Contacts of the helix formed by residues 210 - 217 (chain B) in PDB entry 4AQD
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 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B GLN* 3.4 18.0 + - - -
206B LEU 3.1 5.5 + - - -
207B HIS 3.8 1.2 + - - -
208B LEU 3.7 0.4 - - - -
209B LEU* 1.3 75.7 - - - +
211B PRO* 1.3 62.5 - - - +
212B GLY 3.6 2.4 + - - -
213B SER* 2.8 30.0 + - - -
214B HIS 3.2 0.5 + - - -
298B PHE* 3.1 55.0 + - - -
299B LEU* 5.9 0.2 - - - -
1530B PEG 3.1 13.1 + - - -
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Residues in contact with PRO 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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209B LEU 3.5 7.3 - - - +
210B SER* 1.3 87.4 - - - +
212B GLY* 1.3 63.4 + - - +
214B HIS* 3.2 17.2 + - - +
215B SER* 4.6 1.6 + - - -
297B ASP 4.9 3.1 - - - +
298B PHE 4.0 7.9 - - - +
300B THR* 4.2 26.0 - - + +
1530B PEG 3.9 31.4 - - - +
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Residues in contact with GLY 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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172B GLN* 3.2 21.0 + - - -
176B GLN* 5.3 3.1 + - - +
210B SER* 3.2 3.0 + - - -
211B PRO* 1.3 81.3 - - - +
213B SER* 1.3 56.7 + - - +
214B HIS 3.4 0.4 + - - -
215B SER* 4.8 2.9 + - - -
216B LEU* 3.2 22.0 - - - +
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Residues in contact with SER 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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172B GLN* 2.7 23.3 + - - +
175B LEU* 5.0 1.3 - - - -
207B HIS* 2.7 47.7 + - - -
210B SER* 2.8 12.0 + - - -
212B GLY* 1.3 76.9 - - - +
214B HIS* 1.3 65.2 + - - +
215B SER 3.3 2.2 - - - -
216B LEU* 3.1 20.4 + - - +
217B PHE* 3.3 18.0 - - - -
298B PHE* 3.8 2.8 - - - -
1530B PEG 4.2 1.3 - - - -
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Residues in contact with HIS 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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210B SER 3.2 3.0 + - - -
211B PRO 3.2 17.2 + - - +
212B GLY 3.4 0.2 - - - -
213B SER* 1.3 77.6 - - - +
215B SER* 1.3 65.0 + - - +
216B LEU 3.4 1.9 + - - -
217B PHE 4.0 0.2 - - - +
312B PHE 5.7 0.2 - - - -
313B LYS* 2.8 68.5 + - + +
314B LYS 5.4 1.6 - - - -
1530B PEG 3.2 40.8 + - - +
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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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179B GLN* 3.7 14.2 - - - +
211B PRO 4.6 0.6 + - - -
212B GLY 4.8 3.1 + - - -
213B SER 3.3 0.2 - - - -
214B HIS* 1.3 84.5 - - - +
216B LEU* 1.3 72.9 + - - +
217B PHE 3.6 2.7 - - - -
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Residues in contact with LEU 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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111B ILE* 5.3 0.5 - - - +
172B GLN* 3.6 35.4 - - + +
175B LEU* 3.9 27.0 - - + +
176B GLN* 4.3 27.6 - - + +
178B VAL* 5.9 0.2 - - - +
179B GLN* 3.5 36.0 + - + +
192B VAL* 4.3 5.5 - - - +
212B GLY 3.2 26.2 - - - +
213B SER* 3.1 12.8 + - - +
215B SER* 1.3 93.2 - - - +
217B PHE* 1.3 63.5 + - - +
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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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175B LEU* 4.4 4.5 - - + -
179B GLN* 5.0 0.7 - - - +
189B PRO 5.6 0.9 - - - -
192B VAL* 3.5 17.0 - - + +
194B LEU* 3.6 41.5 - - + -
204B VAL 5.1 0.4 - - - -
207B HIS* 3.5 32.5 - - + -
208B LEU* 4.1 18.8 - - + -
213B SER 3.3 21.8 - - - -
214B HIS* 4.0 1.5 - - - +
215B SER 3.6 2.5 + - - -
216B LEU* 1.3 80.5 - - - +
218B THR* 1.3 73.4 + - - +
219B ARG 3.4 24.9 - - - -
220B ALA* 4.3 3.1 - - + -
313B LYS* 3.0 44.1 + - + -
315B THR* 5.2 0.2 - - + -
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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