Contacts of the helix formed by residues 191 - 207 (chain A) in PDB entry 3NO1
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 SER 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A LEU* 1.3 81.4 - - - +
192A ALA* 1.3 64.5 + - - +
193A ALA* 3.6 7.4 + - - +
194A GLU* 3.2 34.4 + - - +
195A ASP* 3.1 19.2 + - - +
224A VAL* 4.7 4.7 - - - -
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A SER* 1.3 74.2 - - - +
193A ALA* 1.3 58.8 + - - +
195A ASP* 3.6 1.1 + - - -
196A ALA* 2.9 32.2 + - - +
220A TYR* 5.6 0.9 - - - -
224A VAL* 3.9 18.1 - - + +
227A ASP* 3.4 44.2 - - + +
228A LEU* 3.7 19.9 - - - +
231A ARG* 3.8 3.5 - - - +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A SER* 3.3 7.2 + - - +
192A ALA* 1.3 79.6 - - - +
194A GLU* 1.3 59.1 + - + +
196A ALA* 3.4 2.6 + - - +
197A ALA* 3.0 28.8 + - - +
231A ARG* 3.9 33.5 - - - +
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 3.7 31.5 - - + +
191A SER* 3.2 32.1 + - - +
193A ALA* 1.3 75.9 - - + +
195A ASP* 1.3 66.2 + - - +
197A ALA* 3.1 8.1 + - - +
198A ARG* 3.0 26.9 + - + +
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Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 2.6 26.8 + - - -
187A VAL* 4.1 8.7 - - + -
190A LEU* 2.9 32.5 + - - +
191A SER 3.1 10.2 + - - +
192A ALA* 4.2 1.8 - - - +
194A GLU* 1.3 77.3 - - - +
196A ALA* 1.3 62.4 + - - +
198A ARG* 3.1 20.3 + - - +
199A ILE* 3.0 27.0 + - - +
220A TYR* 2.4 31.3 + - - +
228A LEU* 4.1 9.0 - - + -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ALA 2.9 20.5 + - - +
193A ALA* 3.6 4.7 - - - +
195A ASP* 1.3 77.3 - - - +
197A ALA* 1.3 58.7 + - - +
199A ILE* 3.4 2.1 + - - +
200A THR* 2.8 33.6 + - - +
228A LEU* 3.6 16.7 - - + +
231A ARG* 3.9 27.1 - - + +
232A ILE* 4.2 8.7 - - + -
235A LEU* 4.6 1.6 - - - +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA 3.0 13.6 + - - +
194A GLU* 3.1 12.1 + - - +
196A ALA* 1.3 74.6 - - - +
198A ARG* 1.3 66.6 + - + +
200A THR* 3.4 8.2 + - - -
201A ALA* 3.1 22.7 + - - +
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Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLY 2.7 30.1 + - - -
160A TYR 4.5 3.0 + - - -
161A TYR* 3.4 21.5 - - - +
163A GLU* 5.9 0.8 + - - -
168A ILE* 3.7 24.0 - - + +
185A PHE* 3.4 33.0 - - + -
186A LYS 3.0 20.0 + - - -
187A VAL* 3.7 4.2 - - - +
190A LEU* 3.7 27.8 - - + -
194A GLU 3.0 10.8 + - - +
195A ASP* 3.1 26.2 + - - +
197A ALA* 1.3 77.2 - - + +
199A ILE* 1.3 62.4 + - - +
201A ALA* 3.3 6.2 + - - +
202A ALA 3.2 14.9 + - - -
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 4.0 20.2 - - + -
187A VAL* 3.9 11.4 - - + -
195A ASP 3.0 16.8 + - - +
196A ALA 3.8 3.8 - - - +
197A ALA 3.3 0.2 - - - -
198A ARG* 1.3 73.2 - - - +
200A THR* 1.3 65.6 + - - +
202A ALA* 3.0 16.2 + - + +
203A ARG* 3.1 12.5 + - - +
212A ILE* 4.7 8.1 - - + -
214A ILE* 3.7 26.5 - - + -
228A LEU* 4.0 21.8 - - + -
232A ILE* 4.0 12.6 - - + -
235A LEU* 3.7 17.9 - - + -
237A ILE* 3.8 22.0 - - + -
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ALA* 2.8 22.5 + - - +
197A ALA* 3.6 8.9 - - - -
198A ARG 3.3 0.2 - - - -
199A ILE* 1.3 75.5 - - - +
201A ALA* 1.3 58.4 + - - +
203A ARG* 3.3 2.8 + - - +
204A GLU* 2.9 54.5 + - + +
235A LEU* 3.7 28.8 - - + +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 3.9 22.0 - - + +
169A ALA* 5.3 0.3 + - - +
197A ALA 3.1 12.8 + - - +
198A ARG 3.5 10.8 - - - +
199A ILE 3.2 0.2 - - - -
200A THR* 1.3 78.1 - - - +
202A ALA* 1.3 57.5 + - - +
204A GLU* 3.8 7.1 - - - +
205A ALA* 3.0 30.5 + - - +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 3.7 15.7 - - + +
172A MSE 4.0 13.2 - - - +
183A VAL* 5.7 0.2 - - + -
185A PHE* 4.2 16.4 - - + -
198A ARG 3.2 10.9 + - - +
199A ILE* 3.0 16.0 + - + +
201A ALA* 1.3 74.5 - - - +
203A ARG* 1.3 60.7 + - - +
205A ALA* 3.4 1.6 + - - +
206A ALA* 2.9 32.9 + - - +
212A ILE* 4.0 16.1 - - + +
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Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ILE* 3.1 8.6 + - + +
200A THR 3.8 6.5 - - - +
202A ALA* 1.3 76.3 - - - +
204A GLU* 1.3 62.9 + - + +
207A GLY* 2.8 53.7 + - - +
208A ASP* 3.4 24.0 + - - +
210A PHE* 2.8 30.1 + - - +
211A ILE* 5.1 0.2 - - - +
212A ILE* 3.8 33.8 - - + +
235A LEU* 3.1 40.4 + - + +
236A ASN* 3.1 36.0 + - - +
237A ILE* 6.1 0.2 - - + -
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A THR* 2.9 45.3 + - + +
201A ALA* 3.8 7.9 - - - +
203A ARG* 1.3 82.3 - - - +
205A ALA* 1.3 61.1 + - - +
207A GLY* 3.9 5.2 + - - -
235A LEU* 5.6 2.4 - - - +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ALA* 3.5 39.0 - - + +
172A MSE 4.4 6.5 - - + -
173A HIS* 3.1 28.2 + - - +
176A GLN* 4.3 0.5 - - - +
201A ALA 3.0 19.5 + - - +
202A ALA 3.8 2.9 - - - +
204A GLU* 1.3 79.5 - - - +
206A ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A MSE 4.3 8.1 - - + -
176A GLN* 3.0 29.8 + - - +
202A ALA 2.9 18.4 + - - +
203A ARG* 4.4 1.6 - - - +
205A ALA* 1.3 79.8 - - - +
207A GLY* 1.3 62.6 + - - +
209A ASP 5.2 1.0 + - - +
210A PHE* 3.4 42.8 - - + +
212A ILE* 4.8 0.7 - - + -
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ARG* 2.8 41.3 + - - -
204A GLU 3.9 4.4 + - - -
205A ALA 3.6 1.8 - - - -
206A ALA* 1.3 79.9 - - - +
208A ASP* 1.3 64.5 + - - -
209A ASP 3.6 1.7 + - - -
210A PHE* 4.0 1.4 - - - +
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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