Contacts of the helix formed by residues 185 - 200 (chain D) in PDB entry 3KHU
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 THR 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D GLN* 5.2 0.9 + - - -
183D ASP* 3.1 19.3 + - + +
184D GLU* 1.3 82.2 - - + +
186D PRO* 1.3 70.4 - - + +
187D GLU* 3.8 5.9 + - - +
188D GLY* 3.1 19.8 + - - -
189D GLN* 2.9 28.7 + - - +
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Residues in contact with PRO 186 (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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184D GLU 4.7 0.9 - - - +
185D THR* 1.3 89.2 - - + +
187D GLU* 1.3 64.2 + - + +
189D GLN* 3.4 6.1 + - + +
190D ARG* 3.1 22.9 + - - +
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Residues in contact with GLU 187 (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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123D TYR* 4.3 14.0 + - - -
153D ASN* 4.0 21.7 + - - +
155D GLN* 3.8 22.7 - - - +
185D THR* 3.3 5.5 + - - +
186D PRO* 1.3 80.1 - - + +
188D GLY* 1.3 65.8 + - - +
190D ARG* 3.2 18.0 + - - +
191D ALA* 3.1 22.2 + - - +
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Residues in contact with GLY 188 (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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155D GLN* 3.9 9.3 + - - -
157D LEU* 4.2 2.4 - - - +
183D ASP* 3.8 22.9 - - - -
185D THR* 3.1 20.3 + - - -
187D GLU* 1.3 76.9 - - - +
189D GLN* 1.3 55.5 + - - +
191D ALA* 3.2 6.8 + - - +
192D VAL* 2.9 32.4 + - - +
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Residues in contact with GLN 189 (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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182D GLY 4.2 6.3 + - - -
183D ASP 2.8 25.6 + - - +
184D GLU* 4.1 10.5 - - - +
185D THR 2.9 20.6 + - - +
186D PRO* 3.9 5.8 - - + +
188D GLY* 1.3 77.0 - - - +
190D ARG* 1.3 58.6 + - - +
192D VAL* 3.7 20.8 - - - +
193D GLN* 3.0 28.8 + - - +
210D THR* 5.3 4.9 + - - -
211D THR 5.2 2.6 + - - -
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Residues in contact with ARG 190 (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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1D MET* 4.1 19.4 - - - +
2D PHE* 3.6 53.5 - - + +
123D TYR* 4.2 27.3 + - - +
186D PRO 3.1 15.9 + - - +
187D GLU* 3.2 18.6 + - - +
189D GLN* 1.3 73.4 - - - +
191D ALA* 1.3 64.9 + - - +
193D GLN* 4.0 4.6 - - - +
194D ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 191 (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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123D TYR* 3.9 13.0 + - - +
125D ILE* 4.0 14.3 - - + +
155D GLN* 3.9 26.2 - - + -
157D LEU* 3.7 22.4 - - + +
187D GLU 3.1 11.5 + - - +
188D GLY* 3.2 9.4 + - - +
190D ARG* 1.3 74.3 - - - +
192D VAL* 1.3 65.6 + - - +
194D ALA* 3.1 4.2 + - - +
195D LEU* 3.1 18.0 + - - +
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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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157D LEU* 3.6 24.5 - - + -
180D ILE* 4.0 13.5 - - + +
181D GLY* 5.1 0.2 - - - -
182D GLY* 3.8 20.2 - - - +
188D GLY 2.9 19.9 + - - +
189D GLN* 3.7 23.3 - - - +
190D ARG 3.4 0.2 - - - -
191D ALA* 1.3 76.7 - - - +
193D GLN* 1.3 57.9 + - - +
195D LEU* 3.2 4.7 + - - +
196D CYS* 2.9 28.3 + - - -
210D THR* 3.7 35.0 - - + -
211D THR 5.2 1.6 - - - +
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Residues in contact with GLN 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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0D SER* 4.6 24.7 - - - +
189D GLN 3.0 17.6 + - - +
190D ARG* 4.1 6.1 - - - +
192D VAL* 1.3 77.7 - - + +
