Contacts of the helix formed by residues 194 - 207 (chain S) in PDB entry 3A68
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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192S GLY 3.8 0.2 + - - -
193S LYS* 1.3 72.7 - - - +
195S HIS* 1.3 67.0 + - - -
196S GLY 3.2 1.3 - - - -
197S VAL* 3.2 8.3 + - - +
198S TRP* 3.1 21.8 + - - +
190T ARG* 3.3 34.1 - - - +
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Residues in contact with HIS 195 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195N HIS* 3.7 21.5 + + + +
193S LYS 3.7 2.0 + - - -
194S GLY* 1.3 70.5 - - - -
196S GLY* 1.3 63.0 + - - +
198S TRP* 3.3 13.2 + + - +
199S HIS* 2.9 20.0 + - + +
190T ARG 3.6 4.6 + - - -
191T VAL* 3.8 23.0 + - + +
195T HIS* 3.7 44.0 + + - +
196T GLY* 3.8 21.7 + - - -
199T HIS* 2.9 30.9 + - - +
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Residues in contact with GLY 196 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195N HIS* 3.8 17.6 + - - -
191S VAL* 3.4 33.0 + - - +
192S GLY 3.6 9.9 + - - -
193S LYS 4.2 2.4 + - - -
194S GLY 3.2 0.8 - - - -
195S HIS* 1.3 78.1 - - - +
197S VAL* 1.3 58.0 + - - +
199S HIS* 3.2 3.3 + - - +
200S PHE 2.9 25.3 + - - -
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Residues in contact with VAL 197 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77S LEU* 4.2 9.6 - - + -
127S GLY* 6.5 0.2 - - - -
128S ASP* 5.0 0.2 - - - +
129S ALA* 3.6 27.6 - - + -
130S LEU* 5.6 2.7 - - + +
188S LEU* 4.0 21.1 - - + +
191S VAL* 4.2 4.3 - - + -
192S GLY 3.1 18.7 + - - +
193S LYS* 3.8 17.5 - - + -
194S GLY 3.2 11.1 + - - +
196S GLY* 1.3 74.3 - - - +
198S TRP* 1.3 59.2 + - - +
200S PHE* 3.3 3.5 + - - +
201S ASP* 2.9 27.0 + - + +
190T ARG* 3.9 20.9 - - - +
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Residues in contact with TRP 198 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S ALA 4.9 5.8 - - - -
77S LEU* 4.4 7.2 - - + -
194S GLY 3.1 11.1 + - - +
195S HIS* 3.6 11.7 - + - +
197S VAL* 1.3 77.2 - - - +
199S HIS* 1.3 63.6 + - - +
201S ASP* 3.3 10.4 + - - +
202S GLN* 2.9 56.8 + - + +
187T GLN* 2.8 44.7 + - + +
190T ARG* 4.1 10.8 - - - -
191T VAL* 3.5 30.7 - - + -
199T HIS* 3.6 38.4 - + + -
200T PHE* 3.8 21.1 - + - -
203T MET* 3.8 28.3 - - + -
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Residues in contact with HIS 199 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195N HIS* 2.9 25.4 + - + +
198N TRP* 3.6 20.2 - + + -
199N HIS* 3.5 47.0 + + - -
202N GLN* 5.8 1.4 - - - +
195S HIS* 2.9 17.2 + - + +
196S GLY 3.5 4.3 - - - +
198S TRP* 1.3 81.3 - - + +
200S PHE* 1.3 65.9 + - - +
202S GLN* 3.0 9.9 + - + +
203S MET* 3.0 20.5 + - + +
199T HIS* 3.5 29.8 + + + -
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Residues in contact with PHE 200 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198N TRP* 3.8 17.8 - + + -
80S LEU* 4.6 8.1 - - + -
129S ALA* 5.9 0.2 - - + -
133S MET* 4.8 0.2 - - + -
184S TYR* 3.7 37.0 - + + -
187S GLN* 3.8 34.3 - - + -
188S LEU* 3.5 37.2 - - + -
