Contacts of the helix formed by residues 190 - 204 (chain D) in PDB entry 3E5X
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 HIS 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C ASN 5.6 4.0 + - - -
188D GLY 3.9 9.8 + - - -
189D VAL* 1.3 82.6 - - - +
191D HIS* 1.3 68.0 + - - +
192D VAL* 3.3 14.4 - - + -
193D THR* 3.1 15.9 + - - +
194D VAL* 3.1 10.0 + - - +
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Residues in contact with HIS 191 (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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180D GLN* 4.4 5.5 - - + +
181D LYS* 6.3 3.4 - - - -
184D GLY* 6.0 1.1 - - - -
189D VAL 3.7 1.2 + - - -
190D HIS* 1.3 74.9 - - - +
192D VAL* 1.3 75.0 + - + +
194D VAL* 3.2 10.4 + - - +
195D SER* 2.8 38.8 + - - +
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Residues in contact with VAL 192 (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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190D HIS* 4.6 11.9 - - + +
191D HIS* 1.3 91.9 + - + +
193D THR* 1.3 69.6 + - - +
195D SER* 3.3 6.9 + - - -
196D ARG* 3.0 40.0 + - + +
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Residues in contact with THR 193 (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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149D PRO* 4.4 7.8 - - + +
150D THR* 3.7 23.6 - - + -
153D ILE* 4.3 2.0 - - + -
189D VAL* 3.6 25.9 - - + +
190D HIS* 3.1 7.4 + - - +
192D VAL* 1.3 83.3 - - - +
194D VAL* 1.3 67.1 + - - +
196D ARG* 3.4 30.4 + - - +
197D VAL* 3.0 26.7 + - + +
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Residues in contact with VAL 194 (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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153D ILE* 4.0 10.3 - - + -
180D GLN* 3.8 37.9 - - + +
183D ILE* 4.0 19.1 - - + -
184D GLY* 4.1 17.9 - - - +
189D VAL* 3.8 22.4 - - + +
190D HIS 3.1 14.4 + - - +
191D HIS* 3.2 9.4 + - - +
193D THR* 1.3 78.4 - - - +
195D SER* 1.3 62.7 + - - +
197D VAL* 4.0 1.0 - - - +
198D LEU* 3.1 31.7 + - + +
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Residues in contact with SER 195 (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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180D GLN* 2.8 28.1 + - - +
191D HIS* 2.8 29.7 + - - +
192D VAL* 3.6 8.1 - - - -
194D VAL* 1.3 73.3 - - - +
196D ARG* 1.3 56.7 + - - +
198D LEU* 3.4 1.9 + - - +
199D ALA* 2.9 30.1 + - - +
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Residues in contact with ARG 196 (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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150D THR* 4.6 8.9 - - - +
192D VAL* 3.0 34.2 + - + +
193D THR* 3.4 40.1 + - - +
195D SER* 1.3 72.9 - - - +
197D VAL* 1.3 66.0 + - + +
199D ALA* 3.3 6.6 + - - +
200D CYS* 2.8 43.3 + - - -
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Residues in contact with VAL 197 (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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150D THR* 3.5 39.3 - - + +
153D ILE* 4.0 27.4 - - + -
154D LEU* 4.3 14.4 - - + -
193D THR* 3.0 22.6 + - + +
194D VAL 4.0 3.1 - - - +
196D ARG* 1.3 80.0 - - + +
198D LEU* 1.4 58.5 + - - +
200D CYS* 3.1 7.4 + - - +
201D LEU* 2.9 45.9 + - + +
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Residues in contact with LEU 198 (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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153D ILE* 5.4 1.3 - - + -
157D PHE* 3.3 36.1 - - + -
180D GLN* 3.4 41.3 - - + +
183D ILE* 4.1 5.6 - - + -
194D VAL* 3.1 25.5 + - + +
195D SER 3.9 3.6 - - - +
197D VAL* 1.4 72.6 - - + +
199D ALA* 1.3 63.9 + - - +
201D LEU* 3.5 4.3 + - + +
202D LYS* 3.0 25.5 + - - +
207D LEU* 4.2 10.4 - - + +
209D LYS* 3.8 33.9 - - + -
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Residues in contact with ALA 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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195D SER 2.9 18.4 + - - +
196D ARG* 3.6 8.7 - - + +
198D LEU* 1.3 77.7 - - - +
200D CYS* 1.3 57.4 + - - +
202D LYS* 3.4 6.5 + - - +
203D ARG* 2.9 46.6 + - - +
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Residues in contact with CYS 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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196D ARG* 2.8 38.0 + - - -
197D VAL* 3.1 7.7 + - - +
199D ALA* 1.3 70.1 - - - +
201D LEU* 1.3 68.8 + - + +
203D ARG* 3.0 21.6 + - - +
204D GLU* 2.9 43.8 + - - +
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Residues in contact with LEU 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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154D LEU* 3.4 29.8 - - + -
157D PHE* 3.7 34.8 - - + -
197D VAL* 2.9 25.7 + - + +
198D LEU* 3.9 6.7 - - + +
200D CYS* 1.3 78.1 - - + +
202D LYS* 1.3 60.0 + - - +
204D GLU* 3.7 0.8 + - - +
205D ASN 3.4 1.6 + - - -
206D ILE* 2.9 63.0 + - + +
207D LEU* 3.2 28.4 + - + +
222D LEU* 4.3 3.4 - - + -
225D LEU* 4.5 5.2 - - + -
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Residues in contact with LYS 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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198D LEU 3.0 18.1 + - - +
199D ALA* 3.7 5.8 - - - +
201D LEU* 1.3 73.4 - - - +
203D ARG* 1.3 68.5 + - - +
205D ASN* 3.0 22.4 + - - +
207D LEU 3.3 12.3 + - - +
208D ASP* 3.5 34.8 + - + +
217D TYR* 6.4 0.4 - - - -
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Residues in contact with ARG 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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199D ALA* 2.9 31.2 + - - +
200D CYS* 3.0 33.1 + - - +
202D LYS* 1.3 77.7 - - - +
204D GLU* 1.3 64.5 + - + +
205D ASN* 3.4 11.3 + - - +
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Residues in contact with GLU 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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200D CYS* 2.9 27.2 + - - +
201D LEU* 5.1 0.3 - - - +
203D ARG* 1.3 82.5 - - + +
205D ASN* 1.3 69.2 + - - +
206D ILE* 3.3 34.4 + - + +
221D GLU* 5.7 0.2 - - - +
225D LEU* 4.5 10.0 - - - +
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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