Contacts of the helix formed by residues 190 - 204 (chain N) 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 ASN 190 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117N ASP* 3.9 8.3 + - - +
158N ARG* 3.6 22.6 - - - +
188N MET* 5.1 0.5 - - - +
189N GLN* 1.3 76.2 + - - +
191N LYS* 1.3 69.0 + - - +
192N GLN* 3.3 30.9 + - - +
193N PHE* 3.8 17.3 - - + +
194N ARG* 2.9 24.8 + - - +
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Residues in contact with LYS 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N GLN 2.9 7.9 + - - +
190N ASN* 1.3 75.0 + - - +
192N GLN* 1.3 59.9 + - - +
194N ARG* 3.4 12.3 + - - +
195N ASN* 2.7 56.6 + - - +
222N PHE 5.7 1.1 + - - -
223N LEU 5.8 2.0 + - - -
224N ASP* 5.6 5.3 + - - -
558N GLY 6.1 1.1 - - - +
560N MET* 6.5 1.3 - - + -
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Residues in contact with GLN 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N ALA 5.3 4.0 + - - -
117N ASP* 4.2 24.4 + - - +
158N ARG* 5.9 0.2 - - - -
190N ASN* 3.2 24.8 + - - +
191N LYS* 1.3 80.2 - - - +
193N PHE* 1.3 63.4 + - - +
195N ASN* 3.2 8.4 + - - +
196N LYS* 3.0 51.3 + - - +
199N ARG* 4.7 0.2 + - - -
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Residues in contact with PHE 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N ALA 4.8 0.2 - - - -
155N LEU* 4.1 13.7 - - + -
158N ARG* 3.4 79.2 - - + +
160N LEU* 3.6 26.2 - - + -
188N MET* 3.5 37.9 - - + -
190N ASN* 3.4 14.0 + - + +
192N GLN* 1.3 81.8 - - + +
194N ARG* 1.3 63.2 + - - +
196N LYS* 2.9 16.3 + - + +
197N VAL* 2.9 33.3 + - + +
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Residues in contact with ARG 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N CYS* 2.8 21.8 + - - +
185N MET* 3.6 23.0 + - - +
188N MET* 3.6 40.3 - - + -
189N GLN 5.2 2.5 - - - -
190N ASN 2.9 18.8 + - - +
191N LYS* 3.6 13.2 + - - +
193N PHE* 1.3 77.7 - - - +
195N ASN* 1.3 67.7 + - - +
197N VAL* 3.1 5.7 + - - +
198N LEU* 3.0 42.9 + - + +
222N PHE* 3.5 43.9 + - - +
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Residues in contact with ASN 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191N LYS* 2.7 52.3 + - - +
192N GLN* 3.2 9.8 + - - +
194N ARG* 1.3 81.6 - - - +
196N LYS* 1.3 62.8 + - - +
198N LEU* 3.0 18.8 + - - +
199N ARG* 3.0 33.0 + - - +
222N PHE 3.6 22.2 + - - -
223N LEU* 3.8 23.4 + - + +
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Residues in contact with LYS 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N ALA 5.5 4.4 + - - -
160N LEU* 3.8 10.3 - - + +
192N GLN* 3.0 42.7 + - + +
193N PHE* 2.9 25.4 + - + +
195N ASN* 1.3 76.5 - - - +
197N VAL* 1.3 60.7 + - - +
199N ARG* 3.6 24.0 + - - +
200N VAL* 3.7 23.0 + - - +
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Residues in contact with VAL 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155N LEU* 4.1 15.3 - - + -
160N LEU* 3.9 34.1 - - + -
163N PHE* 4.5 16.4 - - + -
180N SER* 5.3 2.7 - - - +
184N CYS* 3.6 22.2 - - - -
188N MET* 4.4 5.6 - - - -
193N PHE* 2.9 36.1 + - + +
194N ARG 3.1 7.4 + - - +
196N LYS* 1.3 74.6 - - - +
198N LEU* 1.3 60.9 + - - +
200N VAL* 3.4 3.3 + - - +
