Contacts of the helix formed by residues 221 - 234 (chain C) in PDB entry 5LEZ
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 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C ILE* 4.2 1.2 + - - -
220C LEU* 1.3 76.7 - - - +
222C PRO* 1.4 71.3 - - + +
223C GLU* 3.9 18.8 - - - +
224C GLU* 2.9 27.9 + - - +
225C ILE* 2.9 26.1 + - - +
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Residues in contact with PRO 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLU* 4.7 20.6 - - - +
204C LYS 5.9 2.7 - - - +
220C LEU 4.8 0.7 - - - +
221C ASN* 1.4 86.8 - - + +
223C GLU* 1.3 57.8 + - - +
225C ILE* 3.9 12.3 - - + +
226C GLU* 3.4 25.1 + - - +
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ASN* 3.2 14.5 - - - +
222C PRO* 1.3 78.7 - - - +
224C GLU* 1.3 61.8 + - - +
225C ILE 3.3 0.7 + - - -
226C GLU* 4.5 1.4 - - - +
227C LYS* 3.6 20.1 + - - +
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Residues in contact with GLU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C LEU* 4.4 14.5 - - + +
221C ASN* 2.9 29.8 + - - +
223C GLU* 1.3 76.5 - - - +
225C ILE* 1.3 60.1 + - - +
227C LYS* 3.9 13.7 - - + +
228C TYR* 3.1 29.5 - - + -
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE* 4.4 14.4 - - + -
203C GLY 4.2 9.9 - - - +
204C LYS 4.8 6.1 - - - +
206C ILE* 4.1 24.2 - - + +
208C LEU* 3.7 36.1 - - + +
220C LEU* 4.4 19.1 - - + +
221C ASN 2.9 16.9 + - - +
222C PRO* 4.1 11.4 - - + +
223C GLU 3.3 0.2 - - - -
224C GLU* 1.3 74.9 - - - +
226C GLU* 1.3 63.4 + - + +
227C LYS 3.2 1.8 - - - -
228C TYR* 3.0 24.4 + - - +
229C VAL* 3.1 25.1 + - + +
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Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLY 4.1 17.5 + - - +
204C LYS* 4.7 1.6 + - - +
222C PRO 3.4 15.7 + - - +
223C GLU* 3.9 2.2 + - - +
224C GLU 3.8 0.2 - - - -
225C ILE* 1.3 75.6 - - + +
227C LYS* 1.3 63.7 + - - +
229C VAL* 3.8 24.2 - - + +
230C ALA* 3.2 30.4 + - + +
233C GLU* 5.1 2.6 - - - +
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASP* 5.6 3.6 - - - -
223C GLU 3.6 16.7 + - - +
224C GLU* 3.9 15.3 - - + +
225C ILE 3.2 0.4 - - - -
226C GLU* 1.3 77.4 - - - +
228C TYR* 1.3 80.4 + - + +
230C ALA* 4.0 2.8 - - - +
231C GLU* 3.1 43.9 + - + +
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Residues in contact with TYR 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASP* 3.1 47.5 + - - -
188C ILE* 3.7 33.5 - - + +
189C LYS* 5.2 8.3 - - + +
192C ILE* 3.6 20.6 - - + +
212C ARG* 5.3 2.8 + - - -
220C LEU* 4.1 20.0 - - + -
224C GLU* 3.1 28.5 - - + -
225C ILE* 3.0 10.0 + - - +
227C LYS* 1.3 94.7 - - + +
229C VAL* 1.3 62.2 + - - +
231C GLU* 3.5 20.0 + - - +
232C ILE* 3.1 24.1 + - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE* 4.4 22.2 - - + -
202C GLY 6.0 0.7 - - - -
203C GLY* 3.4 29.8 - - - +
225C ILE* 3.1 21.0 + - + +
226C GLU* 3.7 27.4 - - - +
227C LYS 3.2 0.4 - - - -
228C TYR* 1.3 75.4 - - - +
230C ALA* 1.3 58.8 + - - +
232C ILE* 3.3 5.7 + - - +
233C GLU* 3.0 43.8 + - - +
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C GLU* 3.2 21.8 + - + +
227C LYS* 4.2 2.2 - - - +
229C VAL* 1.3 80.0 - - - +
231C GLU* 1.3 56.7 + - - +
233C GLU* 4.2 10.3 - - - +
234C LYS* 3.1 57.1 + - - +
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASP* 4.1 14.7 - - - +
227C LYS* 3.1 34.5 + - + +
228C TYR* 3.6 33.2 - - - +
230C ALA* 1.3 76.1 - - - +
232C ILE* 1.3 54.7 + - - +
234C LYS* 5.2 2.0 - - - +
235C GLU* 3.7 27.1 - - - +
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Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LYS* 5.2 15.0 - - + +
192C ILE* 6.2 4.7 - - + -
193C LYS* 6.1 5.6 - - + +
228C TYR 3.1 14.5 + - - +
229C VAL* 3.8 4.3 - - - +
231C GLU* 1.3 74.3 - - - +
233C GLU* 1.3 61.2 + - - +
234C LYS 3.5 1.8 - - - -
235C GLU* 3.3 12.3 + - - +
236C LYS* 3.1 37.0 + - + +
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Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C GLU* 5.1 2.8 - - - +
229C VAL* 3.0 32.6 + - - +
230C ALA* 3.5 9.3 + - - +
232C ILE* 1.3 73.0 - - - +
234C LYS* 1.3 66.3 + - + +
235C GLU 3.5 0.2 + - - -
236C LYS* 3.6 16.0 + - - +
237C GLU* 3.6 13.6 - - - +
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA* 3.1 43.6 + - - +
231C GLU* 5.2 2.0 - - - +
233C GLU* 1.3 81.5 - - + +
235C GLU* 1.3 60.9 + - - +
237C GLU* 3.5 33.7 - - - +
238C GLU* 4.5 4.9 - - - +
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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