Contacts of the helix formed by residues 208 - 213 (chain B) in PDB entry 5FQU
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 GLY 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR* 3.4 8.0 - - - +
164B VAL* 3.5 26.2 + - - +
165B SER* 3.6 9.4 - - - -
166B THR* 3.5 11.4 - - - -
188B SER 3.7 3.0 + - - -
206B VAL 3.2 1.8 + - - -
207B ASP* 1.3 71.7 + - - +
209B GLY* 1.3 58.7 + - - +
210B MSE 3.3 2.5 - - - -
211B VAL* 3.4 1.7 + - - +
212B ASP 3.0 33.3 + - - +
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 3.4 2.1 - - - +
207B ASP* 3.1 22.1 + - - -
208B GLY* 1.3 78.2 - - - +
210B MSE 1.3 57.2 + - - +
211B VAL 3.2 0.2 + - - -
213B ASN* 3.6 26.4 + - - +
257B THR* 3.5 19.1 - - - +
260B ASN* 2.8 22.0 + - - -
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Residues in contact with MSE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 5.8 0.2 - - + -
252A SER* 3.7 28.3 - - - +
255A LEU* 5.0 4.5 - - + -
166B THR* 3.5 31.2 - - + +
168B ILE* 4.4 12.3 - - + -
192B PRO* 3.9 31.4 - - + -
206B VAL* 4.0 14.4 - - + -
207B ASP* 4.0 13.2 + - - +
209B GLY* 1.3 76.1 - - - +
211B VAL* 1.3 59.0 + - + +
253B ILE* 4.4 19.9 - - + +
256B MSE 3.3 42.1 - - + +
257B THR* 4.2 6.9 + - - -
260B ASN* 3.2 11.2 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 5.8 1.3 - - + -
164B VAL* 4.8 0.7 - - + -
165B SER 3.8 13.7 - - - +
166B THR* 3.3 29.6 - - + +
171B GLY* 3.5 25.6 - - - +
173B LYS* 3.9 24.7 - - + +
208B GLY 3.8 3.8 - - - +
209B GLY 3.2 0.2 - - - -
210B MSE 1.3 87.9 - - + +
212B ASP* 1.3 67.5 + - + +
256B MSE 5.3 4.3 - - + -
260B ASN* 3.4 21.8 - - - +
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Residues in contact with ASP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 2.9 19.4 + - - -
164B VAL* 4.0 10.1 - - + +
173B LYS* 3.4 28.1 + - + +
208B GLY 3.0 11.3 + - - +
211B VAL* 1.3 80.2 - - - +
213B ASN* 1.3 60.0 + - - +
214B ILE 3.4 18.2 + - - +
215B PRO* 3.4 15.1 - - - +
217B ASP* 2.7 31.7 - - - +
218B VAL* 3.9 1.2 - - - +
260B ASN* 3.7 1.7 - - - +
264B GLN* 3.5 14.9 - - - +
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Residues in contact with ASN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 3.2 9.8 - - - -
31B GLY* 3.1 46.8 + - - +
59B THR* 3.7 4.0 + - - -
60B SER* 4.8 0.2 + - - -
209B GLY* 3.6 28.2 + - - +
212B ASP* 1.3 74.0 - - - +
214B ILE* 1.3 68.8 + - - +
215B PRO* 3.5 3.8 - - - +
231B ASP* 4.9 1.0 + - - -
234B ASN* 3.4 19.5 - - - +
257B THR* 3.7 14.4 - - + +
260B ASN* 3.0 7.2 + - - +
261B SER* 3.3 25.1 + - - +
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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