Contacts of the helix formed by residues 221 - 234 (chain H) in PDB entry 5LN3
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 221 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176H ASP* 4.7 1.3 - - - -
180H CYS* 4.5 18.4 - - - +
183H GLN* 4.0 3.1 - - - +
219H GLY 3.5 3.6 - - - -
220H THR* 1.4 76.8 - - - +
222H LYS* 1.3 64.7 + - - +
223H THR* 3.2 2.9 + - - -
224H LEU* 3.5 28.5 - - - +
225H CYS* 3.3 23.6 + - - +
386H ARG* 4.2 0.8 - - - +
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Residues in contact with LYS 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H GLN* 3.9 15.9 - - - +
214H LEU* 3.5 43.4 - - + +
215H PHE* 4.1 19.3 - - - +
216H GLY 3.4 14.1 + - - -
217H PRO 3.6 18.2 - - - +
218H PRO* 4.1 10.5 - - + +
220H THR* 3.4 5.7 + - - +
221H GLY* 1.3 80.5 - - - +
223H THR* 1.3 77.9 + - + +
225H CYS* 3.5 6.8 - - - +
226H ALA* 4.0 1.4 + - - +
273H PHE* 6.0 4.3 - - + -
276H GLU* 3.8 24.3 + - - -
320H ALA* 4.2 13.9 - - - -
321H THR 3.2 24.8 + - - -
322H ASN* 5.2 0.2 - - - +
343H PHE* 5.7 4.0 - - + -
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Residues in contact with THR 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PRO* 3.5 19.3 - - + -
219H GLY* 2.9 39.2 + - - +
221H GLY* 3.8 4.0 + - - -
222H LYS* 1.3 83.9 - - + +
224H LEU* 1.4 68.9 + - - +
225H CYS 3.3 0.5 + - - -
226H ALA* 3.7 15.8 + - - +
227H ARG* 3.9 10.3 + - - +
273H PHE* 5.5 11.0 - - + -
276H GLU* 5.6 0.9 - - - +
317I ASP* 4.7 14.9 + - + +
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Residues in contact with LEU 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H VAL* 4.5 21.5 - - + +
175H SER* 4.0 22.7 - - - +
176H ASP* 4.6 4.7 - - + +
219H GLY 6.2 0.7 - - - -
221H GLY* 3.4 21.7 + - - +
222H LYS 3.4 0.6 - - - -
223H THR* 1.4 85.5 + - - +
225H CYS* 1.4 52.8 - - - +
227H ARG* 3.3 14.4 + - - +
228H ALA* 2.8 33.7 + - + +
386H ARG* 3.7 28.7 - - - +
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Residues in contact with CYS 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H CYS* 6.1 2.2 - - + -
183H GLN* 3.2 48.0 - - - +
184H ILE* 4.7 13.5 - - - -
187H LEU* 3.5 26.2 - - - +
214H LEU* 4.8 1.8 - - + -
221H GLY 3.3 11.4 + - - +
222H LYS 3.5 4.5 - - - +
224H LEU* 1.4 76.2 - - - +
226H ALA* 1.3 58.7 + - - +
228H ALA* 3.4 7.8 + - - +
229H VAL* 3.0 26.3 + - - +
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Residues in contact with ALA 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H LEU* 4.6 5.8 - - - +
214H LEU* 4.8 6.4 - - + +
222H LYS 4.0 5.0 + - - +
223H THR 3.7 10.7 + - - +
225H CYS* 1.3 77.3 - - - +
227H ARG* 1.4 64.1 + - + +
229H VAL* 4.0 1.7 - - - +
230H ALA* 3.0 22.3 + - - +
237H PHE* 3.6 17.3 - - + -
271H LEU* 5.7 0.7 - - - +
273H PHE* 4.1 17.3 - - + -
318H LEU* 3.8 28.0 - - + +
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Residues in contact with ARG 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H GLU* 3.5 18.0 + - - +
170H PRO* 3.8 20.8 - - + +
172H VAL* 4.3 13.0 - - + -
223H THR 4.3 10.7 + - - +
224H LEU* 3.3 15.4 + - - +
226H ALA* 1.4 78.1 - - + +
