Contacts of the helix formed by residues 183 - 199 (chain A) in PDB entry 1NH1
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 ASP 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASP 4.7 2.1 - - - +
157A LEU* 4.1 10.5 - - + +
158A ASN* 2.5 53.4 + - - +
181A ALA* 3.7 1.8 - - - +
182A THR* 1.3 75.7 - - - +
184A THR* 1.3 65.5 + - - +
185A GLU* 3.5 2.7 - - - -
186A TYR* 3.5 21.4 + - + -
187A LEU* 3.1 28.6 + - + +
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Residues in contact with THR 184 (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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181A ALA 5.3 2.7 + - - -
182A THR* 3.0 12.7 + - - -
183A ASP* 1.3 70.8 - - - +
185A GLU* 1.3 74.1 + - - +
187A LEU* 3.1 9.5 + - - +
188A ARG* 2.8 37.9 + - + +
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Residues in contact with GLU 185 (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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183A ASP 5.5 0.2 - - - -
184A THR* 1.3 88.8 - - - +
186A TYR* 1.3 65.3 + - - +
188A ARG* 2.9 19.4 + - - +
189A ASP* 3.1 18.0 + - - +
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Residues in contact with TYR 186 (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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154A PHE* 2.8 31.3 + - + -
156A ASP 5.4 1.8 - - - -
157A LEU* 3.9 24.7 - - + -
183A ASP* 3.5 19.2 + - + +
184A THR 3.3 0.4 - - - -
185A GLU* 1.3 78.0 - - - +
187A LEU* 1.3 61.9 + - + +
189A ASP* 3.3 11.7 + - + +
190A ARG* 2.7 66.8 + - + +
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Residues in contact with LEU 187 (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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154A PHE* 3.1 36.6 - - + -
157A LEU* 3.6 26.2 - - + -
181A ALA* 3.2 36.1 - - + +
183A ASP 3.1 19.5 + - - +
184A THR* 3.1 9.1 + - - +
186A TYR* 1.3 75.2 - - + +
188A ARG* 1.3 66.2 + - - +
189A ASP 3.1 2.5 + - - -
190A ARG* 4.6 1.8 - - - -
191A VAL* 3.2 31.8 + - + +
212A PRO* 4.4 6.7 - - + -
213A ASP* 5.0 5.2 - - - +
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 2.8 21.0 + - + +
185A GLU* 3.2 15.0 - - - +
187A LEU* 1.3 73.0 - - - +
189A ASP* 1.3 69.8 + - - +
191A VAL* 4.3 2.7 - - - +
192A ALA* 3.7 12.8 + - - +
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU* 3.1 14.6 + - - +
186A TYR* 3.4 10.7 - - + +
187A LEU 3.1 1.0 - - - -
188A ARG* 1.3 76.2 - - - +
190A ARG* 1.3 56.8 + - + +
191A VAL 2.5 18.3 + - - -
192A ALA* 2.5 22.8 + - - +
193A HIS* 3.1 8.8 + - + -
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Residues in contact with ARG 190 (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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153A LEU 2.9 23.4 + - - -
154A PHE* 4.1 19.4 - - + +
186A TYR* 2.7 60.2 + - + +
187A LEU 4.2 0.7 - - - +
189A ASP* 1.3 76.2 - - + +
191A VAL* 1.3 52.2 + - - +
193A HIS* 3.1 29.6 + - - +
194A LEU* 2.6 78.4 + - + +
197A GLU* 3.8 3.4 + - - -
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Residues in contact with VAL 191 (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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154A PHE* 3.4 29.8 - - + -
187A LEU* 3.2 21.0 + - + +
188A ARG* 4.3 3.6 - - - +
189A ASP 2.5 5.7 + - - -
190A ARG* 1.3 70.5 - - - +
192A ALA* 1.3 57.6 + - - +
194A LEU* 4.4 4.5 - - - +
195A ARG* 2.6 46.5 + - - +
203A LEU* 4.0 17.4 - - + +
207A LEU* 5.2 7.4 - - + -
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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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188A ARG 3.7 8.4 + - - +
189A ASP* 2.5 16.5 + - - +
191A VAL* 1.3 77.0 - - - +
193A HIS* 1.3 65.6 + - - +
195A ARG* 3.2 33.7 + - - +
196A THR* 3.3 21.1 + - - -
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Residues in contact with HIS 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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189A ASP 3.1 3.8 + - - +
190A ARG* 3.1 37.5 + - - +
192A ALA* 1.3 83.4 - - - +
194A LEU* 1.3 51.9 + - - +
196A THR* 3.0 4.0 + - - +
197A GLU* 2.7 77.2 + - + +
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Residues in contact with LEU 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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153A LEU* 3.6 44.0 - - + +
154A PHE* 4.4 15.3 - - + -
190A ARG* 2.6 54.7 + - - +
191A VAL* 4.0 2.7 - - - +
193A HIS* 1.3 73.0 - - - +
195A ARG* 1.3 56.1 + - - +
197A GLU* 3.9 12.8 - - - +
198A LEU* 2.7 61.1 + - + +
203A LEU* 4.3 10.7 - - + +
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Residues in contact with ARG 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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191A VAL* 2.6 27.0 + - - +
192A ALA* 3.2 43.0 + - - +
194A LEU* 1.3 72.4 - - - +
196A THR* 1.3 61.4 + - - +
199A GLY* 2.6 36.6 + - - -
200A ALA* 3.1 23.6 + - + +
203A LEU* 3.8 22.4 - - + +
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Residues in contact with THR 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 3.3 9.5 + - - -
193A HIS* 3.0 8.2 + - - +
195A ARG* 1.3 86.7 + - - +
197A GLU* 1.3 66.3 + - - +
198A LEU 3.1 2.8 + - - -
199A GLY* 3.5 6.1 + - - -
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Residues in contact with GLU 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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190A ARG* 3.8 9.5 + - - -
193A HIS* 2.7 55.6 + - + +
194A LEU* 3.9 10.3 - - - +
196A THR* 1.3 75.7 - - + +
198A LEU* 1.3 70.8 + - + +
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Residues in contact with LEU 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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153A LEU* 4.2 27.1 - - + -
194A LEU* 2.7 45.7 + - + +
197A GLU* 1.3 90.0 - - + +
199A GLY* 1.3 69.6 + - - +
202A ALA* 3.5 22.3 - - + +
203A LEU* 4.9 8.3 - - + +
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Residues in contact with GLY 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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195A ARG 2.6 22.1 + - - +
196A THR* 3.5 6.7 + - - -
198A LEU* 1.3 81.1 - - - +
200A ALA* 1.3 65.0 + - - -
201A LYS* 3.3 3.6 + - - -
202A ALA 3.3 1.9 + - - -
203A LEU* 3.3 15.9 + - - +
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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