Contacts of the helix formed by residues 214 - 224 (chain B) in PDB entry 2Q41
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 GLU 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B LYS* 3.1 46.7 - - - +
211B GLU* 3.3 27.0 + - + +
213B PHE* 1.3 82.8 - - - +
215B LYS* 1.3 67.0 + - - +
216B PRO* 3.3 11.6 - - + +
217B PHE* 3.2 14.2 + - - +
218B PHE* 3.3 13.8 + - - -
251B ASN* 4.1 4.3 - - - +
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Residues in contact with LYS 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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214B GLU* 1.3 70.4 - - - +
216B PRO* 1.3 72.8 - - + +
218B PHE* 2.9 9.9 + - - +
219B GLN* 2.8 25.6 + - - +
251B ASN* 3.3 37.8 + - + +
254B GLU* 3.2 44.7 + - + +
255B ILE* 4.0 21.2 - - + +
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Residues in contact with PRO 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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184B VAL* 5.9 1.1 - - + -
211B GLU* 5.6 9.0 - - + +
214B GLU* 3.4 14.6 - - + +
215B LYS* 1.3 94.3 - - + +
217B PHE* 1.3 63.2 + - - +
219B GLN* 3.3 7.6 + - + +
220B SER* 3.1 19.9 + - - -
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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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127B ILE* 4.3 9.9 - - + -
184B VAL* 3.9 31.5 - - + +
187B LEU* 4.0 16.6 - - + -
200B VAL* 4.0 24.7 - - + -
211B GLU* 3.3 21.6 + - + +
212B LEU* 3.2 57.9 - - + -
214B GLU 3.2 4.0 + - - +
216B PRO* 1.3 80.5 - - - +
218B PHE* 1.3 67.8 + + - +
220B SER* 3.0 10.3 - - - -
221B VAL* 2.9 49.1 + - + +
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Residues in contact with PHE 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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212B LEU 3.7 21.3 - - - -
213B PHE* 3.4 26.5 - - - -
214B GLU 3.3 11.6 + - - -
215B LYS* 2.9 6.3 + - - +
217B PHE* 1.3 86.2 - + - +
219B GLN* 1.3 56.1 + - - +
221B VAL* 2.8 12.4 + - + +
222B ALA* 2.6 34.7 + - - +
231B VAL* 6.0 3.8 - - + -
233B THR* 4.1 21.5 - - + -
248B ILE* 4.2 12.3 - - + -
251B ASN* 3.8 23.6 - - + -
252B CYS* 3.5 32.8 - - - -
255B ILE* 4.1 13.5 - - + +
256B PHE* 4.2 14.4 - + + -
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Residues in contact with GLN 219 (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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215B LYS 2.8 15.0 + - - +
216B PRO* 3.5 11.0 - - + +
218B PHE* 1.3 71.5 - - - +
220B SER* 1.3 53.3 + - - +
222B ALA* 3.0 11.4 + - - +
223B ARG* 2.7 40.2 + - + +
255B ILE* 3.3 37.6 + - + +
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Residues in contact with SER 220 (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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184B VAL* 4.3 4.1 + - - -
187B LEU* 3.0 38.6 + - - +
188B LYS* 3.4 12.6 + - - -
216B PRO 3.1 13.5 + - - -
217B PHE* 3.0 18.8 - - - -
219B GLN* 1.3 74.8 - - - +
221B VAL* 1.3 61.2 + - - +
223B ARG* 3.4 9.9 + - - +
224B ALA* 3.1 23.4 + - - +
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Residues in contact with VAL 221 (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 LEU* 3.5 22.0 - - + -
198B VAL* 4.3 14.1 - - + +
200B VAL* 4.9 1.6 - - + -
217B PHE* 2.9 45.6 + - + +
218B PHE* 2.8 17.2 + - + +
220B SER* 1.3 72.7 - - - +
222B ALA* 1.3 61.8 + - - +
224B ALA* 3.5 2.6 + - - +
225B LEU* 3.1 28.3 + - + +
231B VAL* 3.8 36.3 - - + -
256B PHE* 4.5 3.8 - - + -
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Residues in contact with ALA 222 (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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218B PHE 2.6 15.0 + - - +
219B GLN* 3.1 15.3 - - - +
221B VAL* 1.3 72.4 - - - +
223B ARG* 1.3 67.2 + - - +
225B LEU* 3.1 20.8 + - - +
255B ILE* 3.7 25.4 - - + +
256B PHE* 4.2 11.2 - - + -
282B THR* 4.2 18.4 - - + +
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Residues in contact with ARG 223 (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 LEU 5.3 4.5 + - - -
188B LYS* 4.9 9.4 + - - +
190B ALA 3.7 21.2 + - - +
191B ALA* 4.8 1.4 - - - +
192B GLU* 3.3 52.4 + - + +
193B GLY* 2.8 29.8 + - - -
219B GLN* 2.7 24.8 + - + +
220B SER* 3.8 9.6 - - - +
222B ALA* 1.3 73.9 - - - +
224B ALA* 1.3 51.5 + - - +
225B LEU 3.5 1.4 + - - +
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Residues in contact with ALA 224 (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 LEU* 3.4 34.3 - - + +
190B ALA* 4.1 11.0 - - + -
191B ALA 4.0 6.5 - - - -
193B GLY 3.7 2.9 - - - +
194B SER 2.8 24.9 + - - -
195B TYR* 3.0 25.7 + - + +
198B VAL* 5.3 1.3 - - + -
220B SER 3.1 6.5 + - - +
221B VAL 3.7 2.9 - - - +
222B ALA 3.1 0.8 - - - -
223B ARG* 1.3 77.2 - - + +
225B LEU* 1.3 59.7 + - + +
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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