Contacts of the helix formed by residues 179 - 190 (chain D) in PDB entry 1P4L
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 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D ILE* 3.6 5.7 - - - +
178D GLU* 1.3 85.6 - - - +
180D GLU* 1.3 67.2 + - + +
181D ASP* 3.7 18.7 + - - +
182D GLU* 3.2 36.4 + - - +
183D LEU 3.3 8.1 + - - -
217D LYS* 4.1 26.7 + - + +
218D LEU* 3.6 10.5 - - - +
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Residues in contact with GLU 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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179D ASP* 1.3 74.6 - - + +
181D ASP* 1.3 77.7 - - - +
183D LEU* 3.3 6.2 + - + +
184D LYS* 3.1 45.0 + - + +
217D LYS 5.3 1.2 + - - -
218D LEU* 3.5 19.7 - - + +
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Residues in contact with ASP 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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146D TYR* 5.3 3.7 + - + +
179D ASP* 3.2 18.2 - - - +
180D GLU* 1.3 91.8 - - - +
182D GLU* 1.3 62.8 + - - +
184D LYS* 3.2 13.2 + - - +
185D PHE* 3.0 22.9 + - - +
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Residues in contact with GLU 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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146D TYR* 5.2 7.0 - - + -
149D LYS* 2.8 26.5 + - + +
151D TYR* 2.4 39.9 + - + +
175D LEU* 4.2 0.9 - - - +
176D LYS 3.5 5.6 - - - +
177D ILE* 4.2 4.7 - - + -
178D GLU* 2.7 41.5 + - - +
179D ASP* 3.2 17.1 + - - +
181D ASP* 1.3 80.1 - - - +
183D LEU* 1.3 55.9 + - - +
185D PHE* 3.5 9.0 - - + +
186D LEU* 3.0 33.9 + - + +
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Residues in contact with LEU 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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177D ILE* 3.3 38.3 - - + +
179D ASP 3.3 3.6 + - - +
180D GLU* 3.3 11.3 + - - +
181D ASP 3.2 0.6 - - - -
182D GLU* 1.3 75.6 - - - +
184D LYS* 1.3 57.6 + - + +
186D LEU* 3.1 5.7 + - + +
187D GLN* 2.7 49.4 + - - +
218D LEU* 4.5 19.7 - - + -
220D MET* 5.4 0.9 - - + -
235D LEU* 3.5 30.1 - - + -
240D ILE* 4.7 20.6 - - + -
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Residues in contact with LYS 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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180D GLU* 3.1 33.2 + - + +
181D ASP* 3.4 13.0 - - - +
183D LEU* 1.3 79.4 - - + +
185D PHE* 1.3 63.8 + - - +
187D GLN* 3.3 9.6 + - - +
188D ARG* 2.9 65.1 + - - +
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Residues in contact with PHE 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 PHE* 3.4 27.4 - + - -
146D TYR* 3.3 72.9 - + + +
151D TYR* 4.0 13.2 - + - -
153D PHE* 5.4 0.2 - + - -
181D ASP 3.0 12.1 + - - +
182D GLU 3.5 11.4 - - - +
184D LYS* 1.3 76.5 - - - +
186D LEU* 1.3 89.5 + - + +
188D ARG* 3.0 9.0 + - - +
189D HIS* 2.8 50.1 + + + +
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Residues in contact with LEU 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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151D TYR* 4.0 20.6 - - + -
153D PHE* 3.9 30.1 - - + -
175D LEU* 3.3 30.5 - - + -
177D ILE* 4.2 21.1 - - + -
182D GLU* 3.0 19.0 + - + +
183D LEU* 3.4 7.6 - - + +
185D PHE* 1.3 98.2 - - + +
187D GLN* 1.3 57.3 + - - +
189D HIS* 4.5 1.6 - - - +
190D VAL* 3.0 36.6 + - - +
235D LEU* 4.1 17.3 - - + -
252D ILE* 4.7 1.3 - - + -
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Residues in contact with GLN 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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134A THR* 4.4 7.6 + - - +
183D LEU* 2.7 36.4 + - + +
184D LYS* 3.9 9.7 - - - +
186D LEU* 1.3 73.0 - - - +
188D ARG* 1.3 60.5 + - + +
190D VAL* 4.8 1.1 - - - -
235D LEU* 3.2 23.5 - - + +
236D SER 2.9 6.6 + - - +
237D LYS* 3.0 47.4 - - - +
238D ALA* 3.3 8.5 - - - -
239D ARG* 2.8 50.6 + - - +
240D ILE* 4.8 1.2 - - - +
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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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136A ALA 5.9 0.7 - - - -
184D LYS* 2.9 58.8 + - - +
185D PHE* 3.7 6.6 - - - +
187D GLN* 1.3 81.5 - - + +
189D HIS* 1.3 59.5 + - - +
237D LYS* 2.9 25.7 + - - +
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Residues in contact with HIS 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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142D TYR* 5.1 8.5 - + - -
144D PHE* 4.0 35.2 - + + +
153D PHE* 3.3 48.6 - + - -
185D PHE* 2.8 40.0 + + + +
186D LEU* 4.1 2.0 - - - +
188D ARG* 1.3 76.2 - - - +
190D VAL* 1.3 70.0 + - - +
191D ILE* 4.5 4.0 - - - +
237D LYS* 4.5 0.7 + - - -
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Residues in contact with VAL 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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153D PHE* 3.7 25.4 - - + -
186D LEU* 3.0 22.5 + - + +
187D GLN* 4.5 1.3 - - - +
188D ARG 3.6 0.4 - - - -
189D HIS* 1.3 90.7 - - - +
191D ILE* 1.3 69.6 + - - +
193D GLY 4.4 3.1 - - - +
195D TYR* 2.9 37.7 - - + -
235D LEU* 4.2 17.9 - - + -
236D SER 5.2 0.9 - - - -
237D LYS* 3.1 42.8 + - + +
252D ILE* 4.6 1.1 - - + -
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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