Contacts of the helix formed by residues 208 - 215 (chain B) in PDB entry 5WQA
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 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B HIS* 5.2 1.3 - - - -
207B VAL* 1.3 79.5 - - - +
209B ASN* 1.3 64.5 + - - +
210B GLN* 3.7 8.6 + - - +
211B PHE 3.3 10.9 + - - -
212B LEU* 3.1 21.3 + - - +
229B LEU* 4.0 4.7 - - - -
343B GLN* 3.2 22.3 + - - -
355B SER* 5.9 0.2 - - - -
501B J20 3.5 30.8 - - - -
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Residues in contact with ASN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER* 1.3 74.2 - - - +
210B GLN* 1.3 57.9 + - - +
212B LEU* 3.1 8.2 + - - +
213B ILE* 2.8 41.1 + - + +
225B ASP 6.0 0.2 - - - +
227B SER* 4.3 2.8 - - - +
228B VAL* 3.4 17.7 - - + +
229B LEU* 2.8 41.3 + - - +
230B GLU* 3.1 29.9 + - - -
272B ASP* 4.2 11.9 + - - -
273B MET 5.8 0.2 - - - +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLN* 5.5 3.2 + - - -
208B SER* 3.3 8.3 + - - +
209B ASN* 1.3 78.2 - - - +
211B PHE* 1.3 57.4 - - - +
213B ILE* 3.3 22.3 + - - +
214B ASN* 2.7 72.4 + - - +
355B SER* 6.0 3.1 - - - +
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Residues in contact with PHE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 3.4 36.6 - - + -
208B SER* 3.3 10.4 + - - +
209B ASN 3.3 0.4 - - - -
210B GLN* 1.3 75.1 - - - +
212B LEU* 1.3 59.2 + - + +
214B ASN* 3.9 5.8 - - - +
215B THR* 2.6 65.9 + - + +
343B GLN* 3.5 25.8 - - + +
346B ARG* 4.4 25.6 - - + -
347B GLU* 3.6 38.1 - - + +
350B ARG* 4.2 17.7 - - - -
352B MET* 4.3 7.4 - - + -
355B SER* 5.9 0.2 - - - -
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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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205B PRO* 4.6 4.0 - - + -
207B VAL* 4.0 20.9 - - + +
208B SER 3.1 14.9 + - - +
209B ASN* 3.1 7.1 + - - +
211B PHE* 1.3 78.5 - - + +
213B ILE* 1.3 63.8 + - - +
215B THR* 3.4 5.3 + - - +
217B SER* 2.9 54.0 + - - +
219B LEU* 4.1 21.1 - - + -
220B ALA* 3.5 2.7 - - - +
228B VAL* 4.3 14.4 - - + -
229B LEU* 3.6 37.9 - - + -
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Residues in contact with ILE 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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258A GLN* 5.9 2.0 - - - +
261A ARG* 5.9 0.2 - - - +
209B ASN* 2.8 27.4 + - + +
210B GLN* 3.5 27.6 - - - +
212B LEU* 1.3 76.5 - - - +
214B ASN* 1.3 61.5 + - - +
216B ASN* 3.0 25.3 + - - +
220B ALA* 3.8 10.2 - - + +
225B ASP* 3.6 57.6 - - + +
228B VAL* 4.5 4.7 - - + -
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Residues in contact with ASN 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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254A LYS* 5.0 18.4 + - - +
258A GLN* 5.0 6.4 - - - +
210B GLN* 2.7 57.4 + - - +
211B PHE* 4.0 2.3 - - - +
213B ILE* 1.3 76.4 - - - +
215B THR* 1.3 58.4 + - - +
216B ASN* 3.3 13.1 + - - -
347B GLU* 5.8 1.4 + - - -
352B MET* 3.9 24.5 - - + +
355B SER* 5.8 1.6 + - - -
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Residues in contact with THR 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 PHE* 2.6 46.9 + - + +
212B LEU* 3.4 9.7 + - - +
214B ASN* 1.3 75.6 - - - +
216B ASN* 1.3 74.2 + - - +
217B SER* 3.2 7.6 + - - -
350B ARG* 4.1 18.1 + - - +
352B MET* 3.6 31.6 - - + -
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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