Contacts of the helix formed by residues 177 - 181 (chain B) in PDB entry 5FS9
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 LYS 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PRO* 3.1 29.5 + - - +
174B PRO 3.1 3.6 + - - -
176B SER* 1.3 84.2 + - - +
178B GLU* 1.3 83.4 + - - +
179B LEU 3.2 1.3 - - - -
180B TRP* 2.9 17.5 + - - +
181B PHE* 3.2 22.2 - - - -
196B TRP* 4.4 7.9 - - + -
314B GLU* 2.8 31.2 + - + +
483B TRP* 4.2 11.9 - - - +
485B ASP* 3.6 37.5 - - + +
487B GLY 6.1 0.2 - - - +
1000B FAD 2.7 38.4 + - - -
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PRO 4.3 0.7 - - - +
174B PRO* 3.5 19.0 + - + +
177B LYS* 1.3 90.3 - - - +
179B LEU* 1.3 63.2 + - - +
181B PHE* 3.0 13.9 + - - +
182B SER* 3.5 9.0 + - - -
193B PHE* 3.5 29.6 - - + +
194B LYS 3.5 27.2 + - - +
195B GLN* 4.3 6.3 - - - -
196B TRP* 3.9 38.4 + - + -
483B TRP* 5.7 1.0 + - - -
485B ASP* 4.7 1.6 - - - +
527B GLY* 4.3 22.5 - - - +
528B ILE* 5.3 3.4 - - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO* 3.1 32.2 + - + +
175B LEU* 3.8 24.0 - - + -
177B LYS 3.1 0.2 + - - -
178B GLU* 1.3 76.4 - - - +
180B TRP* 1.3 61.2 + - + +
181B PHE 3.6 0.2 + - - -
182B SER* 3.8 8.4 + - - +
187B VAL* 3.3 38.6 - - + +
191B LEU* 4.2 22.2 - - + -
193B PHE* 3.7 21.1 - - + -
203B ILE* 4.0 14.8 - - + -
290B PHE* 3.7 34.5 - - + -
322B LYS* 4.9 2.3 + - - -
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Residues in contact with TRP 180 (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 2.7 28.7 + - - -
176B SER* 3.7 21.0 - - - +
177B LYS 2.9 9.1 + - - +
179B LEU* 1.3 76.8 - - - +
181B PHE* 1.3 62.1 + - + +
182B SER 3.4 0.4 - - - -
284B PHE* 4.5 4.9 - + - -
290B PHE* 3.6 23.0 - + - -
293B LEU* 3.9 21.8 - - + -
294B GLU* 3.6 42.2 - - + -
297B SER* 4.5 2.9 - - - -
315B LEU* 4.3 6.5 - - + +
318B ALA* 3.5 27.1 - - + +
319B LEU* 3.7 28.0 - - + -
321B ARG* 3.3 12.2 + - - -
322B LYS* 3.1 53.8 + - + +
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER 5.5 0.2 - - - -
177B LYS* 3.2 22.4 - - - -
178B GLU* 3.0 9.8 + - - +
180B TRP* 1.3 80.0 - - - +
182B SER* 1.3 62.0 + - - +
183B ASP 3.8 0.9 + - - -
194B LYS 5.9 1.1 - - - +
196B TRP* 3.6 30.5 - + + -
314B GLU 5.9 0.2 - - - -
317B CYS* 4.7 10.3 - - + -
318B ALA* 4.3 24.5 - - + -
321B ARG* 3.5 46.7 + - + +
359B GLU* 6.0 2.5 - - - -
487B GLY* 3.8 17.9 - - - -
488B PRO* 3.9 19.3 - - + -
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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