Contacts of the helix formed by residues 175 - 180 (chain B) in PDB entry 2E4Y
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 SER 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 2.9 27.0 + - - -
155B ILE* 4.5 6.1 - - - +
173B SER 3.8 0.2 - - - -
174B THR* 1.3 74.9 - - - +
176B ALA* 1.3 61.1 + - - +
177B LYS* 2.9 28.3 + - - +
178B LEU* 3.1 10.4 + - - +
189B ARG* 2.6 23.6 + - - +
194B ASP* 3.6 11.0 + - - -
221B ASP 3.8 8.6 + - - -
222B TYR* 4.8 0.7 - - - -
225B THR* 3.3 15.4 + - - +
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Residues in contact with ALA 176 (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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174B THR 3.2 2.6 + - - -
175B SER* 1.3 73.1 + - - +
177B LYS* 1.3 64.8 + - - +
179B SER* 3.0 21.0 + - - +
180B ASP* 4.1 1.6 + - - +
193B PRO* 4.0 20.9 - - + -
194B ASP* 4.3 5.2 + - + +
195B PHE* 4.6 20.4 - - + +
225B THR* 4.2 12.7 + - - +
229B ALA* 6.0 3.1 - - + -
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Residues in contact with LYS 177 (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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155B ILE* 4.3 8.7 - - + +
175B SER* 2.9 15.4 + - - +
176B ALA* 1.3 78.6 - - - +
178B LEU* 1.3 59.9 + - - +
180B ASP* 3.3 18.1 + - - +
183B ARG* 6.1 3.8 - - - +
184B TYR* 3.1 35.4 - - + +
221B ASP* 3.0 27.8 + - - +
225B THR* 4.4 17.8 + - + +
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Residues in contact with LEU 178 (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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151B SER 4.9 0.7 - - - +
154B SER* 4.1 6.7 - - - -
155B ILE* 3.6 38.1 - - + +
158B ALA* 4.8 0.4 - - + -
173B SER* 3.9 20.6 - - - -
175B SER* 3.1 14.5 + - - +
176B ALA 3.1 0.6 - - - -
177B LYS* 1.3 73.1 - - - +
179B SER* 1.3 52.9 + - - +
180B ASP 3.0 2.6 + - - -
181B LYS* 2.5 33.1 + - - -
184B TYR* 3.3 31.1 - - + +
187B PHE* 3.6 41.1 - - + -
189B ARG* 3.7 17.6 + - - +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA* 3.0 12.8 + - - -
178B LEU* 1.3 77.8 - - - +
180B ASP* 1.3 50.3 + - - +
181B LYS* 2.8 30.6 + - - +
189B ARG* 3.1 14.7 + - - +
193B PRO* 3.6 15.6 - - - +
459B PHE* 3.5 24.1 - - - +
461B ASP* 2.7 27.4 + - - -
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Residues in contact with ASP 180 (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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176B ALA 4.1 1.4 + - - +
177B LYS* 3.3 15.7 + - - +
178B LEU 3.0 1.0 - - - -
179B SER* 1.3 74.0 - - - +
181B LYS* 1.3 60.7 + - - +
182B SER* 2.4 32.5 + - - -
183B ARG* 3.2 41.6 + - - +
184B TYR* 3.3 11.8 + - - -
459B PHE* 5.6 0.7 - - - -
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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