Contacts of the helix formed by residues 191 - 196 (chain B) in PDB entry 4FGU
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 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.8 1.8 - - - -
186B ILE* 3.7 17.6 + - - +
188B ALA* 3.1 36.9 + - - -
189B CYS 2.9 2.2 + - - -
190B GLU* 1.3 72.0 - - - +
192B GLY* 1.3 56.0 + - - +
193B SER* 3.0 6.5 - - - -
194B MET* 3.1 30.1 + - - +
195B MET 4.0 0.2 + - - -
208B THR* 3.3 28.2 - - - +
209B ALA 3.3 10.9 + - - -
210B ALA 3.6 4.6 + - - -
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU 3.2 1.4 - - - -
191B SER* 1.3 76.5 - - - +
193B SER* 1.3 56.1 + - - +
194B MET 3.2 0.7 - - - -
195B MET 4.1 0.4 - - - -
196B ASN* 3.2 34.5 + - - +
208B THR* 3.6 14.4 - - - -
210B ALA 2.9 20.8 + - - -
212B PRO* 3.5 12.6 - - - +
270B TYR* 4.0 12.4 + - - -
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER 3.0 15.6 + - - -
151B THR* 3.9 3.4 - - - -
152B GLY* 3.2 18.2 + - - -
163B VAL* 4.5 9.9 - - - +
190B GLU 2.6 24.0 + - - -
192B GLY* 1.3 78.8 - - - +
194B MET* 1.3 62.0 + - - +
196B ASN* 2.9 17.8 - - - +
197B HIS* 4.9 3.1 - - - +
212B PRO* 3.5 22.0 - - - +
373B LEU* 3.8 17.9 - - - +
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Residues in contact with MET 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY* 3.5 31.9 - - - +
153B ILE* 3.6 7.6 - - - +
154B LEU* 3.7 45.3 - - + -
161B LEU* 3.8 11.4 - - + +
162B HIS 4.0 2.2 - - - +
163B VAL* 3.4 47.8 - - - +
166B LEU* 4.0 14.8 - - + -
186B ILE* 5.1 3.4 - - + -
191B SER* 3.1 12.5 + - - +
193B SER* 1.3 85.2 - - - +
195B MET* 1.3 81.1 + - + +
196B ASN* 4.4 0.7 - - - -
197B HIS* 4.7 4.9 + - - +
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Residues in contact with MET 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 5.7 0.2 - - + -
166B LEU* 3.9 24.5 - - + -
170B ILE* 6.2 4.3 - - + -
184B PHE* 3.9 22.0 - - + -
186B ILE* 3.6 24.7 - - + -
191B SER 4.0 1.2 + - - -
192B GLY 3.7 1.6 + - - -
194B MET* 1.3 97.0 - - + +
196B ASN* 1.3 64.5 + - - +
197B HIS 3.2 3.5 + - - +
198B LEU* 3.3 39.0 + - + +
204B VAL* 5.6 0.2 - - - -
206B ALA* 3.6 27.6 - - + -
208B THR* 4.1 8.5 - - + -
270B TYR* 3.2 36.2 - - + +
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Residues in contact with ASN 196 (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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192B GLY 3.2 18.1 + - - +
193B SER* 2.9 23.6 - - - +
195B MET* 1.3 76.4 - - - +
197B HIS* 1.3 80.2 + - - +
198B LEU 3.4 4.6 + - - +
212B PRO* 4.6 7.9 - - + +
270B TYR* 3.7 24.6 - - + +
373B LEU* 3.5 24.5 - - - +
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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