Contacts of the helix formed by residues 184 - 205 (chain D) in PDB entry 1IB1
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 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D TYR* 2.8 20.7 + - - +
179D TYR* 3.9 0.8 + - - -
182D LEU* 3.2 23.6 + - - +
183D ASN* 1.3 76.1 + - - +
185D PRO* 1.3 60.1 - - - +
186D GLU* 3.2 18.4 - - - -
187D LYS* 3.4 20.6 + - - +
188D ALA* 2.9 29.0 + - - +
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Residues in contact with PRO 185 (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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179D TYR* 3.7 37.6 - - + +
183D ASN* 3.5 9.6 - - - +
184D SER* 1.3 86.1 - - - +
186D GLU* 1.3 67.0 + - - +
188D ALA* 3.1 1.4 + - - +
189D CYS* 2.8 39.4 + - - -
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Residues in contact with GLU 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 SER* 3.2 30.7 - - - -
185D PRO* 1.3 87.6 - - - +
187D LYS* 1.3 73.5 + - + +
189D CYS* 3.3 5.7 + - - +
190D SER* 3.0 31.2 + - - -
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Residues in contact with LYS 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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146D GLN* 5.5 1.0 + - - -
178D TYR* 4.1 34.8 - - + -
182D LEU* 5.5 3.0 - - - +
184D SER* 3.9 17.8 + - - +
186D GLU* 1.3 97.0 + - + +
188D ALA* 1.3 62.6 + - - +
190D SER* 3.2 9.6 + - - -
191D LEU* 3.0 27.0 + - - +
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Residues in contact with ALA 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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175D SER* 3.2 48.1 - - - +
178D TYR* 3.8 6.2 - - - +
179D TYR* 3.6 25.8 - - + +
184D SER 2.9 18.9 + - - +
185D PRO 3.3 5.4 - - - +
187D LYS* 1.3 78.1 - - - +
189D CYS* 1.3 61.8 + - - +
192D ALA* 3.2 10.6 + - - +
228D TRP* 4.2 5.4 - - + -
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Residues in contact with CYS 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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179D TYR* 5.3 0.4 - - - -
185D PRO* 2.8 27.2 + - - +
186D GLU* 3.7 4.9 - - - +
188D ALA* 1.3 70.2 - - - +
190D SER* 1.3 59.5 + - - +
192D ALA* 3.9 0.7 - - - +
193D LYS* 2.8 35.2 + - + +
225D LEU* 3.9 17.7 - - + +
228D TRP* 3.8 39.0 - - - -
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Residues in contact with SER 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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186D GLU 3.0 16.3 + - - -
187D LYS* 3.2 12.7 + - - -
189D CYS* 1.3 76.4 - - - +
191D LEU* 1.3 56.1 + - - +
193D LYS* 4.7 3.1 - - - -
194D THR* 2.8 42.7 + - - -
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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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153D PHE* 3.6 37.4 - - + -
171D ALA* 3.7 26.2 - - + +
174D PHE* 4.2 14.1 - - + -
175D SER* 3.7 19.3 - - - +
178D TYR* 4.0 22.4 - - + -
187D LYS 3.0 11.1 + - - +
188D ALA* 3.5 9.6 - - - +
190D SER* 1.3 76.0 - - - +
192D ALA* 1.3 62.6 + - - +
194D THR* 3.9 3.6 - - - -
195D ALA* 3.1 25.3 + - + +
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Residues in contact with ALA 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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171D ALA 5.2 0.2 - - - -
175D SER* 4.0 10.9 - - - +
188D ALA 3.2 13.4 + - - +
189D CYS 3.9 3.4 - - - +
191D LEU* 1.3 80.1 - - - +
193D LYS* 1.3 62.4 + - - +
195D ALA* 3.4 3.8 + - - +
196D PHE* 3.0 24.3 + - - +
221D LEU* 3.8 31.6 - - + +
224D ASN* 5.7 0.7 - - + -
225D LEU* 3.9 20.6 - - + -
228D TRP* 4.7 5.6 - - + -
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Residues in contact with LYS 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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189D CYS* 2.8 22.7 + - + +
190D SER* 4.0 3.4 - - - +
192D ALA* 1.3 70.8 - - - +
194D THR* 1.3 61.4 + - - +
196D PHE* 3.3 1.6 + - - +
197D ASP* 2.8 63.0 + - - +
225D LEU* 3.9 19.9 - - + +
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Residues in contact with THR 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 PHE* 6.4 2.0 - - + -
190D SER* 2.8 29.6 + - - -
191D LEU* 3.9 4.3 - - - -
193D LYS* 1.3 72.5 - - - +
195D ALA* 1.3 58.7 + - - +
197D ASP* 3.3 5.4 + - - +
198D GLU* 2.8 61.6 + - + +
