Contacts of the helix formed by residues 194 - 213 (chain C) in PDB entry 1ZKK
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 SER 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C LYS* 1.3 75.5 - - - +
195C LYS* 1.3 63.3 + - - +
196C ALA* 3.4 10.5 + - - +
197C GLU* 2.8 39.0 + - - +
198C LEU* 3.1 24.3 + - - +
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Residues in contact with LYS 195 (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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194C SER* 1.3 74.7 - - - +
196C ALA* 1.3 57.3 + - - +
198C LEU* 3.3 12.0 + - + +
199C GLN* 2.8 58.1 + - + +
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Residues in contact with ALA 196 (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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194C SER* 3.2 9.7 + - - +
195C LYS* 1.3 78.9 - - - +
197C GLU* 1.3 57.6 + - + +
199C GLN* 3.4 13.2 + - - +
200C SER* 3.0 31.4 + - - -
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Residues in contact with GLU 197 (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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193C LYS* 3.2 17.8 - - + +
194C SER* 2.8 43.9 + - - +
196C ALA* 1.3 78.8 - - + +
198C LEU* 1.3 57.1 + - - +
200C SER* 3.0 9.5 + - - +
201C GLU* 2.9 47.4 + - - +
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LYS* 4.1 35.7 - - + +
194C SER 3.1 25.8 + - - +
195C LYS* 3.3 8.7 + - + +
197C GLU* 1.3 76.7 - - - +
199C GLN* 1.3 58.3 + - + +
201C GLU* 3.9 7.3 - - - +
202C GLU* 3.0 29.5 + - - +
205C ARG* 4.9 1.7 + - - -
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Residues in contact with GLN 199 (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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195C LYS* 2.8 60.0 + - + +
196C ALA* 3.7 9.5 - - - +
198C LEU* 1.3 75.5 - - + +
200C SER* 1.3 57.4 + - - +
202C GLU* 3.3 6.5 + - - +
203C ARG* 2.8 30.4 + - - +
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Residues in contact with SER 200 (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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196C ALA 3.0 14.9 + - - -
197C GLU* 3.0 18.9 + - - -
199C GLN* 1.3 76.3 - - - +
201C GLU* 1.3 58.7 + - - +
203C ARG* 3.4 9.3 + - - +
204C LYS* 3.0 52.2 + - - +
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Residues in contact with GLU 201 (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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193C LYS* 2.7 42.1 + - - +
197C GLU* 2.9 32.4 + - - +
198C LEU* 3.9 6.2 - - - +
200C SER* 1.3 79.7 - - - +
202C GLU* 1.3 61.8 + - - +
204C LYS* 3.5 9.0 + - - +
205C ARG* 3.1 44.9 + - - +
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Residues in contact with GLU 202 (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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198C LEU 3.0 18.3 + - - +
199C GLN* 3.5 7.0 - - - +
201C GLU* 1.3 74.5 - - - +
203C ARG* 1.3 66.2 + - - +
205C ARG* 3.0 35.1 + - - +
206C ILE* 3.1 44.7 + - + +
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Residues in contact with ARG 203 (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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199C GLN 2.8 20.1 + - - +
200C SER* 3.7 9.0 - - - +
202C GLU* 1.3 74.6 - - - +
204C LYS* 1.3 62.0 + - + +
206C ILE* 3.3 2.4 + - - +
207C ASP* 2.8 53.5 + - - +
310C HIS* 4.3 14.5 + - + +
311C ASP* 5.5 9.9 + - - +
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Residues in contact with LYS 204 (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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200C SER* 3.0 39.1 + - - +
201C GLU* 3.8 9.1 - - + +
203C ARG* 1.3 78.6 - - + +
205C ARG* 1.3 66.2 + - + +
207C ASP* 3.6 8.6 - - - +