201N LEU* 2.9 26.9 + - + +
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Residues in contact with LEU 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N LEU* 5.6 0.4 - - + -
184N CYS* 3.8 24.0 - - + -
185N MET* 6.2 1.3 - - - -
194N ARG* 3.0 48.4 + - - +
195N ASN* 3.0 13.0 + - - +
197N VAL* 1.3 77.7 - - - +
199N ARG* 1.3 57.6 + - - +
201N LEU* 3.1 9.1 + - + +
202N VAL* 2.9 32.1 + - - +
219N CYS* 3.7 34.5 - - + +
222N PHE* 3.8 29.2 - - + +
223N LEU* 4.4 10.5 - - + +
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Residues in contact with ARG 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N GLN 4.7 0.2 + - - -
195N ASN* 3.0 22.1 + - - +
196N LYS* 3.6 44.6 - - - +
197N VAL 3.3 0.2 - - - -
198N LEU* 1.3 76.1 - - - +
200N VAL* 1.3 60.1 + - + +
202N VAL* 2.8 26.3 + - - +
203N LYS* 3.1 24.6 + - - +
223N LEU* 3.7 37.3 + - + +
225N ASP* 4.9 5.5 + - - -
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Residues in contact with VAL 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N LEU* 3.9 22.2 - - + +
163N PHE* 3.9 20.9 - - + -
164N GLU* 3.6 32.3 - - + -
196N LYS 3.7 14.5 + - - +
197N VAL 3.4 7.5 + - - +
198N LEU 3.4 0.2 - - - -
199N ARG* 1.3 78.1 - - + +
201N LEU* 1.3 59.7 + - - +
203N LYS* 3.5 9.4 + - + +
204N ILE* 3.4 25.3 + - + +
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Residues in contact with LEU 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N PHE* 4.9 5.1 - - + -
177N LEU* 3.7 29.2 - - + -
180N SER* 3.7 29.4 - - - +
181N LEU* 3.6 19.7 - - + -
184N CYS* 4.5 4.0 - - - -
197N VAL* 2.9 14.6 + - + +
198N LEU* 3.3 20.9 - - + +
199N ARG 3.1 0.2 - - - -
200N VAL* 1.3 77.2 - - - +
202N VAL* 1.3 59.5 + - - +
204N ILE* 3.5 11.9 - - + +
205N TYR* 3.1 37.2 - - + -
219N CYS* 3.6 27.6 - - - -
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Residues in contact with VAL 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198N LEU* 2.9 18.5 + - + +
199N ARG* 2.8 13.3 + - - +
201N LEU* 1.3 77.9 - - - +
203N LYS* 1.3 78.1 + - - +
204N ILE 3.2 0.2 - - - -
205N TYR* 3.2 16.6 + - - +
206N MET* 3.6 33.1 - - + +
216N VAL* 5.0 9.6 - - + +
219N CYS* 4.2 15.9 - - + -
220N LEU* 4.0 29.6 - - + +
223N LEU* 5.0 8.1 - - + -
232N ILE* 5.2 1.3 - - + -
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Residues in contact with LYS 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164N GLU* 6.5 0.2 - - + -
199N ARG* 3.1 27.0 + - - +
200N VAL* 3.5 10.7 + - + +
202N VAL* 1.3 91.6 - - + +
204N ILE* 1.3 61.3 + - + +
206N MET* 3.4 15.9 + - - +
207N ASN* 2.8 43.9 + - - +
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Residues in contact with ILE 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N PHE* 4.6 9.0 - - + -
164N GLU* 3.3 31.0 - - + +
167N ILE* 3.2 29.4 - - + -
177N LEU* 3.5 31.6 - - + +
180N SER* 5.3 0.2 - - - +
200N VAL* 3.4 20.9 - - + +
201N LEU* 3.5 20.0 - - + +
203N LYS* 1.3 76.6 - - + +
205N TYR* 1.3 59.1 + - - +
206N MET 3.3 4.9 - - - -
207N ASN* 4.4 0.9 - - - -
208N LEU* 3.2 44.2 - - + +
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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