Contacts of the helix formed by residues 198 - 212 (chain D) in PDB entry 1ZUM
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 PRO 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.2 6.7 - - + -
39D THR* 3.7 5.4 - - - +
51D VAL* 4.1 26.2 - - + -
109D ASP* 3.3 11.2 - - - +
193D VAL* 3.8 21.9 - - + +
194D ALA 3.3 11.7 - - - +
195D GLU* 3.3 14.8 - - - +
196D GLN 3.6 0.9 - - - -
197D THR* 1.3 90.5 - - - +
199D LEU* 1.3 63.6 + - + +
200D THR 3.7 0.4 - - - -
201D ALA* 3.6 5.9 + - - +
202D LEU* 3.2 28.6 + - + +
222D PRO* 4.3 13.9 - - + -
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Residues in contact with LEU 199 (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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17D VAL* 3.7 27.1 - - + -
19D CYS 3.9 10.4 - - - +
20D ASN* 4.9 0.7 - - + -
39D THR* 4.0 12.3 - - + -
48D ILE* 3.9 26.7 - - + -
49D CYS* 3.8 11.2 - - - -
51D VAL* 4.4 11.0 - - + -
105D LEU* 3.8 34.3 - - + +
109D ASP* 3.5 26.2 + - + +
197D THR 3.5 1.2 - - - -
198D PRO* 1.3 77.1 - - - +
200D THR* 1.3 63.8 + - - +
202D LEU* 3.1 8.5 + - + +
203D TYR* 3.1 20.1 + - - +
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Residues in contact with THR 200 (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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102D LEU* 3.8 17.3 - - + +
105D LEU* 3.7 19.5 - - + +
106D GLU* 2.7 53.2 + - + +
109D ASP* 5.2 1.9 + - + +
171D PRO* 3.7 13.9 - - - +
172D LEU* 3.6 17.2 - - + +
197D THR* 4.8 1.9 + - - -
199D LEU* 1.3 77.6 - - - +
201D ALA* 1.3 58.2 + - - +
203D TYR* 3.3 3.3 + - - +
204D VAL* 3.0 32.1 + - - +
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Residues in contact with ALA 201 (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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166D ILE* 5.1 1.3 - - + -
171D PRO* 5.2 4.5 - - + +
172D LEU* 4.9 0.2 - - - -
175D GLN* 3.2 39.1 - - + +
193D VAL* 3.4 33.0 - - + -
197D THR 5.2 2.4 + - - +
198D PRO 3.6 6.0 + - - +
199D LEU 3.3 0.8 - - - -
200D THR* 1.3 81.9 + - - +
202D LEU* 1.3 57.5 + - - +
204D VAL 3.4 0.5 + - - -
205D ALA 3.1 20.4 + - - -
220D ILE* 3.4 8.8 - - + +
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Residues in contact with LEU 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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19D CYS* 3.9 15.3 - - + +
20D ASN* 3.9 27.4 - - - -
21D GLN 3.3 23.3 - - - +
28D TRP* 3.0 35.6 - - + -
51D VAL* 4.2 14.1 - - + -
193D VAL* 5.1 0.4 - - + -
198D PRO* 3.2 24.2 + - + +
199D LEU* 3.1 9.3 + - + +
201D ALA* 1.3 75.5 - - - +
203D TYR* 1.3 65.9 + - - +
205D ALA* 3.2 8.1 - - - +
206D ASN 3.4 0.2 + - - -
220D ILE* 3.9 28.9 - - + +
222D PRO* 4.4 7.9 - - + -
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Residues in contact with TYR 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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18D PHE* 4.3 16.7 - + + -
19D CYS* 4.0 20.6 - - + +
97D ARG* 4.5 2.4 + - - -
98D ASP* 2.7 33.7 + - + -
101D TYR* 3.8 42.0 - + + -
102D LEU* 3.8 20.6 - - + -
105D LEU* 4.7 4.9 - - + -
199D LEU 3.1 12.2 + - - +
200D THR* 3.3 9.6 + - - +
202D LEU* 1.3 75.8 - - - +
204D VAL* 1.3 59.6 + - - +
206D ASN* 2.9 37.7 + - + +
207D LEU* 3.2 24.6 + - + +
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Residues in contact with VAL 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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91D LEU* 4.5 6.5 - - + -
95D ILE* 4.4 24.2 - - + -
102D LEU* 4.5 14.1 - - + -
172D LEU* 3.4 25.1 - - + -
175D GLN* 3.3 26.9 - - - +
179D LEU* 5.1 1.6 - - + -
200D THR 3.0 19.2 + - - +
201D ALA 3.6 2.7 - - - +
203D TYR* 1.3 75.3 - - - +
205D ALA* 1.3 57.5 + - - +
207D LEU* 2.8 10.8 + - - +
208D ILE* 2.8 39.9 + - + +
