Contacts of the helix formed by residues 210 - 218 (chain B) in PDB entry 2Q8I
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 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B TYR* 3.8 5.4 - - - -
208B VAL* 2.9 23.4 - - - +
209B GLU* 1.3 96.5 + - + +
211B GLU* 1.3 63.8 + - - +
212B ALA* 3.4 10.5 - - + +
213B ASP* 3.3 26.5 + - - +
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Residues in contact with GLU 211 (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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157B GLY 4.4 6.6 - - - +
185B TYR* 3.6 44.2 + - + +
210B LYS* 1.3 70.4 - - - +
212B ALA* 1.3 59.6 + - - +
213B ASP 2.9 5.2 - - - -
214B ILE* 2.9 38.1 + - + +
215B SER* 4.6 0.7 + - - -
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Residues in contact with ALA 212 (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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210B LYS* 4.2 9.8 - - + +
211B GLU* 1.3 79.1 - - - +
213B ASP* 1.3 60.9 + - - +
214B ILE 3.3 0.4 - - - -
215B SER* 3.5 18.6 + - - -
216B ALA* 5.0 0.9 + - - +
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Residues in contact with ASP 213 (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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130B PRO* 3.3 32.4 - - + +
131B PRO* 5.5 2.3 - - - +
208B VAL* 3.4 26.1 - - + +
209B GLU* 5.2 0.9 + - - +
210B LYS* 3.3 31.2 + - - +
211B GLU 2.9 1.6 - - - -
212B ALA* 1.3 81.5 - - - +
214B ILE* 1.4 58.5 + - - +
215B SER 3.5 0.9 - - - -
216B ALA* 3.4 5.6 - - - +
217B PHE* 2.9 30.0 - - - -
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Residues in contact with ILE 214 (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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156B VAL* 4.2 23.8 - - + -
157B GLY* 3.7 28.0 - - - +
185B TYR* 3.8 22.0 - - + -
186B LEU 3.8 10.8 - - - +
187B ALA* 4.1 12.5 - - - +
208B VAL* 4.2 7.6 - - + -
211B GLU* 2.9 37.0 + - + +
213B ASP* 1.4 76.5 - - - +
215B SER* 1.3 69.6 + - - +
217B PHE* 3.2 18.0 + - - +
218B ALA 4.2 2.4 + - - -
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Residues in contact with SER 215 (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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211B GLU 4.6 0.6 + - - -
212B ALA 3.5 14.9 + - - -
214B ILE* 1.3 74.1 - - - +
216B ALA* 1.3 53.1 + - - +
217B PHE 2.6 19.0 + - - -
218B ALA* 3.4 17.1 + - - +
219B ASP* 4.5 4.2 + - - +
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Residues in contact with ALA 216 (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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129B TYR* 3.4 24.5 - - + -
130B PRO* 3.3 36.6 - - + -
212B ALA 5.0 0.4 + - - +
213B ASP* 3.4 16.2 + - - +
214B ILE 3.2 1.4 - - - -
215B SER* 1.3 76.8 + - - +
217B PHE* 1.5 50.4 + - + +
219B ASP* 4.2 9.9 - - - +
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Residues in contact with PHE 217 (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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129B TYR* 3.6 37.9 - + + -
130B PRO* 3.4 27.4 - - + -
132B HIS* 4.0 22.9 - + + -
187B ALA* 4.1 23.6 - - + +
188B LYS* 3.2 29.0 - - + +
206B ILE* 4.2 18.4 - - + -
208B VAL* 4.1 12.8 - - + -
213B ASP 2.9 29.4 - - - -
214B ILE 3.2 8.8 + - - +
215B SER 2.6 11.3 + - - -
216B ALA* 1.5 66.3 - - + +
218B ALA* 1.3 58.8 + - - +
219B ASP 2.8 6.4 + - - +
220B TYR* 3.3 16.4 + + - +
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Residues in contact with ALA 218 (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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187B ALA 5.1 1.4 + - - -
188B LYS* 4.9 14.2 + - - +
214B ILE 4.2 3.6 + - - +
215B SER* 3.4 13.1 + - - +
217B PHE* 1.3 76.5 - - - +
219B ASP* 1.3 60.2 + - - +
220B TYR 3.6 0.5 + - - -
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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