191S VAL* 4.4 6.7 - - + -
196S GLY 2.9 13.9 + - - +
197S VAL 3.6 6.7 - - - +
199S HIS* 1.3 75.1 - - - +
201S ASP* 1.3 67.2 + - + +
203S MET* 3.1 32.6 + - + +
204S LEU* 2.9 40.9 + - + +
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Residues in contact with ASP 201 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S ALA 4.9 0.3 - - - +
77S LEU* 3.3 33.0 - - + +
78S ARG* 3.1 10.0 + - - +
79S GLY* 2.8 21.3 + - - -
80S LEU* 2.7 33.1 + - + +
197S VAL* 2.9 14.3 + - + +
198S TRP* 3.3 11.5 - - + +
200S PHE* 1.3 84.2 - - + +
202S GLN* 1.3 64.1 + - - +
204S LEU* 3.2 4.1 + - - +
205S LEU* 2.9 25.6 + - - +
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Residues in contact with GLN 202 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78S ARG* 3.1 25.9 + - - +
198S TRP* 2.9 54.3 + - + +
199S HIS* 3.0 15.0 + - + +
201S ASP* 1.3 80.3 + - - +
203S MET* 1.3 64.5 + - - +
205S LEU* 3.3 11.0 + - - +
206S HIS* 3.1 51.7 + - - +
199T HIS* 5.5 1.3 - - - +
203T MET* 3.4 20.8 - - - +
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Residues in contact with MET 203 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78N ARG* 3.8 9.9 - - - +
198N TRP* 3.8 11.7 - - + -
202N GLN* 3.3 28.9 - - - +
206N HIS* 6.0 0.9 - - + -
184S TYR* 4.8 2.7 - - + -
187S GLN* 3.7 15.0 - - - +
199S HIS* 3.0 13.1 + - + +
200S PHE* 3.3 47.1 - - + +
202S GLN* 1.3 74.9 - - - +
204S LEU* 1.3 61.5 + - + +
206S HIS* 3.1 5.5 + - - +
207S GLU* 2.8 58.4 + - - +
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Residues in contact with LEU 204 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S GLY* 3.9 13.8 - - - +
80S LEU* 3.6 31.9 - - + +
82S LYS* 4.7 5.9 - - - +
83S PHE* 3.8 24.6 - - + +
133S MET* 4.0 6.7 - - + -
180S ARG* 5.5 0.4 - - - +
184S TYR* 3.4 39.3 - - + +
200S PHE* 2.9 25.3 + - + +
201S ASP* 3.6 8.5 - - - +
203S MET* 1.3 78.6 - - + +
205S LEU* 1.3 63.5 + - - +
206S HIS 3.2 1.0 + - - -
207S GLU* 3.2 24.5 + - - +
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Residues in contact with LEU 205 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S ARG* 3.9 54.5 - - + +
79S GLY* 3.6 9.1 - - - +
82S LYS* 3.6 32.6 - - + +
201S ASP* 2.9 13.4 + - - +
202S GLN* 3.5 25.4 - - - +
203S MET 3.2 0.2 - - - -
204S LEU* 1.3 77.1 - - - +
206S HIS* 1.3 80.1 + - + +
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Residues in contact with HIS 206 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202S GLN* 3.1 40.3 + - - +
203S MET* 3.1 5.7 + - - +
205S LEU* 1.3 97.4 - - + +
207S GLU* 1.3 65.6 + - - +
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Residues in contact with GLU 207 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78N ARG* 3.3 26.5 + - - +
82S LYS* 5.4 5.2 - - - -
180S ARG* 4.2 8.1 + - - -
184S TYR* 2.5 37.8 + - - -
203S MET* 2.8 32.2 + - - +
204S LEU* 3.2 19.0 + - + +
205S LEU 4.9 1.0 - - - +
206S HIS* 1.3 82.6 - - - +
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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