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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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23D PHE* 3.2 46.8 - - + -
28D TRP* 3.8 3.1 - - + -
201D ALA 3.1 12.9 + - - +
202D LEU* 3.2 14.1 - - - +
204D VAL* 1.3 74.9 - - - +
206D ASN* 1.3 62.1 + - - +
208D ILE* 3.1 15.0 + - - +
209D LYS 3.1 17.0 + - - -
218D VAL* 5.9 0.2 - - + -
220D ILE* 4.0 12.3 - - + -
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Residues in contact with ASN 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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18D PHE* 5.3 3.8 - - - +
19D CYS* 3.5 26.6 - - - -
23D PHE* 4.6 3.5 - - - -
28D TRP* 2.9 24.9 + - - +
202D LEU 3.4 1.6 + - - -
203D TYR* 2.9 26.6 + - + +
205D ALA* 1.3 80.7 - - - +
207D LEU* 1.3 56.8 + - + +
209D LYS* 3.3 12.8 + - - +
210D GLU* 3.0 26.0 + - - +
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Residues in contact with LEU 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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91D LEU* 3.8 13.6 - - + +
94D LEU* 3.4 14.5 - - + +
95D ILE* 3.8 39.0 - - + +
97D ARG* 3.5 28.0 - - - +
98D ASP* 3.7 6.5 - - - +
102D LEU* 4.3 5.2 - - + -
203D TYR* 3.8 35.0 - - + +
204D VAL* 2.8 10.4 + - - +
206D ASN* 1.3 77.1 - - + +
208D ILE* 1.3 56.1 + - - +
210D GLU* 3.6 11.9 - - - +
211D ALA* 2.8 35.7 + - - +
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Residues in contact with ILE 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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23D PHE* 4.9 6.3 - - + -
26D ASN* 5.1 3.1 - - - +
91D LEU* 3.8 24.5 - - + -
175D GLN* 4.9 2.5 - - - +
179D LEU* 3.7 30.3 - - + -
183D LEU* 5.6 0.7 - - + -
204D VAL* 2.8 22.9 + - + +
205D ALA* 3.3 16.4 - - - +
207D LEU* 1.3 77.9 - - - +
209D LYS* 1.3 62.4 + - - +
212D GLY 3.4 2.6 + - - -
213D PHE* 3.4 49.6 + - + -
218D VAL* 3.8 33.9 - - + +
220D ILE* 5.4 0.2 - - + -
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Residues in contact with LYS 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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23D PHE* 4.1 7.8 - - + -
26D ASN* 3.3 57.1 + - + +
27D GLU* 5.5 1.8 - - - +
28D TRP* 6.0 3.7 - - - +
205D ALA 3.1 11.0 + - - +
206D ASN* 3.5 15.3 - - - +
208D ILE* 1.3 75.8 - - - +
210D GLU* 1.3 65.3 + - - +
212D GLY* 3.1 14.9 + - - -
213D PHE 4.9 0.7 - - - -
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Residues in contact with GLU 210 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D ARG* 4.6 12.0 + - - +
94D LEU* 3.4 15.4 - - + +
97D ARG* 2.7 44.7 + - - -
206D ASN 3.0 16.6 + - - +
207D LEU* 3.6 13.6 - - - +
209D LYS* 1.3 77.2 - - - +
211D ALA* 1.3 62.3 + - - +
212D GLY* 3.3 1.6 + - - -
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Residues in contact with ALA 211 (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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87D LEU* 3.6 17.4 - - - +
90D ARG* 3.7 27.9 + - + +
91D LEU* 4.0 14.6 - - + +
94D LEU* 3.5 11.8 - - + +
207D LEU 2.8 21.0 + - - +
208D ILE 3.6 6.7 - - - +
209D LYS 3.2 0.2 - - - -
210D GLU* 1.3 72.7 - - - +
212D GLY* 1.3 57.8 + - - +
213D PHE* 4.0 15.0 - - + -
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Residues in contact with GLY 212 (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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79D MET* 5.7 0.3 - - - +
87D LEU* 4.2 11.8 - - - +
208D ILE 3.4 0.4 + - - -
209D LYS 3.1 13.1 + - - -
210D GLU 3.2 1.3 - - - -
211D ALA* 1.3 80.1 - - - +
213D PHE* 1.3 67.4 + - - +
214D PRO* 3.4 7.3 - - - +
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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