Contacts of the helix formed by residues 183 - 201 (chain D) in PDB entry 3JCK
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 ASP 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D LYS* 3.3 23.4 + - - +
178D GLY 3.5 6.5 + - - +
181D TYR* 3.4 5.4 - - + +
182D ASN* 1.3 76.0 - - - +
184D GLN* 1.3 65.6 + - - +
185D LEU* 3.3 17.5 + - - +
186D TYR* 3.1 26.6 + - + +
187D VAL* 3.2 26.1 + - - +
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Residues in contact with GLN 184 (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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178D GLY 5.3 1.0 + - - -
179D PHE* 4.9 7.7 - - - +
182D ASN* 3.9 23.3 + - - +
183D ASP* 1.3 74.5 + - - +
185D LEU* 1.3 62.2 + - - +
187D VAL* 3.4 9.9 - - - +
188D LYS* 2.9 25.1 + - - +
217D HIS* 2.7 42.1 + - + -
220D ALA* 3.3 34.0 - - + +
221D VAL* 5.0 2.0 - - + -
321D TYR* 4.5 11.7 - - - -
59I ILE* 3.8 23.3 - - + -
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ASP* 3.3 8.0 + - - +
184D GLN* 1.3 74.1 - - - +
186D TYR* 1.3 59.6 + - - +
187D VAL 3.0 1.3 - - - -
188D LYS* 2.5 35.8 + - + +
189D GLU* 2.9 24.3 + - + +
59I ILE* 3.9 30.7 - - + -
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Residues in contact with TYR 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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147D LYS* 3.4 42.0 + - + +
151D GLU* 4.1 26.7 - - - +
174D ILE* 3.6 22.8 + - - +
177D LEU* 4.4 5.4 - - + +
178D GLY* 3.4 35.7 - - - -
183D ASP* 3.1 28.5 + - - +
185D LEU* 1.3 76.7 - - - +
187D VAL* 1.3 59.8 + - - +
189D GLU* 4.3 7.6 + - - -
190D LYS* 3.0 72.1 + - + +
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Residues in contact with VAL 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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175D ALA* 4.1 12.3 - - + +
178D GLY* 3.5 28.9 - - - -
179D PHE* 3.5 33.2 - - + +
183D ASP 3.2 17.2 + - - +
184D GLN* 3.4 12.6 - - - +
185D LEU 3.0 0.2 - - - -
186D TYR* 1.3 76.7 - - - +
188D LYS* 1.3 67.3 + - - +
190D LYS* 2.7 15.1 + - - +
191D LEU* 2.9 34.7 + - + +
217D HIS* 4.1 9.0 - - + +
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Residues in contact with LYS 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D GLN 2.9 15.7 + - - +
185D LEU* 2.5 26.9 + - + +
187D VAL* 1.3 72.5 - - - +
189D GLU* 1.3 65.8 + - + +
191D LEU* 3.3 6.1 + - + +
192D GLU* 2.7 58.2 + - - +
214D TYR* 5.8 7.4 - - + -
217D HIS* 4.3 19.7 - - + +
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Residues in contact with GLU 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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185D LEU* 2.9 23.8 + - + +
186D TYR* 4.5 5.7 - - - +
188D LYS* 1.3 76.5 - - + +
190D LYS* 1.3 76.9 + - + +
192D GLU* 3.0 14.1 - - - +
193D ALA* 3.0 22.3 + - - +
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Residues in contact with LYS 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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151D GLU* 4.8 9.8 + - - -
171D MET* 5.2 4.7 - - + +
174D ILE* 3.7 26.9 - - + -
175D ALA* 3.9 19.1 - - + +
186D TYR* 3.0 62.9 + - + +
187D VAL 2.7 14.4 + - - +
189D GLU* 1.3 83.8 + - + +
191D LEU* 1.3 59.6 + - - +
192D GLU 3.0 1.6 - - - -
193D ALA* 2.9 12.7 + - + +
194D VAL* 2.8 33.0 + - + +
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Residues in contact with LEU 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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172D LEU* 4.8 7.6 - - + -
175D ALA* 4.8 11.0 - - + -
179D PHE* 4.5 0.9 - - + -
187D VAL* 2.9 36.2 + - + +
188D LYS* 3.9 9.2 - - + +
190D LYS* 1.3 76.6 - - - +
192D GLU* 1.3 60.9 + - - +
194D VAL* 4.5 3.1 - - + +
195D ASN* 2.9 27.9 + - - +
210D TYR* 4.0 26.4 + - + +
213D TYR* 4.1 25.8 - - + -
214D TYR* 3.8 38.8 - - + +
217D HIS* 4.3 10.1 - - + -
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Residues in contact with GLU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LYS* 2.7 52.3 + - - +
