Contacts of the helix formed by residues 168 - 173 (chain B) in PDB entry 3E4E
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 PRO 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B PHE* 3.5 23.5 - - + +
167B ASP* 1.3 90.7 - - - +
169B THR* 1.3 65.6 + - - +
171B LEU* 2.8 14.0 + - + -
172B ILE* 3.0 34.1 + - + +
309B ARG* 4.4 8.3 - - + -
312B LEU* 4.5 6.3 - - + -
485B TYR* 3.5 42.6 - - + +
487B LEU* 3.7 15.0 - - + -
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ASP* 2.5 31.5 + - - -
168B PRO* 1.3 77.7 - - - +
170B PHE* 1.3 83.5 + - + +
172B ILE* 4.7 1.0 - - - +
173B GLY* 3.3 20.1 + - - -
204B ASN* 3.9 20.6 - - + +
305B SER* 4.4 4.5 + - - -
309B ARG* 3.7 38.6 + - - +
484B ARG* 6.0 1.7 - - - +
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Residues in contact with PHE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 4.2 8.1 + - - -
168B PRO 3.0 1.2 + - - -
169B THR* 1.3 96.8 - - + +
171B LEU* 1.3 58.9 + - - +
173B GLY 4.5 1.3 - - - +
174B CYS* 3.2 19.5 - - - -
191B TYR* 4.8 2.1 - - - +
197B LEU* 4.0 25.5 - - + +
200B MET* 3.7 49.6 - - + -
201B TYR* 3.7 27.8 - + + -
204B ASN* 4.0 19.1 - - + -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.8 14.7 - - + +
157B ALA* 3.7 36.1 - - + +
158B LEU* 3.8 22.2 - - + -
161B THR* 3.6 30.3 - - + -
166B PHE* 3.9 17.5 - - + -
167B ASP 4.5 4.0 + - - +
168B PRO* 2.8 11.0 + - + +
170B PHE* 1.3 78.8 - - - +
172B ILE* 1.3 68.5 + - + +
173B GLY 3.1 1.1 + - - -
174B CYS* 3.1 22.5 + - - +
191B TYR* 4.0 7.0 - - + -
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.1 20.9 - - + -
158B LEU* 4.7 15.9 - - + -
166B PHE* 5.8 0.7 - - + -
168B PRO* 3.0 34.9 + - + +
169B THR* 4.7 0.9 - - - +
171B LEU* 1.3 72.0 - - + +
173B GLY* 1.3 65.5 + - - +
174B CYS 3.3 0.5 + - - -
175B ALA* 3.3 7.8 + - - +
176B PRO* 3.1 17.2 - - - +
305B SER* 4.2 9.9 - - - +
308B LEU* 3.5 39.6 - - + +
309B ARG* 4.4 5.8 - - + +
312B LEU* 3.9 21.1 - - + -
454B ILE* 4.4 15.9 - - + -
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B THR 3.3 18.5 + - - -
171B LEU 3.1 2.0 + - - -
172B ILE* 1.3 77.9 - - - +
174B CYS* 1.3 64.3 + - - +
176B PRO* 3.0 13.0 - - - +
177B CYS* 3.1 13.9 + - - +
200B MET* 3.7 12.3 - - - +
301B THR* 4.3 4.0 - - - +
305B SER* 3.7 22.0 + - - -
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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