Contacts of the helix formed by residues 185 - 191 (chain A) in PDB entry 3E88
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 LYS 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU 3.8 1.8 + - - -
184A ARG* 1.3 70.6 - - - +
186A GLU* 1.3 56.6 + - - +
188A ILE* 3.2 9.8 + - - +
189A ILE* 2.8 41.0 + - + +
220A GLN* 3.2 23.9 + - - +
221A THR 2.8 26.1 + - - -
222A HIS* 3.7 17.1 + - - +
223A ASP* 3.0 23.7 + - - +
224A ARG 3.7 11.0 - - - +
225A LEU* 3.9 14.4 - - + -
468A THR* 2.6 32.1 + - - +
469A HIS* 4.3 0.2 - - - +
470A PHE* 3.9 28.0 - - + -
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Residues in contact with GLU 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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184A ARG* 3.2 16.9 + - + +
185A LYS* 1.3 77.4 - - - +
187A VAL* 1.3 61.7 - - + +
189A ILE* 4.0 6.9 - - - +
190A ALA* 3.0 30.0 + - + +
223A ASP* 4.6 3.4 + - + +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A THR 4.1 13.7 - - - +
163A PHE* 4.3 15.5 - - + +
184A ARG* 3.3 25.4 + - + +
186A GLU* 1.3 76.2 - - + +
188A ILE* 1.3 65.7 + - - +
190A ALA* 3.5 5.8 + - - +
191A LYS* 3.1 53.8 + - + +
150B ASN* 4.1 20.4 - - - +
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Residues in contact with ILE 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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163A PHE* 4.3 19.7 - - + -
183A LEU* 3.8 25.8 - - + -
184A ARG 3.2 12.1 + - - +
185A LYS* 3.2 8.6 + - - +
187A VAL* 1.3 76.7 - - - +
189A ILE* 1.3 62.7 + - - +
191A LYS* 3.1 5.9 + - - +
192A ASP 3.1 17.3 + - - -
193A GLU* 3.1 41.9 + - + +
194A VAL* 4.0 10.3 - - + +
197A THR* 3.7 13.7 - - - +
225A LEU* 3.4 31.2 - - + -
470A PHE* 4.5 7.4 - - + -
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Residues in contact with ILE 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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185A LYS* 2.8 30.4 + - + +
186A GLU* 4.0 5.8 - - - +
188A ILE* 1.3 72.8 - - - +
190A ALA* 1.3 63.8 + - - +
192A ASP* 3.2 12.8 + - - +
194A VAL* 4.4 14.5 - - + +
468A THR* 4.8 10.8 - - - +
470A PHE* 4.4 24.0 - - + -
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Residues in contact with ALA 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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186A GLU* 3.0 21.3 + - + +
187A VAL* 3.7 7.9 - - - +
188A ILE 3.2 0.2 - - - -
189A ILE* 1.3 77.4 - - - +
191A LYS* 1.3 59.1 + - - +
192A ASP* 3.3 1.1 + - - +
146B LYS* 4.2 13.3 - - - +
148B THR* 3.7 22.0 - - + +
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Residues in contact with LYS 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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162A THR* 4.4 13.9 + - - +
163A PHE* 3.2 49.7 - - + -
187A VAL* 3.1 31.6 + - + +
188A ILE 3.1 4.0 + - - +
190A ALA* 1.3 75.1 - - + +
192A ASP* 1.3 71.2 + - - +
193A GLU* 3.4 14.9 + - + +
146B LYS* 3.5 36.3 + - - +
148B THR* 3.6 30.1 - - + -
150B ASN* 4.1 3.6 + - - -
151B ASP* 3.5 22.4 + - - -
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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