Contacts of the helix formed by residues 174 - 185 (chain D) in PDB entry 2IBS
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 PHE 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D TYR* 3.7 22.7 - + - -
141D ASN* 3.7 26.7 - - + -
143D TYR* 3.3 34.1 - + - -
144D GLY* 4.2 5.8 - - - -
167D THR* 3.7 9.0 - - - -
168D TRP* 3.6 35.4 - - + +
171D LEU* 3.2 21.6 + - + +
172D GLU 3.0 0.8 - - - -
173D ASP* 1.3 90.6 - - + +
175D ALA* 1.3 57.0 + - - +
176D LEU 3.3 2.0 - - - -
177D LEU* 3.3 28.1 + - + -
178D ARG* 2.9 32.9 + - - +
4E C 5.1 2.2 - - - -
5E G 4.4 7.4 - - - -
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Residues in contact with ALA 175 (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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137D LYS* 3.8 13.9 - - + +
171D LEU 3.8 0.6 + - - -
172D GLU* 3.1 27.1 + - - +
174D PHE* 1.3 78.3 - - - +
176D LEU* 1.3 63.5 + - + +
178D ARG* 3.5 24.1 + - - +
179D GLU* 3.2 38.3 + - - +
240D GLY 4.6 0.7 - - - +
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Residues in contact with LEU 176 (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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134D SER 3.6 19.5 - - - +
135D THR* 3.6 27.8 - - + +
136D TRP 4.3 4.5 - - - +
137D LYS* 4.2 25.9 - - + +
173D ASP 5.0 0.4 + - - -
174D PHE* 3.3 0.4 - - - +
175D ALA* 1.3 74.5 - - + +
177D LEU* 1.3 60.3 + - - +
179D GLU* 3.6 18.7 + - - +
180D PHE* 3.0 29.8 + - - +
183D ARG* 5.0 1.7 + - - -
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Residues in contact with LEU 177 (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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135D THR* 3.8 17.6 + - + +
140D TYR* 3.6 22.0 - - - +
143D TYR* 5.1 0.4 - - + -
144D GLY* 3.8 16.4 - - - +
147D LEU* 3.8 34.1 - - + -
148D GLU* 4.4 6.3 - - + +
168D TRP* 4.3 16.4 - - + -
174D PHE* 3.3 36.7 + - + +
176D LEU* 1.3 76.1 - - - +
178D ARG* 1.3 58.6 + - - +
180D PHE* 3.4 4.6 + - + +
181D LEU* 3.0 47.2 + - + +
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Residues in contact with ARG 178 (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 TRP* 2.9 45.6 + - + +
169D LEU* 3.7 19.4 + - - +
170D VAL 3.7 5.7 + - - -
171D LEU 2.9 25.0 + - - -
172D GLU* 4.9 1.2 - - - +
174D PHE 2.9 16.3 + - - +
175D ALA* 3.6 27.6 - - - +
177D LEU* 1.3 74.9 - - - +
179D GLU* 1.3 57.4 + - - +
181D LEU* 3.4 3.6 + - - -
182D ALA* 3.1 24.6 + - - +
238D TRP* 3.4 22.2 - - + -
240D GLY* 3.1 26.9 + - - +
241D GLU 3.6 17.7 + - - -
242D ILE* 3.8 19.0 - - - +
243D ILE* 4.6 1.8 - - - -
398D ARG* 4.7 6.9 - - - +
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Residues in contact with GLU 179 (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* 3.2 24.6 + - - +
176D LEU* 4.0 21.3 - - - +
178D ARG* 1.3 73.7 - - - +
180D PHE* 1.3 64.0 + - - +
182D ALA* 3.4 2.9 + - - +
183D ARG* 3.2 47.2 + - - +
239D GLU 3.4 25.2 - - - +
240D GLY* 4.0 8.7 - - - +
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Residues in contact with PHE 180 (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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134D SER* 4.4 3.4 - - - -
135D THR* 3.6 16.6 - - + -
148D GLU* 3.7 28.3 - - + -
151D VAL* 3.7 32.5 - - + -
152D ARG* 3.5 37.0 - - + -
176D LEU 3.0 20.0 + - - +
177D LEU* 3.4 8.3 - - + +
179D GLU* 1.3 76.3 - - - +
181D LEU* 1.3 71.5 + - + +
183D ARG* 3.2 21.8 + - - +
184D GLU* 3.1 54.1 + - + +
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Residues in contact with LEU 181 (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 LEU* 5.2 7.2 - - + +
151D VAL* 3.9 27.4 - - + -
168D TRP* 3.7 32.8 - - + -
177D LEU* 3.0 37.3 + - + +
178D ARG* 3.8 4.5 - - - +
180D PHE* 1.3 79.1 - - + +
182D ALA* 1.3 60.5 + - - +
184D GLU* 4.6 0.7 - - - -
185D GLY 3.3 11.8 + - - +
187D THR* 3.9 13.3 + - - +
206D ILE* 3.8 21.8 - - + -
208D PHE* 3.3 36.1 - - + -
238D TRP* 4.2 5.6 - - + -
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Residues in contact with ALA 182 (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 ARG 3.1 17.6 + - - +
179D GLU 3.6 4.0 - - - +
180D PHE 3.2 0.2 - - - -
181D LEU* 1.3 78.5 - - - +
183D ARG* 1.3 57.7 + - - +
184D GLU 3.5 0.2 - - - -
185D GLY 3.6 12.1 + - - +
213D LYS* 4.8 10.2 - - - +
214D GLY 4.9 1.3 + - - +
238D TRP* 3.5 39.9 - - + +
239D GLU* 3.6 7.4 - - - -
240D GLY 3.6 15.9 - - - +
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Residues in contact with ARG 183 (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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176D LEU 5.0 1.0 + - - -
179D GLU* 3.2 35.5 + - - +
180D PHE* 3.4 39.3 - - - +
182D ALA* 1.3 75.9 - - + +
184D GLU* 1.3 76.0 + - + +
185D GLY 3.6 0.4 - - - -
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Residues in contact with GLU 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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151D VAL* 4.1 6.8 - - + +
180D PHE* 3.1 57.3 + - + +
181D LEU* 4.6 0.4 - - - -
182D ALA 3.5 0.2 - - - -
183D ARG* 1.3 93.7 - - + +
185D GLY* 1.3 57.3 + - - +
208D PHE* 3.6 17.0 - - + -
210D LYS* 3.7 45.1 + - + +
211D SER* 4.9 0.3 - - - -
212D GLY 4.9 0.4 - - - -
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Residues in contact with GLY 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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181D LEU 3.3 13.2 + - - +
182D ALA* 3.6 12.1 - - - +
183D ARG 3.6 1.6 - - - -
184D GLU* 1.3 80.9 - - - +
186D LYS* 1.3 60.9 + - - -
187D THR 4.3 0.3 + - - -
208D PHE* 3.5 6.0 - - - -
209D GLN 3.3 12.1 - - - -
211D SER 3.9 5.4 - - - -
212D GLY 3.5 18.5 + - - -
213D LYS* 3.6 8.3 - - - -
214D GLY 4.2 1.6 + - - +
238D TRP* 5.9 0.2 - - - -
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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