Contacts of the helix formed by residues 194 - 204 (chain R) in PDB entry 5L4K
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 PHE 194 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188R CYS 4.3 1.2 + - - -
189R VAL* 4.2 7.8 - - + +
192R ARG* 4.1 4.3 - - + -
193R ASP* 1.3 90.7 + - - +
195R LYS* 1.3 53.7 + - - +
197R ALA* 2.8 14.5 + - - +
198R ALA* 2.3 39.4 + - - +
226R VAL* 3.7 25.5 - - + +
229R ILE* 4.2 25.6 - - + -
230R ALA* 4.0 8.1 - - + -
288R PHE* 3.7 32.3 - + - -
289R ALA* 5.3 0.2 - - + -
291R HIS* 4.0 28.7 - + - -
294R TYR* 4.2 22.0 - + - -
295R TYR* 4.2 21.8 - + + -
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Residues in contact with LYS 195 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402Q GLU* 5.9 0.8 + - - -
193R ASP* 2.3 33.2 + - - +
194R PHE* 1.3 71.1 - - - +
196R GLN* 1.3 77.0 + - - +
198R ALA* 2.8 9.7 + - - +
199R GLU* 3.0 11.5 + - - +
230R ALA* 3.6 18.8 - - + +
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Residues in contact with GLN 196 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R CYS* 3.7 16.4 - - - -
193R ASP* 2.7 23.6 + - - +
195R LYS* 1.3 88.7 - - - +
197R ALA* 1.3 60.5 + - - +
199R GLU* 3.1 24.2 + - - +
200R LEU* 2.9 42.8 + - + +
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Residues in contact with ALA 197 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185R GLY 4.5 2.5 - - - +
188R CYS* 3.8 23.2 - - + +
189R VAL* 4.0 23.6 - - + -
193R ASP* 3.1 4.6 + - - -
194R PHE* 2.8 27.3 + - - +
196R GLN* 1.3 77.8 - - - +
198R ALA* 1.3 55.1 + - - +
200R LEU* 3.9 3.8 - - - +
201R PHE* 2.9 38.7 + - + +
226R VAL* 4.9 1.6 - - + -
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Residues in contact with ALA 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194R PHE 2.3 28.9 + - - +
195R LYS 3.5 3.8 - - - +
197R ALA* 1.3 67.0 - - - +
199R GLU* 1.3 62.4 + - - +
202R LEU* 2.8 33.8 + - - +
226R VAL* 4.2 21.7 - - + +
227R SER* 4.5 12.6 - - - -
230R ALA* 4.0 18.4 - - + -
231R LEU* 4.7 13.9 - - + +
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Residues in contact with GLU 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195R LYS 3.0 11.4 + - - +
196R GLN* 3.1 27.6 + - - +
198R ALA* 1.3 77.2 - - - +
200R LEU* 1.3 68.9 + - + +
202R LEU* 4.9 0.9 - - - -
203R ASP* 2.9 41.4 + - + +
231R LEU* 5.9 1.1 - - - +
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Residues in contact with LEU 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R LYS* 3.7 52.5 - - + +
184R GLN* 3.9 23.6 - - + +
185R GLY* 3.7 30.1 - - - +
188R CYS* 4.6 4.3 - - + -
196R GLN* 2.9 40.2 + - + +
197R ALA 3.9 2.5 - - - +
199R GLU* 1.3 81.0 - - + +
201R PHE* 1.3 68.0 + - - +
203R ASP* 3.0 8.1 + - - +
204R THR* 3.6 16.5 + - - +
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Residues in contact with PHE 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R LYS 5.2 2.5 - - - -
182R VAL* 4.2 8.7 - - - -
185R GLY* 3.5 25.4 - - - -
186R LEU* 3.5 30.5 - - + -
189R VAL* 3.9 27.8 - - + -
197R ALA* 2.9 23.4 + - + +
198R ALA 4.5 0.7 - - - +
200R LEU* 1.3 75.0 - - - +
202R LEU* 1.3 63.8 + - - +
203R ASP 3.2 0.2 + - - -
204R THR* 3.3 14.9 + - - -
205R VAL* 3.6 12.1 + - - +
219R PHE* 3.7 33.0 - + - -
222R TYR* 4.9 12.3 - - + -
223R THR* 4.2 22.7 - - + +
226R VAL* 4.1 21.5 - - + -
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Residues in contact with LEU 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198R ALA* 2.8 22.8 + - - +
199R GLU* 4.0 1.3 - - - +
201R PHE* 1.3 78.7 - - - +
203R ASP* 1.3 69.6 + - - +
204R THR 3.5 1.0 + - - -
205R VAL* 3.7 18.3 - - + +
223R THR* 4.0 17.7 - - + -
227R SER* 3.5 31.4 - - - +
231R LEU* 3.8 13.2 - - + -
239R LYS* 3.6 37.2 - - + +
240R VAL* 3.7 18.2 - - + -
246R ILE* 6.0 2.2 - - + -
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Residues in contact with ASP 203 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R LYS* 5.9 3.6 - - + -
199R GLU* 2.9 33.4 + - + +
200R LEU* 3.0 3.5 + - - +
202R LEU* 1.3 90.4 - - - +
204R THR* 1.3 64.1 + - + +
205R VAL* 3.7 0.9 - - - -
206R SER* 5.3 1.5 - - - -
207R THR* 5.6 0.3 + - - -
239R LYS* 4.3 12.2 + - - -
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Residues in contact with THR 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R ASN* 4.1 21.3 - - - +
181R LYS* 3.6 37.8 - - + +
182R VAL* 4.1 12.9 - - - +
200R LEU 3.7 9.4 + - - +
201R PHE* 3.5 10.4 + - - -
202R LEU 3.3 0.6 - - - -
203R ASP* 1.3 82.8 - - + +
205R VAL* 1.3 67.5 + - - +
206R SER 3.0 4.0 - - - +
207R THR* 3.0 19.8 + - - +
208R PHE* 3.2 12.3 + - - +
219R PHE* 4.1 12.9 - - - -
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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