228H ALA* 1.4 64.0 + - - +
230H ALA* 3.0 17.6 + - - +
231H ASN* 3.1 14.7 + - - +
237H PHE* 4.3 15.7 - - + -
239H ARG* 3.1 39.0 - - - +
318I GLY* 3.0 33.5 + - - -
319I PHE* 5.7 0.4 - - - +
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Residues in contact with ALA 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H VAL* 3.9 21.9 - - + +
173H THR* 4.8 2.9 - - - -
174H TYR 5.0 2.5 - - - +
184H ILE* 6.3 2.2 - - + -
224H LEU* 2.8 20.6 + - + +
225H CYS* 3.4 10.7 + - - +
227H ARG* 1.4 73.9 - - - +
229H VAL* 1.4 63.2 + - + +
231H ASN* 3.4 4.7 - - - +
232H ARG* 3.3 47.0 + - - +
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Residues in contact with VAL 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H ILE* 5.5 3.8 - - + +
187H LEU* 3.8 34.1 - - + +
188H ARG* 4.6 14.6 - - + +
191H VAL* 4.0 24.0 - - + -
192H GLU* 4.2 10.3 - - + +
225H CYS* 3.0 13.4 + - - +
226H ALA 4.4 2.0 - - - +
228H ALA* 1.4 73.7 - - + +
230H ALA* 1.4 58.2 + - - +
232H ARG* 3.1 20.9 + - - +
233H THR* 2.9 44.6 + - + +
271H LEU* 5.3 2.2 - - + -
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Residues in contact with ALA 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LYS* 4.7 4.3 - - - +
170H PRO* 4.5 8.3 - - + -
226H ALA 3.0 16.4 + - - +
227H ARG* 3.0 13.5 + - - +
229H VAL* 1.4 76.6 - - - +
231H ASN* 1.3 62.0 + - - +
233H THR* 3.7 9.5 - - - +
234H ASP* 3.6 14.4 + - - -
235H ALA 4.2 8.7 - - - +
237H PHE* 3.6 39.0 - - + -
271H LEU* 5.3 2.7 - - - +
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Residues in contact with ASN 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LYS* 3.9 11.6 - - - +
170H PRO* 3.0 35.9 - - + +
171H ASP* 3.4 20.6 + - - +
172H VAL 3.2 21.1 + - - +
173H THR* 3.7 10.6 - - - +
227H ARG 3.1 7.0 + - - +
228H ALA 3.4 10.1 - - - +
230H ALA* 1.3 81.2 - - - +
232H ARG* 1.4 61.7 + - - +
234H ASP* 3.4 18.7 - - - +
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Residues in contact with ARG 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H THR* 3.8 21.5 - - + +
174H TYR* 3.1 67.9 + - - +
184H ILE* 4.0 15.4 - - - +
188H ARG* 3.3 31.4 - - - +
192H GLU* 3.6 24.8 - - - +
228H ALA* 3.3 29.4 + - - +
229H VAL* 3.1 16.1 + - - +
231H ASN* 1.4 76.4 - - - +
233H THR* 1.4 57.3 + - - +
234H ASP* 2.8 15.8 - - - +
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Residues in contact with THR 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H VAL* 3.8 8.6 - - + +
192H GLU* 3.4 38.6 + - - +
195H LEU* 4.0 14.9 - - - +
196H LEU* 5.9 2.9 - - - +
229H VAL* 2.9 33.2 + - + +
230H ALA* 3.7 14.4 - - - +
232H ARG* 1.4 71.1 - - - +
234H ASP* 1.3 68.8 + - - +
235H ALA* 4.3 4.6 - - + +
271H LEU* 4.0 24.9 - - + -
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Residues in contact with ASP 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LYS* 3.0 37.6 + - - +
230H ALA 3.6 7.9 + - - -
231H ASN 3.4 11.3 - - - +
232H ARG* 2.8 25.3 - - - +
233H THR* 1.3 79.9 - - - +
235H ALA* 1.4 57.8 + - - +
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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