Contacts of the helix formed by residues 181 - 194 (chain D) in PDB entry 1PL8
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 GLY 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D GLY 3.5 3.2 - - - -
180D ALA* 1.3 85.2 - - - +
182D PRO* 1.3 75.2 - - - +
183D ILE 3.0 3.7 + - - -
184D GLY 3.1 1.3 + - - +
185D MET* 2.9 17.4 + - - +
208D ARG* 3.3 10.5 - - - -
249D CYS 5.6 0.4 + - - -
343D LEU* 4.3 1.1 - - - -
400D NAD 3.3 26.9 + - - -
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Residues in contact with PRO 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D CYS* 5.9 3.1 - - + -
156D PRO* 5.7 3.8 - - + -
181D GLY* 1.3 81.5 - - - +
183D ILE* 1.3 59.4 + - + +
185D MET* 3.6 8.0 - - + +
186D VAL* 3.0 34.9 + - + +
208D ARG* 4.5 3.8 - - - +
320D LEU* 5.0 5.7 - - + +
337D PHE* 6.3 2.9 - - + -
343D LEU* 4.0 40.6 - - + +
344D LYS* 4.6 20.4 - - + +
400D NAD 3.3 32.3 - - - +
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Residues in contact with ILE 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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156D PRO* 4.5 16.4 - - + +
159D VAL* 4.0 22.9 - - + -
182D PRO* 1.3 77.4 - - + +
184D GLY* 1.3 65.1 + - - +
186D VAL* 3.1 4.9 - - + +
187D THR* 2.8 31.3 + - - +
249D CYS* 3.9 12.8 - - + -
272D VAL* 3.8 27.6 - - + -
400D NAD 3.0 65.0 + - + +
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Residues in contact with GLY 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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177D VAL* 3.6 15.8 - - - +
179D GLY 3.3 22.4 - - - -
181D GLY 3.1 5.8 + - - +
183D ILE* 1.3 79.0 - - - +
185D MET* 1.3 64.0 + - - +
187D THR* 3.3 2.4 + - - -
188D LEU* 2.9 28.8 + - - +
249D CYS* 3.9 11.5 - - - +
400D NAD 4.2 0.8 + - - -
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Residues in contact with MET 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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180D ALA* 3.5 32.1 - - + +
181D GLY 2.9 20.2 + - - +
182D PRO* 3.6 5.6 - - + +
183D ILE 3.1 0.2 - - - -
184D GLY* 1.3 79.8 - - - +
186D VAL* 1.3 65.1 + - - +
188D LEU* 3.2 11.3 + - + +
189D LEU* 3.0 26.9 + - - +
201D VAL* 3.9 9.0 - - + -
208D ARG 4.5 1.6 - - - +
211D LYS* 4.6 4.3 - - - -
212D ALA* 3.5 44.4 - - + -
215D ILE* 3.7 13.8 - - + +
320D LEU* 3.9 17.7 - - + -
343D LEU* 4.2 15.3 - - + -
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Residues in contact with VAL 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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153D LEU 5.5 0.2 - - - +
156D PRO* 3.3 26.9 - - + +
157D LEU* 3.9 35.4 - - + +
160D GLY 4.1 9.6 - - - +
182D PRO* 3.0 18.0 + - + +
183D ILE* 3.1 22.7 - - + +
185D MET* 1.3 72.5 - - - +
187D THR* 1.3 60.5 + - - +
189D LEU* 3.2 10.0 + - + +
190D VAL* 2.9 35.0 + - - +
317D VAL* 5.4 0.4 - - + -
320D LEU* 3.6 24.9 - - + -
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Residues in contact with THR 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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159D VAL* 5.1 0.3 + - - +
160D GLY* 3.8 20.5 - - - +
163D ALA* 4.7 1.9 - - - +
164D CYS* 3.8 4.5 - - - -
177D VAL* 3.9 12.3 - - + -
183D ILE* 2.8 23.9 + - - +
184D GLY* 3.4 8.7 - - - -
186D VAL* 1.3 77.2 - - - +
188D LEU* 1.3 55.9 + - - +
190D VAL* 3.3 2.5 + - - +
191D ALA* 2.8 29.9 + - - +
247D ILE* 3.2 48.7 - - + +
249D CYS* 3.8 9.6 - - - -