208C GLU* 2.9 47.6 + - - +
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Residues in contact with ARG 205 (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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198C LEU 4.9 1.2 + - - -
201C GLU* 3.1 35.8 + - - +
202C GLU* 3.0 42.2 + - - +
204C LYS* 1.3 77.4 - - + +
206C ILE* 1.3 60.1 + - + +
208C GLU* 3.3 9.5 + - - +
209C LEU* 2.9 39.4 + - + +
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Residues in contact with ILE 206 (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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202C GLU* 3.1 37.7 + - + +
205C ARG* 1.3 73.5 - - + +
207C ASP* 1.3 67.8 + - - +
209C LEU* 3.2 10.6 + - + +
210C ILE* 3.0 30.6 + - + +
241C PHE* 4.2 30.1 - - + +
310C HIS* 3.5 41.1 - - + +
319C ILE* 3.9 14.8 - - + -
321C ILE* 6.3 1.1 - - + -
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Residues in contact with ASP 207 (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 ARG* 2.8 42.3 + - - +
204C LYS* 3.6 10.8 - - - +
206C ILE* 1.3 71.7 - - - +
208C GLU* 1.3 60.0 + - + +
210C ILE* 3.4 2.3 + - - +
211C GLU* 2.9 43.2 + - - +
310C HIS* 2.8 30.9 + - - -
311C ASP 4.5 1.4 - - - +
312C ILE* 3.5 35.4 - - + +
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Residues in contact with GLU 208 (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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204C LYS* 2.9 39.6 + - - +
205C ARG* 3.9 8.0 - - - +
207C ASP* 1.3 76.9 - - + +
209C LEU* 1.3 60.9 + - - +
211C GLU* 4.2 11.2 - - - +
212C SER* 2.8 34.7 + - - -
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Residues in contact with LEU 209 (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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205C ARG* 2.9 25.2 + - + +
206C ILE* 3.7 13.2 - - + +
208C GLU* 1.3 75.0 - - - +
210C ILE* 1.3 62.8 + - - +
212C SER* 3.3 5.1 + - - +
213C GLY* 3.3 19.2 + - - -
214C LYS* 4.5 19.4 + - - +
241C PHE* 3.8 53.9 - - + -
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Residues in contact with ILE 210 (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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206C ILE* 3.0 19.0 + - + +
207C ASP 3.5 6.3 - - - +
209C LEU* 1.3 77.8 - - - +
211C GLU* 1.3 65.6 + - + +
213C GLY* 3.3 13.0 + - - -
241C PHE* 4.1 10.3 - - + -
244C GLU* 3.4 28.5 - - + +
246C HIS* 5.7 0.3 - - - -
292C ARG* 4.9 4.5 + - - -
310C HIS* 3.5 33.0 - - + -
312C ILE* 4.0 13.2 - - + -
317C HIS* 3.7 27.8 - - + +
319C ILE* 3.7 31.2 - - + -
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Residues in contact with GLU 211 (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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207C ASP* 2.9 31.2 + - - +
208C GLU* 4.2 11.3 - - + +
210C ILE* 1.3 76.9 - - + +
212C SER* 1.3 61.8 + - - +
213C GLY 3.6 0.2 + - - -
292C ARG* 5.5 2.4 + - - -
312C ILE* 3.9 30.8 - - + +
317C HIS* 6.4 0.4 - - + -
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Residues in contact with SER 212 (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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208C GLU 2.8 21.5 + - - -
209C LEU* 3.3 8.1 + - - -
211C GLU* 1.3 77.8 - - - +
213C GLY* 1.3 66.3 + - - +
214C LYS* 3.2 35.7 + - - +
292C ARG* 5.4 0.2 - - - -
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Residues in contact with GLY 213 (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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209C LEU 3.3 10.1 + - - -
210C ILE 3.3 9.6 + - - -
212C SER* 1.3 80.5 + - - +
214C LYS* 1.3 62.4 + - - +
215C GLU* 3.3 14.8 - - - +
292C ARG* 3.8 32.9 + - - -
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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