Contacts of the helix formed by residues 194 - 206 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N GLY 3.9 0.2 + - - -
193N LYS* 1.3 73.2 - - - +
195N HIS* 1.3 66.4 + - - -
196N GLY 3.2 1.3 - - - -
197N VAL* 3.3 6.2 + - - +
198N TRP* 3.1 18.7 + - - +
190S ARG* 3.3 39.3 - - - +
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Residues in contact with HIS 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N LYS 3.7 2.4 + - - -
194N GLY* 1.3 70.8 - - - -
196N GLY* 1.3 63.2 + - - +
198N TRP* 3.3 12.7 + + - +
199N HIS* 2.9 20.2 + - + +
190S ARG 3.7 3.8 + - - -
191S VAL* 3.7 25.0 + - + +
195S HIS* 3.7 43.3 + + - +
196S GLY* 3.8 22.0 + - - -
199S HIS* 2.9 31.3 + - + +
195U HIS* 3.7 22.7 + + + +
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Residues in contact with GLY 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191N VAL* 3.4 33.8 + - - +
192N GLY 3.6 9.7 + - - -
193N LYS 4.2 2.0 + - - -
194N GLY 3.2 1.4 - - - -
195N HIS* 1.3 78.9 - - - +
197N VAL* 1.3 56.2 + - - +
199N HIS* 3.1 3.5 + - - +
200N PHE 2.9 25.6 + - - -
195U HIS* 3.8 15.4 + - - -
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Residues in contact with VAL 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77N LEU* 4.3 9.2 - - + -
126N LYS 6.1 0.4 - - - +
128N ASP* 5.0 0.7 - - - +
129N ALA* 3.7 27.6 - - + -
130N LEU* 5.8 2.5 - - + +
188N LEU* 4.1 20.0 - - + +
191N VAL* 4.3 5.2 - - + -
192N GLY 3.1 19.6 + - - +
193N LYS* 3.7 17.9 - - + -
194N GLY 3.3 10.1 + - - +
196N GLY* 1.3 73.0 - - - +
198N TRP* 1.3 58.6 + - - +
200N PHE* 3.3 4.3 + - + +
201N ASP* 2.9 27.8 + - + +
190S ARG* 3.8 21.8 - - - +
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Residues in contact with TRP 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N ALA 5.2 0.9 - - - -
77N LEU* 4.5 8.1 - - + -
194N GLY 3.1 13.6 + - - +
195N HIS* 3.6 13.9 - + - +
197N VAL* 1.3 78.1 - - - +
199N HIS* 1.3 61.9 + - - +
201N ASP* 3.3 10.0 + - - +
202N GLN* 3.0 55.1 + - + +
187S GLN* 2.9 43.7 + - + +
190S ARG* 4.1 14.1 - - - +
191S VAL* 3.5 28.3 - - + -
199S HIS* 3.6 37.5 - + + -
200S PHE* 3.8 28.0 - + - -
203S MET* 3.8 23.8 - - + -
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Residues in contact with HIS 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195N HIS* 2.9 17.0 + - + +
196N GLY 3.5 4.3 - - - +
198N TRP* 1.3 80.7 - - + +
200N PHE* 1.3 65.7 + - - +
202N GLN* 3.1 9.7 + - + +
203N MET* 3.0 21.8 + - + +
199S HIS* 3.5 32.7 + + + -
195U HIS* 2.9 25.3 + - + +
198U TRP* 3.6 20.5 - + + -
199U HIS* 3.5 41.5 + + - -
202U GLN* 5.6 2.0 - - - +
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Residues in contact with PHE 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N LEU* 4.2 8.3 - - + -
133N MET* 4.7 1.3 - - + -
184N TYR* 3.6 42.0 - + + -
187N GLN* 3.9 32.5 - - + -
188N LEU* 3.6 36.8 - - + -
191N VAL* 4.4 7.2 - - + -
196N GLY 2.9 12.2 + - - +
197N VAL 3.6 7.4 - - - +
199N HIS* 1.3 76.0 - - - +
201N ASP* 1.3 62.3 + - - +
203N MET* 3.1 31.3 + - + +
204N LEU* 2.9 46.4 + - + +
198U TRP* 3.9 15.5 - + + -
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Residues in contact with ASP 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N ALA 4.8 0.3 - - - +
77N LEU* 3.3 28.4 - - + +
78N ARG* 3.1 10.9 + - - +
79N GLY* 2.9 18.7 + - - -
80N LEU* 2.8 39.3 + - + +
197N VAL* 2.9 13.5 + - + +
198N TRP* 3.4 11.1 - - + +
199N HIS 3.2 0.2 - - - -
200N PHE* 1.3 83.4 - - - +
202N GLN* 1.3 63.5 + - - +
204N LEU* 3.2 3.4 + - - -
205N LEU* 2.8 27.2 + - - +
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Residues in contact with GLN 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N ARG* 2.9 28.1 + - - +
198N TRP* 3.0 54.2 + - + +
199N HIS* 3.1 14.3 + - + +
201N ASP* 1.3 78.6 - - - +
203N MET* 1.3 66.6 + - - +
205N LEU* 3.3 8.9 + - - +
206N HIS* 3.1 51.9 + - - +
199S HIS* 5.8 0.9 - - - +
203S MET* 3.3 22.3 - - - +
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Residues in contact with MET 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N TYR* 4.9 7.4 - - + -
187N GLN* 3.9 4.7 - - - +
199N HIS* 3.0 13.3 + - + +
200N PHE* 3.2 43.3 - - + +
202N GLN* 1.3 77.4 - - - +
204N LEU* 1.3 68.4 + - + +
206N HIS* 3.2 5.0 + - - +
207N GLU* 2.9 38.5 + - - +
78U ARG* 3.7 28.5 - - - +
198U TRP* 3.8 11.0 - - + -
202U GLN* 3.4 31.0 - - - +
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Residues in contact with LEU 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N GLY* 3.7 25.5 - - - +
80N LEU* 3.9 19.1 - - + -
82N LYS* 4.5 8.3 + - - -
83N PHE* 3.9 18.8 - - + -
133N MET* 4.0 14.8 - - + -
184N TYR* 3.4 40.4 - - + +
200N PHE* 2.9 21.3 + - + +
201N ASP* 3.6 8.3 - - - +
203N MET* 1.3 79.6 - - + +
205N LEU* 1.3 64.5 + - - +
206N HIS 3.2 0.9 + - - -
207N GLU* 3.3 26.2 + - - +
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Residues in contact with LEU 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N ARG* 3.8 59.9 - - + +
79N GLY* 3.7 8.9 - - - +
82N LYS* 3.2 38.8 + - + +
201N ASP* 2.8 17.9 + - - +
202N GLN* 3.5 14.1 - - - +
203N MET 3.3 0.2 - - - -
204N LEU* 1.3 78.0 - - - +
206N HIS* 1.3 81.4 + - + +
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Residues in contact with HIS 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N GLN* 3.1 36.1 + - - +
203N MET* 3.2 5.5 + - - +
204N LEU 3.2 0.4 - - - -
205N LEU* 1.3 102.3 - - + +
207N GLU* 1.3 66.7 + - - +
203S MET* 6.0 0.7 - - + -
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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