194D ALA* 1.3 59.6 + - - +
196D CYS* 3.3 11.4 + - + +
197D ALA* 2.9 30.5 + - + +
200D GLU* 5.1 2.0 - - - +
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Residues in contact with ALA 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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2D PHE* 3.8 32.3 - - + +
4D ILE* 3.5 18.5 + - + +
125D ILE* 3.8 20.4 - - + -
190D ARG 3.1 15.1 + - - +
191D ALA 3.1 9.2 + - - +
193D GLN* 1.3 77.3 - - - +
195D LEU* 1.3 61.8 + - - +
197D ALA* 3.4 12.7 + - - +
198D VAL* 3.5 9.4 + - - +
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Residues in contact with LEU 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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4D ILE* 4.0 5.8 - - + +
23D ILE* 6.2 0.2 - - + -
84D LEU* 3.9 29.4 - - + -
86D PHE* 4.2 7.4 - - + -
125D ILE* 5.7 0.2 - - + -
127D THR* 4.1 9.0 - - + +
157D LEU* 4.0 21.8 - - + -
159D ASN* 3.9 27.1 - - + +
180D ILE* 3.8 24.0 - - + -
191D ALA 3.1 11.8 + - - +
192D VAL 3.7 7.0 - - - +
194D ALA* 1.3 73.8 - - - +
196D CYS* 1.3 65.5 + - - +
198D VAL* 3.1 22.4 + - + +
199D TYR* 3.3 25.0 + - + -
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Residues in contact with CYS 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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180D ILE* 3.8 10.9 - - - +
192D VAL* 2.9 24.9 + - - -
193D GLN* 3.3 12.3 + - + +
195D LEU* 1.3 77.6 - - - +
197D ALA* 1.3 56.8 + - - +
199D TYR* 3.1 5.4 + - - +
200D GLU* 2.8 42.5 + - - +
205D ARG* 4.4 11.9 - - - +
208D ILE* 3.7 22.3 - - + +
210D THR* 3.6 30.1 - - - -
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Residues in contact with ALA 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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2D PHE 5.6 3.6 - - - +
3D GLU* 6.5 2.2 - - + -
193D GLN* 2.9 15.8 + - + +
194D ALA* 3.6 12.6 - - - +
195D LEU 3.2 0.2 - - - -
196D CYS* 1.3 76.6 - - - +
198D VAL* 1.3 62.2 + - + +
200D GLU* 3.4 21.1 + - - +
201D HIS* 3.0 23.5 + - + -
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Residues in contact with VAL 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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4D ILE* 3.9 31.6 - - + +
7D ILE* 4.6 6.1 - - + -
23D ILE* 3.9 33.9 - - + -
27D CYS* 3.7 7.7 - - - -
30D ILE* 4.2 14.1 - - + -
84D LEU* 5.5 0.2 - - + -
194D ALA 3.5 14.1 + - - +
195D LEU* 3.1 18.9 + - + +
197D ALA* 1.3 77.0 - - + +
199D TYR* 1.3 66.8 + - + +
201D HIS* 3.0 29.6 + - + +
202D TRP* 3.6 7.0 - - + -
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Residues in contact with TYR 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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19D THR* 4.6 15.8 - - + +
23D ILE* 4.8 8.7 - - + +
86D PHE* 4.6 4.7 - + - -
159D ASN* 2.6 33.3 + - - -
172D LEU* 6.1 2.9 - - + -
178D VAL* 3.8 40.6 - - + -
180D ILE* 4.2 5.8 - - + -
195D LEU* 3.3 35.8 + - + -
196D CYS 3.1 6.9 + - - +
198D VAL* 1.3 81.1 - - + +
200D GLU* 1.3 59.6 + - - +
201D HIS 3.0 1.7 + - - -
202D TRP* 3.0 39.1 + + - -
203D VAL* 2.9 29.9 + - + +
208D ILE* 4.0 16.2 - - + -
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Residues in contact with GLU 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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193D GLN* 5.1 2.1 - - - +
196D CYS* 2.8 34.5 + - - +
197D ALA* 3.8 14.3 + - - +
198D VAL 3.2 0.6 - - - -
199D TYR* 1.3 72.3 - - - +
201D HIS* 1.3 60.8 + - - +
202D TRP* 3.1 2.0 + - - -
203D VAL 3.6 13.8 - - - +
205D ARG* 3.7 32.0 + - - +
208D ILE* 3.6 15.7 - - + -
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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