Contacts of the helix formed by residues 182 - 192 (chain D) in PDB entry 1USK
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D ILE* 3.7 39.0 - - + -
179D GLU* 3.2 35.0 - - + -
180D LYS 4.4 0.4 - - - -
181D ASP* 1.3 75.0 - - - +
183D SER* 1.3 59.0 + - - +
184D ALA 3.2 3.1 - - - -
185D LEU* 3.1 26.8 + - + +
186D ILE* 2.9 37.2 + - + +
205D GLU* 3.9 20.9 - - + -
208D GLN* 3.7 19.7 - - + -
209D MET* 3.9 26.9 - - + -
212D GLN* 3.0 28.9 + - - +
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Residues in contact with SER 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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181D ASP* 2.7 29.1 + - - -
182D PHE* 1.3 78.0 - - - +
184D ALA* 1.3 58.8 + - - +
186D ILE* 4.0 7.3 - - - +
187D ALA* 3.1 27.4 + - - +
212D GLN* 3.7 5.8 + - - -
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Residues in contact with ALA 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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181D ASP* 5.1 2.1 + - - +
182D PHE 3.2 1.0 - - - -
183D SER* 1.3 80.5 + - - +
185D LEU* 1.3 63.2 + - - +
187D ALA* 3.5 6.2 + - - +
188D ARG* 3.2 22.0 + - - +
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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
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144D ILE* 3.7 39.5 - - + -
171D PHE* 4.3 15.0 - - + -
173D ASP* 5.2 7.0 - - - +
175D ILE* 4.6 10.3 - - + -
182D PHE* 3.1 28.9 + - + +
184D ALA* 1.3 76.2 - - - +
186D ILE* 1.3 61.4 + - + +
188D ARG* 3.2 9.9 + - + +
189D LEU* 3.0 42.0 + - + +
209D MET* 3.9 32.8 - - + -
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Residues in contact with ILE 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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182D PHE* 2.9 27.6 + - + +
183D SER* 4.0 7.4 - - - +
185D LEU* 1.3 75.7 - - + +
187D ALA* 1.3 63.6 + - - +
189D LEU* 3.2 15.7 + - + +
190D LYS* 3.1 21.9 + - + +
209D MET* 3.9 17.3 - - + +
212D GLN* 4.4 11.0 - - + +
213D ALA* 3.5 36.8 - - + +
216D VAL* 3.4 36.3 - - + -
218D LEU* 3.9 13.5 - - + +
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Residues in contact with ALA 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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183D SER 3.1 20.1 + - - +
184D ALA* 3.7 8.1 - - - +
185D LEU 3.2 0.4 - - - -
186D ILE* 1.3 76.1 - - - +
188D ARG* 1.3 57.3 + - - +
190D LYS* 3.3 8.7 + - - +
191D LYS* 3.0 53.6 + - - +
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Residues in contact with ARG 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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171D PHE* 3.4 56.9 - - + +
172D PHE 5.3 1.0 + - - -
173D ASP* 4.2 19.4 + - - +
184D ALA 3.2 11.2 + - - +
185D LEU* 3.2 15.3 + - - +
187D ALA* 1.3 78.2 - - - +
189D LEU* 1.3 59.4 + - - +
191D LYS* 4.5 6.7 - - + +
192D GLU* 3.0 59.6 + - + +
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Residues in contact with LEU 189 (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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142D ALA* 4.0 1.6 - - + -
144D ILE* 5.9 1.1 - - + -
171D PHE* 3.9 16.6 - - + -
185D LEU* 3.0 33.8 + - + +
186D ILE* 3.2 18.6 + - + +
188D ARG* 1.3 76.3 - - - +
190D LYS* 1.3 60.2 + - - +
193D ASN* 3.2 2.3 + - - -
194D ILE* 3.1 54.1 + - + +
197D VAL* 3.6 33.4 - - + -
209D MET* 5.6 0.2 - - - -
218D LEU* 3.9 29.0 - - + +
220D THR* 4.8 2.5 - - + +
222D PHE* 4.6 9.9 - - + -
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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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186D ILE* 3.1 12.7 + - + +
187D ALA* 3.5 11.9 - - - +
189D LEU* 1.3 76.0 - - - +
191D LYS* 1.3 67.6 + - + +
193D ASN* 3.3 15.2 + - - +
216D VAL* 3.1 38.8 + - + +
217D GLY 4.7 7.5 + - - -
218D LEU* 4.1 17.3 - - + +
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Residues in contact with LYS 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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187D ALA* 3.0 42.3 + - + +
188D ARG* 4.1 7.0 - - + +
190D LYS* 1.3 79.0 - - - +
192D GLU* 1.3 61.8 + - + +
193D ASN* 3.3 6.8 + - - +
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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
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140D ARG* 2.9 33.1 + - - +
170D VAL* 3.3 23.2 - - - +
171D PHE* 4.6 2.7 - - + -
188D ARG* 3.0 52.2 + - + +
189D LEU 4.0 0.2 - - - -
191D LYS* 1.3 79.0 - - + +
193D ASN* 1.3 63.9 + - - +
194D ILE* 3.3 17.9 + - + +
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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