 - - - +
199E HIS* 1.3 63.4 + - - +
201E ASP* 3.3 10.7 + - + +
202E GLN* 3.0 58.3 + - + +
187W GLN* 2.9 43.6 + - + +
190W ARG* 4.1 14.6 - - - +
191W VAL* 3.5 28.0 - - + -
199W HIS* 3.5 39.0 - + + -
200W PHE* 3.9 20.4 - + - -
203W MET* 3.9 30.1 - - + -
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Residues in contact with HIS 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E HIS 2.9 16.8 + - - +
196E GLY 3.5 4.7 - - - +
198E TRP* 1.3 81.2 - - + +
200E PHE* 1.3 66.1 + - - +
202E GLN* 3.1 9.7 + - + +
203E MET* 3.0 21.3 + - + +
195L HIS* 2.9 25.7 + - + +
198L TRP* 3.5 20.1 - + + -
199L HIS* 3.6 45.8 + + - -
202L GLN* 5.7 1.6 - - - +
199W HIS* 3.6 28.1 + + + -
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Residues in contact with PHE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 4.5 8.3 - - + -
133E MET* 4.7 1.1 - - + -
184E TYR* 3.7 36.1 - + + -
187E GLN* 3.8 35.2 - - + -
188E LEU* 3.6 35.7 - - + -
191E VAL* 4.3 6.5 - - + -
196E GLY 2.9 14.5 + - - +
197E VAL 3.6 7.2 - - - +
199E HIS* 1.3 73.7 - - - +
201E ASP* 1.3 62.9 - - + +
203E MET* 3.1 31.0 + - + +
204E LEU* 2.9 47.4 + - + +
198L TRP* 3.8 16.4 - + + -
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Residues in contact with ASP 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ALA 5.0 0.2 - - - +
77E LEU* 3.3 25.7 - - + +
78E ARG* 3.2 8.7 + - - +
79E GLY* 2.8 22.0 + - - -
80E LEU* 2.8 42.2 + - + +
197E VAL 2.9 13.6 + - - +
198E TRP* 3.3 12.2 - - + +
199E HIS 3.1 0.2 - - - -
200E PHE* 1.3 84.0 - - - +
202E GLN* 1.3 66.0 + - - +
204E LEU* 3.2 4.1 + - - +
205E LEU* 2.8 27.5 + - - +
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Residues in contact with GLN 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ARG* 3.3 24.3 + - - +
198E TRP* 3.0 54.6 + - + +
199E HIS* 3.1 14.5 + - + +
201E ASP* 1.3 80.1 + - - +
203E MET* 1.3 62.5 + - - +
205E LEU* 3.3 10.7 + - - +
206E HIS* 2.9 50.9 + - + -
199W HIS* 5.6 1.1 - - - +
203W MET* 3.4 23.0 - - - +
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Residues in contact with MET 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E TYR* 5.0 2.0 - - + -
187E GLN* 3.7 15.5 - - - +
199E HIS* 3.0 12.7 + - + +
200E PHE* 3.2 46.9 - - + +
202E GLN* 1.3 77.3 - - - +
204E LEU* 1.3 64.9 + - + +
206E HIS* 3.1 7.1 + - - +
207E GLU* 3.0 49.0 + - - +
78L ARG* 3.9 9.9 - - - +
198L TRP* 3.9 11.2 - - + -
202L GLN* 3.4 29.4 - - - +
206L HIS* 5.9 0.2 - - - +
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Residues in contact with LEU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E GLY* 3.9 17.7 - - - +
80E LEU* 3.5 32.3 - - + +
82E LYS* 5.0 5.5 - - - +
83E PHE* 4.0 13.9 - - + -
133E MET* 4.0 10.1 - - + -
180E ARG* 5.2 0.7 - - - +
184E TYR* 3.5 24.9 - - + +
200E PHE* 2.9 27.4 + - + +
201E ASP* 3.5 9.0 - - - +
203E MET* 1.3 80.2 - - + +
205E LEU* 1.3 63.2 + - - +
207E GLU* 3.2 38.1 + - + +
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Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ARG* 3.7 61.0 - - + +
79E GLY* 3.6 8.9 - - - +
82E LYS* 3.7 32.3 - - + -
201E ASP 2.8 17.0 + - - +
202E GLN* 3.4 16.2 - - - +
203E MET 3.2 0.2 - - - -
204E LEU* 1.3 77.5 - - - +
206E HIS* 1.3 82.2 + - + +
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Residues in contact with HIS 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E GLN* 2.9 40.7 + - + +
203E MET* 3.1 7.0 + - - +
205E LEU* 1.3 100.2 + - + +
207E GLU* 1.3 64.3 + - - +
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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