Contacts of the helix formed by residues 201 - 210 (chain D) in PDB entry 3ZKJ
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 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D TYR* 3.8 3.9 - - - -
194D ASN* 3.6 21.9 + - - -
196D GLY* 4.2 0.9 - - - +
199D GLN 3.5 4.6 + - - -
200D ASP* 1.3 73.7 - - - +
202D PRO* 1.3 67.7 - - - +
203D LEU* 3.7 9.7 + - - +
204D HIS* 2.8 60.9 + - - +
205D ALA 3.2 5.2 + - - -
224D ASP 5.0 3.3 + - - -
227D ALA* 4.9 9.9 - - - +
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Residues in contact with PRO 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.7 22.9 - - + -
172D TYR* 4.1 12.8 - - + -
175D CYS* 4.4 7.6 - - - -
193D VAL 3.3 20.2 - - - +
194D ASN 3.6 4.3 - - - +
195D GLN 3.5 17.0 - - - +
196D GLY* 3.4 20.4 - - - +
201D SER* 1.3 87.4 - - - +
203D LEU* 1.3 63.0 + - - +
205D ALA* 3.1 4.4 + - + +
206D VAL* 3.0 26.3 + - - +
218D LEU* 3.4 18.6 - - + -
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Residues in contact with LEU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D VAL 5.1 0.8 + - - -
194D ASN* 6.0 0.2 - - - +
201D SER* 3.2 9.3 + - - +
202D PRO* 1.3 78.1 - - - +
204D HIS* 1.3 62.0 + - - +
206D VAL* 4.4 2.5 - - + -
207D ALA* 3.2 20.4 + - - +
215D ALA* 4.4 17.9 - - + +
218D LEU* 3.2 25.5 - - + +
219D MET* 4.4 3.4 - - + -
223D ALA* 3.7 24.0 - - + -
224D ASP 3.8 16.8 - - - +
225D THR* 4.0 24.5 - - + -
235D PRO* 4.0 15.7 - - + +
249D PHE* 4.1 20.9 - - + -
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Residues in contact with HIS 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D GLN 4.6 1.6 - - - -
200D ASP* 3.0 22.9 + - - +
201D SER* 2.8 42.7 + - - +
203D LEU* 1.3 74.5 - - - +
205D ALA* 1.3 62.7 + - - +
207D ALA* 3.1 14.2 + - - +
208D ARG* 3.3 11.4 + - - -
227D ALA* 3.2 29.5 + - + -
228D LYS 4.2 0.7 - - - -
229D ASN* 3.7 19.2 + - + -
233D LYS 2.8 26.2 + - - -
234D ARG 4.0 0.2 - - - -
235D PRO* 3.4 22.3 - - + -
238D LEU* 3.6 30.4 - - + +
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Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D TYR* 3.6 35.4 - - + +
175D CYS* 4.8 9.2 - - + -
176D GLU* 4.5 17.0 - - + +
201D SER 3.2 1.6 + - - -
202D PRO* 3.1 8.4 + - + +
204D HIS* 1.3 78.3 - - - +
206D VAL* 1.3 62.5 + - - +
208D ARG* 3.2 26.6 + - - +
209D THR* 3.4 14.8 + - - -
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D CYS* 3.7 32.1 - - + +
202D PRO 3.0 17.8 + - - +
203D LEU* 4.0 7.4 - - + +
205D ALA* 1.3 78.3 - - - +
207D ALA* 1.3 60.9 + - - +
209D THR* 3.3 9.0 - - - -
210D ALA 3.1 15.9 + - - -
211D SER* 3.3 15.3 + - - +
214D LEU* 3.8 19.7 - - + -
215D ALA* 3.4 37.7 - - + +
218D LEU* 4.1 7.0 - - + -
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 3.2 13.7 + - - +
204D HIS 3.1 11.4 + - - +
206D VAL* 1.3 76.8 - - - +
208D ARG* 1.3 63.2 + - - +
210D ALA* 3.2 11.9 + - - +
235D PRO 3.7 25.6 - - - +
238D LEU* 3.5 16.6 - - + +
239D VAL* 3.9 18.3 - - + +
240D PRO* 4.6 1.0 - - - +
245D LEU* 4.6 8.5 - - - -
249D PHE* 4.4 8.5 - - + -
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D TYR* 4.2 2.2 + - - -
200D ASP* 2.9 42.2 + - - -
204D HIS 3.3 5.7 + - - +
205D ALA* 3.2 36.4 + - - +
207D ALA* 1.3 76.3 - - - +
209D THR* 1.3 64.8 + - - +
210D ALA* 3.3 3.3 + - - +
229D ASN* 4.0 7.5 - - - +
238D LEU* 3.6 42.7 - - + +
240D PRO* 5.5 3.3 - - - +
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Residues in contact with THR 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 4.9 3.1 + - - -
175D CYS 4.7 4.8 + - - +
176D GLU* 4.6 8.0 + - - -
178D GLN* 3.2 33.7 + - + +
205D ALA 3.4 9.1 + - - -
206D VAL* 3.3 11.7 - - - +
208D ARG* 1.3 75.3 - - - +
210D ALA* 1.3 64.3 + - - +
211D SER* 3.0 35.4 - - - +
214D LEU* 5.4 1.3 - - + -
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 3.6 27.6 + - + +
206D VAL 3.1 7.1 + - - -
207D ALA 3.2 10.4 + - - +
208D ARG 3.2 7.0 - - - +
209D THR* 1.3 78.1 - - - +
211D SER* 1.3 59.1 + - - +
212D GLU* 3.1 13.6 + - - +
240D PRO* 4.7 18.6 - - + -
243D SER* 4.9 10.5 + - - +
245D LEU* 4.3 11.6 - - + +
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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