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Residues in contact with ALA 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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153D PHE* 6.3 1.6 - - + -
162D PRO* 4.6 1.0 - - - +
168D LEU* 4.0 16.0 - - + +
171D ALA* 3.5 28.3 - - + -
191D LEU* 3.1 18.1 + - + +
192D ALA 3.6 3.8 - - - +
194D THR* 1.3 79.8 - - - +
196D PHE* 1.3 61.4 + - - +
198D GLU* 4.0 9.8 - - - +
199D ALA* 3.1 24.4 + - - +
221D LEU* 4.4 3.4 - - + -
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Residues in contact with PHE 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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192D ALA 3.0 17.3 + - - +
193D LYS* 3.7 6.1 - - + +
195D ALA* 1.3 75.1 - - - +
197D ASP* 1.3 72.4 + - - +
199D ALA* 3.2 4.4 + - - +
200D ILE* 2.9 57.5 + - + +
218D MET* 3.5 52.2 - - + +
221D LEU* 4.4 10.7 - - + +
222D ARG* 3.7 54.1 - - + -
225D LEU* 4.9 7.0 - - + -
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Residues in contact with ASP 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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193D LYS* 2.8 60.3 + - - +
194D THR* 3.8 4.9 - - - +
196D PHE* 1.3 86.6 - - - +
198D GLU* 1.3 58.0 + - + +
200D ILE* 3.2 7.8 + - - +
201D ALA* 2.8 29.9 + - - +
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Residues in contact with GLU 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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162D PRO* 3.6 24.4 - - + +
167D ARG* 3.2 26.5 + - - -
194D THR* 2.8 46.1 + - + +
195D ALA* 4.0 7.2 - - - +
197D ASP* 1.3 73.2 - - + +
199D ALA* 1.3 61.8 + - - +
201D ALA* 3.3 9.0 + - - +
202D GLU* 3.1 19.1 + - - +
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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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162D PRO* 3.8 14.3 - - - +
163D THR* 3.3 29.1 - - + +
168D LEU* 4.3 6.3 - - + -
195D ALA 3.1 18.6 + - - +
196D PHE* 3.5 4.7 - - - +
198D GLU* 1.3 76.8 - - - +
200D ILE* 1.3 61.8 + - - +
202D GLU 3.3 1.6 + - - -
203D LEU* 3.1 21.3 + - - +
218D MET* 3.5 23.1 - - + -
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Residues in contact with ILE 200 (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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196D PHE* 2.9 47.2 + - + +
197D ASP* 3.5 9.9 - - - +
199D ALA* 1.3 74.8 - - - +
201D ALA* 1.3 63.5 + - - +
203D LEU* 3.3 14.8 + - + +
204D ASP* 3.0 39.8 + - - +
218D MET* 3.6 17.5 - - + -
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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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197D ASP 2.8 14.1 + - - +
198D GLU* 3.4 14.1 - - - +
200D ILE* 1.3 76.4 - - - +
202D GLU* 1.3 61.9 + - - +
204D ASP* 3.0 27.6 + - - +
205D THR* 3.4 12.6 + - - +
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Residues in contact with GLU 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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161D GLN* 3.4 24.2 + - - +
162D PRO* 3.1 27.1 - - + +
163D THR* 3.1 26.0 + - + -
198D GLU 3.1 9.7 + - - +
199D ALA 3.3 6.7 + - - +
201D ALA* 1.3 77.7 - - - +
203D LEU* 1.3 61.0 + - - +
205D THR* 2.9 27.3 + - - +
206D LEU 4.1 1.4 + - - -
207D SER* 4.2 7.4 + - - +
209D GLU* 4.3 1.7 - - - +
210D SER* 3.1 35.8 + - - +
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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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163D THR* 3.9 7.9 - - + -
199D ALA 3.1 19.3 + - - +
200D ILE* 3.6 18.4 - - + +
202D GLU* 1.3 77.3 - - - +
204D ASP* 1.3 63.2 + - - +
206D LEU* 3.4 13.5 + - - +
210D SER* 3.9 23.6 - - - -
212D LYS* 4.1 34.8 - - + +
218D MET* 4.3 22.0 - - - -
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Residues in contact with ASP 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 ILE* 3.0 39.2 + - - +
201D ALA* 3.0 16.6 + - - +
203D LEU* 1.3 73.3 - - - +
205D THR* 1.3 56.8 + - + +
206D LEU* 3.0 26.4 + - - +
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Residues in contact with THR 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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201D ALA 3.6 14.6 - - - +
202D GLU* 2.9 19.9 + - - +
204D ASP* 1.3 73.8 - - + +
206D LEU* 1.3 74.2 + - - +
207D SER* 3.4 16.7 + - - -
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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