Contacts of the helix formed by residues 184 - 191 (chain N) in PDB entry 3HAE
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 THR 184 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131N ASN* 6.0 0.2 - - - +
132N LYS* 5.4 0.4 - - - +
133N ALA* 4.2 0.2 - - - -
183N LEU* 1.3 74.4 - - - +
185N PRO* 1.3 65.6 - - + +
186N GLU* 2.3 36.1 + - + +
187N GLN* 3.0 37.6 + - - +
188N TRP* 3.4 6.2 + - - +
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Residues in contact with PRO 185 (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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128N LEU* 3.7 31.1 - - + +
131N ASN* 3.1 42.6 - - - +
132N LYS* 3.7 8.5 - - - -
133N ALA* 3.6 20.4 - - + +
183N LEU 3.6 0.2 - - - -
184N THR* 1.3 84.0 - - + +
186N GLU* 1.3 65.1 + - + +
188N TRP* 4.0 4.3 - - + +
189N LYS* 3.3 27.2 + - - +
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Residues in contact with GLU 186 (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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131N ASN* 5.9 0.9 + - - -
184N THR* 2.3 35.5 + - - +
185N PRO* 1.3 72.6 - - + +
187N GLN* 1.3 65.4 + - + +
188N TRP 3.0 1.1 - - - -
189N LYS* 3.0 15.5 + - - +
190N SER* 2.9 14.1 + - - -
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Residues in contact with GLN 187 (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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160N ALA 5.6 1.0 - - - +
182N SER 4.6 1.4 - - - +
183N LEU* 3.3 38.1 - - + +
184N THR* 3.0 23.5 + - - +
186N GLU* 1.3 69.5 - - + +
188N TRP* 1.3 58.3 + - - +
190N SER* 2.7 26.3 + - - -
191N HIS* 3.3 14.2 + - + -
194N TYR* 2.5 20.1 + - - +
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Residues in contact with TRP 188 (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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122N PRO* 4.3 11.7 - - + -
123N PRO* 3.4 27.1 - - + -
128N LEU* 3.5 37.5 - - + +
133N ALA* 4.3 10.8 - - + -
135N LEU* 3.9 22.7 - - + -
183N LEU* 4.3 7.0 - - + +
184N THR 3.4 7.6 + - - +
185N PRO 4.0 7.6 - - - +
186N GLU 3.0 0.4 - - - -
187N GLN* 1.3 79.7 - - - +
189N LYS* 1.3 83.4 + - + +
190N SER 3.5 0.5 + - - -
191N HIS 3.9 1.7 - - - +
194N TYR* 3.7 39.1 - + - -
209N VAL* 4.4 8.7 - - + -
210N ALA 3.8 7.9 - - - -
211N PRO* 3.4 48.8 - - + +
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Residues in contact with LYS 189 (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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128N LEU* 5.5 3.6 - - + -
185N PRO 3.3 17.3 - - - +
186N GLU 3.0 8.2 + - - +
188N TRP* 1.3 98.0 - - + +
190N SER* 1.3 65.2 + - - +
191N HIS 4.0 3.4 - - - +
211N PRO* 4.2 19.1 - - + +
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Residues in contact with SER 190 (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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186N GLU 2.9 6.1 + - - -
187N GLN* 2.7 33.7 + - - -
188N TRP 3.3 0.2 - - - -
189N LYS* 1.3 76.6 - - - +
191N HIS* 1.3 78.4 + - - +
192N ARG* 3.8 2.6 + - - +
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Residues in contact with HIS 191 (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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153N ALA* 4.1 18.3 + - + +
154N ASP* 3.1 28.7 - - - +
183N LEU* 5.5 1.1 - - + -
187N GLN* 3.3 15.6 + - + -
188N TRP 3.9 12.6 - - - +
189N LYS 4.0 1.7 - - - +
190N SER* 1.3 87.2 - - - +
192N ARG* 1.3 61.5 + - - +
193N SER 3.5 4.4 + - - +
194N TYR* 2.8 45.3 + + + -
211N PRO* 3.9 8.3 - - - +
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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