Contacts of the helix formed by residues 206 - 210 (chain B) in PDB entry 2E98
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 LEU 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 3.6 44.3 - - - +
207A TRP* 4.4 5.4 - - - +
209A ILE* 5.0 0.2 - - + -
210A ALA* 3.8 26.2 - - + +
147B GLY* 3.9 4.6 - - - -
148B ARG* 3.6 27.8 - - + +
151B ILE* 4.3 11.0 - - + -
201B ILE* 3.9 20.2 - - + -
203B ASN* 3.6 21.8 - - - +
204B PHE 3.4 7.6 + - - +
205B LEU* 1.3 84.6 - - - +
207B TRP* 1.3 70.7 + - - +
208B GLN* 3.2 3.1 + - - -
209B ILE* 3.2 17.9 + - - +
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Residues in contact with TRP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 2.9 85.6 + - + +
151A ILE* 4.0 21.1 - - + -
152A VAL* 4.0 12.6 - - + -
206A LEU* 4.4 7.0 - - - -
147B GLY 5.4 0.2 + - - -
151B ILE* 4.0 22.7 - - + +
174B GLU* 3.6 26.9 - - + -
177B LEU* 3.7 29.4 - - + -
178B ASN* 2.8 38.7 + - + +
181B VAL* 3.6 23.6 - - + -
206B LEU* 1.3 80.5 - - - +
208B GLN* 1.3 73.3 + - + +
209B ILE 3.3 0.3 + - - -
210B ALA* 3.4 5.5 + - - +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 4.2 9.6 + - - +
145B TYR* 4.0 2.6 + - - -
147B GLY 5.6 0.9 - - - +
150B ASP* 2.8 29.3 + - - +
151B ILE* 5.7 0.5 - - - +
178B ASN* 6.0 0.2 - - - +
181B VAL* 3.8 16.8 - - + +
182B CYS* 2.9 32.0 + - - +
183B MET* 4.8 6.7 - - + +
188B PRO* 6.0 0.2 - - - +
189B VAL* 3.9 28.4 + - + +
205B LEU* 4.0 28.1 - - + +
206B LEU 3.2 7.8 + - - -
207B TRP* 1.3 86.1 + - + +
209B ILE* 1.3 57.7 + - - +
210B ALA 3.3 2.2 + - - -
211B TYR 4.9 1.0 + - - -
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 4.7 11.0 - - + +
206A LEU* 4.9 5.2 - - + -
189B VAL* 4.5 3.1 - - + -
192B VAL* 3.5 28.9 - - + -
201B ILE* 3.2 38.8 - - + -
204B PHE* 6.0 0.4 - - + -
205B LEU* 3.4 38.8 - - + +
206B LEU* 3.2 13.8 + - - +
208B GLN* 1.3 80.5 - - - +
210B ALA* 1.3 65.2 + - - +
211B TYR 3.1 4.4 + - - -
212B ALA* 3.3 23.0 + - + +
214B LEU* 4.3 16.9 - - + +
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Residues in contact with ALA 210 (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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148A ARG* 3.6 32.8 - - - +
201A ILE 4.0 0.5 - - - -
202A SER* 3.2 11.8 + - - -
203A ASN* 2.9 30.8 + - + +
206A LEU* 3.8 24.7 - - + -
206B LEU 3.8 1.6 + - - -
207B TRP 3.4 4.8 + - - +
208B GLN 3.3 2.6 + - - -
209B ILE* 1.3 76.7 - - - +
211B TYR* 1.3 71.4 + - + +
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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