Contacts of the helix formed by residues 181 - 189 (chain A) in PDB entry 3NNJ
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLN 4.2 0.7 + - - +
180A GLY* 1.3 72.3 - - - +
182A LEU* 1.3 57.9 + - - +
183A ASN* 3.3 5.2 + - - +
184A GLU* 3.0 52.8 + - - +
185A TYR* 3.0 27.5 + - - +
273A TYR* 3.6 13.4 + - - +
274A TYR* 2.3 35.0 + - - -
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Residues in contact with LEU 182 (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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175A TRP* 3.4 49.4 - - + +
180A GLY 3.3 3.2 + - - -
181A ASP* 1.3 75.5 + - - +
183A ASN* 1.3 63.8 + - - +
185A TYR* 3.2 3.5 + - - +
186A VAL* 3.2 24.3 + - + +
266A TYR* 4.4 15.0 - - + +
269A LEU* 4.0 9.9 - - + +
270A HIS* 3.1 60.6 - - + +
273A TYR* 3.7 11.2 - - + -
274A TYR* 3.4 14.1 + - + +
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Residues in contact with ASN 183 (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 ASP* 3.5 5.2 - - - +
182A LEU* 1.3 73.2 - - - +
184A GLU* 1.3 62.6 + - + +
186A VAL* 3.8 7.7 + - - +
187A ALA* 3.3 22.0 + - - +
266A TYR* 5.4 0.3 + - - -
270A HIS* 3.6 19.3 - - - -
274A TYR* 2.9 45.3 + - - +
279A ARG* 5.2 8.0 + - - -
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Residues in contact with GLU 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 ASP* 3.0 38.3 + - + +
182A LEU 3.2 0.4 - - - -
183A ASN* 1.3 76.6 - - + +
185A TYR* 1.3 58.8 + - - +
187A ALA* 3.0 5.8 + - + -
188A ASN* 2.8 50.1 + - - +
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Residues in contact with TYR 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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171A ASN* 3.0 47.3 + - - -
172A ASN* 4.0 5.4 - - - -
174A LYS* 3.9 7.3 + - - +
175A TRP* 3.5 47.1 + + + -
179A GLN* 3.6 37.1 + - + +
181A ASP 3.0 13.8 + - - +
182A LEU 3.4 8.1 - - - +
184A GLU* 1.3 75.6 - - - +
186A VAL* 1.3 74.9 + - + +
188A ASN* 3.0 4.8 + - - +
189A ALA* 2.9 26.2 + - + +
203B TYR* 4.0 11.0 + + - -
206B LYS* 4.7 2.6 + - - -
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Residues in contact with VAL 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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168A HIS* 3.7 17.3 - - - +
172A ASN* 3.3 33.4 - - + +
182A LEU* 3.2 15.7 + - + +
183A ASN* 4.0 6.5 - - - +
185A TYR* 1.3 90.3 - - + +
187A ALA* 1.3 63.3 + - + +
189A ALA* 3.7 3.9 + - - +
194A ASN* 3.1 18.0 + - - +
266A TYR* 3.2 29.6 - - + +
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Residues in contact with ALA 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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183A ASN 3.3 15.7 + - - +
184A GLU* 3.0 7.8 + - + +
186A VAL* 1.3 82.8 - - + +
188A ASN* 1.3 66.9 + - - +
189A ALA 3.5 0.2 - - - -
194A ASN* 3.5 14.7 + - - +
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Residues in contact with ASN 188 (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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184A GLU* 2.8 35.6 + - - +
185A TYR* 3.6 3.4 - - - +
187A ALA* 1.3 86.7 - - - +
189A ALA* 1.3 64.8 + - - +
190A ASN* 3.4 2.8 + - - +
195A LYS* 5.1 2.8 + - - -
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Residues in contact with ALA 189 (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 HIS* 5.0 1.3 - - + -
171A ASN* 3.4 16.6 - - - +
185A TYR* 2.9 17.8 + - + +
186A VAL* 4.0 5.2 - - - +
187A ALA 3.5 1.6 - - - -
188A ASN* 1.3 78.5 - - - +
190A ASN* 1.3 57.2 + - - +
191A THR* 2.9 15.3 + - + -
194A ASN* 2.7 33.4 + - - +
195A LYS* 4.0 2.3 + - - -
203B TYR* 3.2 23.6 - - - +
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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