189D GLU* 3.0 14.6 - - - +
190D LYS 3.0 0.4 - - - -
191D LEU* 1.3 78.3 - - - +
193D ALA* 1.3 64.4 + - - +
195D ASN* 3.0 20.3 + - - +
196D SER* 2.9 21.7 + - - -
214D TYR* 5.7 3.6 - - - -
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Residues in contact with ALA 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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171D MET* 3.9 22.4 - - + -
189D GLU 3.0 9.3 + - - +
190D LYS* 2.9 17.0 + - + +
192D GLU* 1.3 73.9 - - - +
194D VAL* 1.3 59.1 + - - +
196D SER* 2.2 38.7 + - - -
197D MET* 3.0 7.6 + - - +
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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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168D ILE* 4.0 19.5 - - + -
171D MET* 3.4 38.4 - - + +
172D LEU* 3.5 34.3 - - + +
175D ALA* 6.0 0.7 - - + -
190D LYS 2.8 22.5 + - - +
191D LEU* 4.3 8.3 - - + +
193D ALA* 1.3 71.7 - - - +
195D ASN* 1.3 63.0 + - - +
197D MET* 3.1 3.0 + - - -
198D ILE* 2.9 28.0 + - + +
210D TYR* 4.0 15.5 - - + -
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Residues in contact with ASN 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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191D LEU 2.9 23.4 + - - +
192D GLU* 3.0 26.5 + - - +
194D VAL* 1.3 77.3 - - - +
196D SER* 1.3 54.4 + - - +
198D ILE* 3.3 3.4 + - - +
199D GLU* 2.8 62.7 + - - +
210D TYR* 3.2 27.8 + - - +
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Residues in contact with SER 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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171D MET* 5.8 0.2 - - - +
192D GLU 2.9 9.2 + - - -
193D ALA* 2.2 36.7 + - - -
195D ASN* 1.3 72.2 - - - +
197D MET* 1.3 69.6 + - - +
199D GLU* 2.9 25.6 + - - +
200D LYS* 3.0 15.8 + - - +
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Residues in contact with MET 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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158D LEU* 4.9 5.6 - - + -
167D LYS* 3.6 42.2 - - + +
168D ILE* 3.7 18.7 - - + +
171D MET* 3.6 31.6 - - + -
193D ALA 3.0 11.6 + - - +
194D VAL* 3.1 8.5 + - - +
196D SER* 1.3 86.7 + - - +
198D ILE* 1.3 50.9 + - - +
200D LYS* 3.1 51.6 - - - +
201D GLY 2.7 21.4 - - - +
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Residues in contact with ILE 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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168D ILE* 4.1 27.4 - - + -
194D VAL* 2.9 29.8 + - + +
195D ASN* 3.6 6.3 - - - +
197D MET* 1.3 73.3 - - - +
199D GLU* 1.3 60.1 + - + +
200D LYS 3.0 2.5 - - - -
201D GLY* 2.7 34.9 + - - +
202D GLY* 4.9 0.9 - - - -
203D ASP 4.7 2.2 - - - +
206D ARG* 4.5 11.7 - - + -
207D ARG* 3.1 57.2 + - + +
210D TYR* 4.9 16.6 - - + -
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Residues in contact with GLU 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 ASN* 2.8 56.7 + - - +
196D SER* 2.9 14.1 + - - +
198D ILE* 1.3 78.6 - - + +
200D LYS* 1.3 60.0 + - - +
207D ARG* 5.4 2.2 + - - +
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Residues in contact with LYS 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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167D LYS* 3.7 18.2 - - - +
196D SER 3.0 11.7 + - - +
197D MET* 3.1 58.6 - - - +
199D GLU* 1.3 79.7 - - - +
201D GLY* 1.3 56.2 + - - +
207D ARG* 5.5 0.2 - - - -
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Residues in contact with GLY 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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167D LYS* 5.9 2.0 - - - -
168D ILE* 4.3 1.8 - - - +
197D MET 2.7 18.3 - - - +
198D ILE* 2.7 26.8 + - - +
200D LYS* 1.3 80.8 - - - +
202D GLY* 1.3 61.5 + - - -
207D ARG* 4.4 7.4 - - - -
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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