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Residues in contact with LEU 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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177D VAL* 4.5 2.0 - - + +
184D GLY 2.9 14.1 + - - +
185D MET* 3.3 13.9 - - + +
187D THR* 1.3 78.5 - - - +
189D LEU* 1.3 64.8 + - - +
191D ALA* 3.3 1.3 + - - +
192D LYS* 3.1 37.5 + - + +
199D VAL* 3.4 36.6 - - + -
201D VAL* 4.2 7.2 - - + -
212D ALA* 3.5 30.1 - - - +
215D ILE* 3.7 23.3 - - + +
216D GLY 4.3 1.3 - - - -
217D ALA* 3.6 29.6 - - + +
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Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 4.9 2.7 - - + -
185D MET 3.0 18.1 + - - +
186D VAL* 3.2 10.1 + - - +
188D LEU* 1.3 77.5 - - - +
190D VAL* 1.3 60.7 + - - +
192D LYS* 3.6 4.5 + - - +
193D ALA* 3.1 24.1 + - - +
215D ILE* 3.6 43.7 - - + +
315D VAL* 3.7 20.1 - - + +
316D ASN 3.8 25.1 - - - +
317D VAL* 4.1 21.5 - - + -
320D LEU* 4.3 16.4 - - + -
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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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171C LEU* 3.8 22.7 - - + -
157D LEU* 3.6 24.0 - - + +
160D GLY 3.8 6.5 - - - +
161D ILE* 3.8 26.9 - - + +
164D CYS* 3.6 26.0 - - + -
186D VAL 2.9 19.7 + - - +
187D THR 3.7 3.6 - - - +
189D LEU* 1.3 73.9 - - - +
191D ALA* 1.3 66.0 + - - +
193D ALA* 3.1 7.4 + - - +
194D MET* 2.9 26.7 + - - +
315D VAL* 5.7 0.9 - - + -
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Residues in contact with ALA 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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164D CYS* 3.8 13.9 - - - -
169D VAL* 4.2 13.3 - - + +
175D VAL* 4.6 11.7 - - + -
187D THR* 2.8 22.6 + - + +
188D LEU* 3.7 4.9 - - - +
190D VAL* 1.3 73.1 - - - +
192D LYS* 1.3 63.4 + - - +
194D MET* 3.2 9.9 + - - +
195D GLY 3.4 0.5 + - - -
196D ALA* 3.1 27.4 + - + +
199D VAL* 3.9 19.3 - - + -
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Residues in contact with LYS 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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193C ALA 4.7 0.7 - - - +
314C SER* 5.1 3.4 + - - -
188D LEU* 3.1 24.5 + - + +
189D LEU* 3.9 5.4 - - - +
191D ALA* 1.3 75.7 - - - +
193D ALA* 1.3 63.2 + - - +
195D GLY* 3.0 14.6 + - - -
196D ALA 3.1 30.3 + - - +
197D ALA 3.4 9.5 + - - -
199D VAL* 4.0 16.8 - - + -
215D ILE 5.7 1.1 - - - +
216D GLY* 3.5 26.0 - - - +
218D ASP* 2.9 29.3 + - - +
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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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171C LEU* 3.8 17.5 - - + -
192C LYS 4.7 0.9 - - - +
193C ALA 3.7 2.6 - - - +
195C GLY* 3.0 29.7 + - - -
189D LEU 3.1 18.8 + - - +
190D VAL* 3.1 6.9 + - - +
192D LYS* 1.3 75.7 - - - +
194D MET* 1.3 57.8 + - - +
195D GLY 3.2 1.2 + - - -
309D MET* 4.9 4.5 - - - -
314D SER* 4.3 18.8 - - - +
315D VAL* 4.9 6.7 - - + -
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Residues in contact with MET 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C THR* 3.6 23.8 - - - +
171C LEU* 4.0 25.8 - - + -
193C ALA 3.6 3.1 - - - -
194C MET* 3.7 19.5 - - - +
161D ILE* 5.3 1.6 - - - +
164D CYS* 3.5 37.7 - - - +
165D ARG* 4.9 13.5 - - + +
169D VAL* 3.3 34.1 - - + +
170D THR* 3.8 3.5 + - - -
171D LEU 3.6 15.9 + - - -
190D VAL* 2.9 22.1 + - - +
191D ALA 3.6 6.3 - - - +
192D LYS 3.1 0.6 - - - -
193D ALA* 1.3 76.4 - - - +
195D GLY* 1.3 58.7 + - - +
196D ALA 3.7 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