Contacts of the helix formed by residues 211 - 220 (chain B) in PDB entry 2QFZ
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 ASP 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B LEU* 3.9 13.4 - - + +
209B ASN 3.3 5.6 + - - +
210B THR* 1.3 73.0 - - - +
212B LEU* 1.3 59.5 + - - +
213B GLU* 3.4 16.7 + - - +
214B GLU* 3.2 28.9 + - + +
215B LEU* 3.0 25.1 + - - +
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Residues in contact with LEU 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 THR* 3.3 13.9 + - + +
211B ASP* 1.3 69.3 + - - +
213B GLU* 1.3 66.8 + - - +
215B LEU* 3.7 9.9 - - + +
216B ARG* 2.9 59.2 + - + +
234B LEU* 4.2 35.4 - - + +
235B LEU* 5.4 2.9 - - + -
239B LEU 6.1 0.4 - - - +
241B ALA* 4.0 29.8 - - + +
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Residues in contact with GLU 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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211B ASP* 3.3 13.5 + - - +
212B LEU* 1.3 79.7 - - - +
214B GLU* 1.3 61.9 + - - +
216B ARG* 3.5 20.3 + - - +
217B ARG* 3.3 20.6 + - - +
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Residues in contact with GLU 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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204B LEU* 4.1 20.4 - - + -
211B ASP* 3.2 26.9 + - + +
213B GLU* 1.3 77.1 - - - +
215B LEU* 1.3 65.6 + - - +
217B ARG* 3.4 7.8 + - + +
218B LEU* 3.2 27.8 + - + +
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Residues in contact with LEU 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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201B PHE* 3.8 28.5 - - + -
204B LEU* 3.8 23.3 - - + +
205B LEU* 3.8 32.5 - - + -
210B THR* 4.3 7.6 - - + -
211B ASP 3.0 14.0 + - - +
212B LEU* 3.2 12.5 + - + +
214B GLU* 1.3 75.0 - - - +
216B ARG* 1.3 59.2 + - - +
218B LEU* 3.3 3.5 + - - +
219B SER* 2.9 33.6 + - - +
231B THR* 4.1 13.7 - - + -
234B LEU* 4.1 22.0 - - + -
235B LEU* 4.0 17.5 - - + -
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Residues in contact with ARG 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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212B LEU* 2.9 42.6 + - - +
213B GLU* 3.6 31.8 - - - +
215B LEU* 1.3 76.5 - - - +
217B ARG* 1.3 57.0 + - - +
219B SER* 4.4 0.4 - - - -
220B TRP* 3.0 27.2 + - - +
235B LEU* 3.6 30.7 + - + +
443B GLN 4.8 3.3 + - - +
444B SER* 3.2 38.7 - - - +
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Residues in contact with ARG 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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213B GLU* 3.3 10.7 + - + +
214B GLU* 3.8 11.4 - - + +
215B LEU 3.3 0.2 - - - -
216B ARG* 1.3 77.8 - - - +
218B LEU* 1.3 67.0 + - + +
220B TRP* 3.7 14.1 - - - +
221B SER* 4.5 4.2 + - - -
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Residues in contact with LEU 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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197B ARG* 2.5 50.6 + - + +
200B LYS* 4.2 40.8 - - + +
201B PHE* 3.7 22.4 - - + +
204B LEU* 3.2 32.5 - - + -
214B GLU* 3.2 15.8 + - + +
215B LEU 3.7 5.8 - - - +
217B ARG* 1.3 81.1 - - + +
219B SER* 1.3 58.4 + - - +
220B TRP 3.2 1.0 + - - -
221B SER* 3.4 3.8 + - - -
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Residues in contact with SER 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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201B PHE* 3.4 14.2 - - - -
215B LEU 2.9 22.6 + - - -
216B ARG 3.3 0.9 + - - -
218B LEU* 1.3 74.3 - - - +
220B TRP* 1.3 58.8 + - - +
221B SER 3.2 0.4 - - - -
222B GLY* 2.9 22.0 + - - -
223B ILE* 3.7 12.6 - - - -
231B THR* 3.3 25.8 - - - +
235B LEU* 3.7 10.6 - - - +
440B ASP* 3.8 10.4 - - - +
444B SER* 3.1 19.8 + - - -
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Residues in contact with TRP 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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216B ARG 3.0 13.4 + - - +
217B ARG* 3.7 12.6 - - - +
218B LEU 3.2 0.6 - - - -
219B SER* 1.3 74.6 - - - +
221B SER* 1.3 67.1 + - - +
222B GLY 3.4 1.7 + - - -
437B ARG* 3.8 3.8 + - - -
441B THR* 2.8 48.3 + - + +
444B SER* 3.3 16.8 + - - -
445B GLU* 2.9 29.6 + - - -
452B PHE* 4.2 7.9 - + - -
498B LEU* 4.0 29.4 - - + -
499B ALA* 4.6 5.4 - - + -
502B TYR* 3.7 36.3 - + + -
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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