Contacts of the helix formed by residues 181 - 194 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C GLY 3.4 3.0 - - - -
180C ALA* 1.3 85.0 - - - +
182C PRO* 1.3 76.6 - - - +
183C ILE 3.1 2.9 - - - -
184C GLY 3.0 2.4 + - - +
185C MET* 2.9 16.4 + - - +
208C ARG* 3.3 11.2 - - - -
249C CYS 5.6 0.2 + - - -
343C LEU* 4.6 0.9 - - - -
400C NAD 3.3 26.8 + - - -
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Residues in contact with PRO 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C CYS* 6.0 2.7 - - + -
156C PRO* 5.7 3.8 - - + -
181C GLY* 1.3 82.0 - - - +
183C ILE* 1.3 58.3 + - + +
185C MET* 3.3 9.3 + - + +
186C VAL* 3.0 34.7 + - + +
208C ARG* 4.4 4.3 - - - +
320C LEU* 5.0 4.9 - - + +
337C PHE* 6.3 2.7 - - + -
343C LEU* 4.3 37.4 - - + +
344C LYS* 4.7 20.2 - - + +
400C NAD 3.2 36.6 - - - +
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Residues in contact with ILE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PRO* 4.5 17.5 - - + +
159C VAL* 4.1 24.0 - - + -
182C PRO* 1.3 76.2 - - + +
184C GLY* 1.3 65.9 + - - +
186C VAL* 3.1 5.4 - - + +
187C THR* 2.8 31.4 + - - +
249C CYS* 3.9 12.6 - - + -
272C VAL* 3.7 29.4 - - + -
400C NAD 3.1 64.8 + - + +
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Residues in contact with GLY 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 3.5 19.9 - - - +
179C GLY 3.3 22.4 - - - -
181C GLY 3.0 6.6 + - - +
183C ILE* 1.3 78.8 - - - +
185C MET* 1.3 63.8 + - - +
187C THR 3.5 0.5 + - - -
188C LEU* 3.0 24.9 + - - +
249C CYS* 3.9 12.2 - - - +
400C NAD 4.1 0.8 + - - -
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Residues in contact with MET 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ALA* 3.5 30.5 - - + +
181C GLY 2.9 17.6 + - - +
182C PRO* 3.5 9.4 - - + +
184C GLY* 1.3 81.1 - - - +
186C VAL* 1.3 61.2 + - - +
188C LEU* 3.2 13.3 + - + +
189C LEU* 3.0 31.8 + - - +
201C VAL* 4.1 7.2 - - + -
208C ARG 4.5 2.0 - - - +
211C LYS* 4.6 4.5 - - - -
212C ALA* 3.4 47.1 - - + -
215C ILE* 3.8 13.0 - - + +
320C LEU* 3.8 17.5 - - + -
343C LEU* 4.4 14.4 - - + -
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LEU 5.4 0.4 - - - +
156C PRO* 3.4 26.9 - - + +
157C LEU* 3.9 32.5 - - + +
160C GLY 4.1 9.0 - - - +
182C PRO* 3.0 15.4 + - + +
183C ILE* 3.1 23.1 - - + +
185C MET* 1.3 72.2 - - - +
187C THR* 1.3 61.4 + - - +
189C LEU* 3.2 9.4 + - + +
190C VAL* 2.9 36.1 + - - +
317C VAL* 5.2 0.7 - - + -
320C LEU* 3.5 29.2 - - + -
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Residues in contact with THR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C GLY* 3.8 20.1 - - - +
163C ALA* 4.6 2.0 - - + +
164C CYS* 3.7 5.4 - - - -
177C VAL* 4.0 11.0 - - + -
183C ILE* 2.8 24.7 + - - +
184C GLY* 3.5 8.7 - - - -
185C MET 3.2 0.2 - - - -
186C VAL* 1.3 77.4 - - - +
188C LEU* 1.3 56.9 + - - +
190C VAL* 3.3 2.9 + - - +
191C ALA* 2.8 29.7 + - + +
247C ILE* 3.3 47.0 - - + +
249C CYS* 3.8 9.8 - - - -
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 4.5 2.9 - - + +
184C GLY 3.0 14.5 + - - +
185C MET* 3.2 20.4 - - + +
187C THR* 1.3 77.1 - - - +
189C LEU* 1.3 64.3 + - - +
191C ALA* 3.3 5.1 + - - +
192C LYS* 3.1 37.9 + - + +
199C VAL* 3.4 37.2 - - + -
201C VAL* 4.3 5.6 - - + -
212C ALA* 3.6 23.3 - - + +
215C ILE* 3.7 22.2 - - + +
216C GLY 4.4 1.3 - - - -
217C ALA* 3.7 26.7 - - + +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU* 5.1 1.1 - - + -
185C MET 3.0 19.0 + - - +
186C VAL* 3.2 13.4 + - - +
188C LEU* 1.3 76.7 - - - +
190C VAL* 1.3 60.0 + - + +
192C LYS* 3.5 5.7 + - - +
193C ALA* 3.0 28.1 + - - +
215C ILE* 3.5 45.3 - - + +
315C VAL* 3.9 18.4 - - + +
316C ASN 3.7 24.5 - - - +
317C VAL* 3.9 23.3 - - + -
320C LEU* 4.4 9.9 - - + -
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU* 3.7 24.0 - - + +
160C GLY 3.8 5.2 - - - +
161C ILE* 3.8 25.8 - - + +
164C CYS* 3.8 20.9 - - + -
186C VAL 2.9 21.0 + - - +
187C THR 3.7 3.6 - - - +
189C LEU* 1.3 73.7 - - - +
191C ALA* 1.3 61.1 + - - +
193C ALA* 3.0 7.2 + - - +
194C MET* 2.8 41.7 + - - +
315C VAL* 5.8 0.9 - - + -
171D LEU* 3.7 23.6 - - + -
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C CYS* 3.8 13.4 - - - -
169C VAL* 4.2 12.0 - - + +
175C VAL* 4.6 11.4 - - + -
177C VAL* 5.5 0.2 - - + -
187C THR* 2.8 22.1 + - + +
188C LEU* 3.6 6.1 - - - +
190C VAL* 1.3 71.5 - - - +
192C LYS* 1.3 63.4 + - - +
194C MET* 3.2 9.4 + - - +
195C GLY 3.3 0.3 + - - -
196C ALA* 3.0 29.3 + - + +
199C VAL* 3.9 20.0 - - + -
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Residues in contact with LYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 3.1 30.2 + - + +
189C LEU* 3.8 5.8 - - + +
191C ALA* 1.3 75.4 - - - +
193C ALA* 1.3 64.0 + - - +
195C GLY* 3.0 14.7 + - - -
196C ALA 3.1 30.2 + - - +
197C ALA 3.5 9.3 + - - -
199C VAL* 4.1 8.3 - - + -
215C ILE 5.6 1.1 - - - +
216C GLY* 3.6 26.7 - - - +
218C ASP* 3.1 27.8 + - - +
193D ALA 4.7 0.5 - - - +
312D SER* 5.6 1.4 + - - -
314D SER* 4.8 5.1 + - - -
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU 3.0 18.3 + - - +
190C VAL* 3.0 8.3 + - - +
192C LYS* 1.3 76.8 - - - +
194C MET* 1.3 60.1 + - - +
195C GLY 3.2 1.1 + - - -
309C MET* 5.2 4.7 - - + -
314C SER* 4.6 16.4 - - - +
315C VAL* 5.1 8.1 - - + -
171D LEU* 3.8 18.2 - - + -
192D LYS 4.7 0.9 - - - +
193D ALA 3.7 2.6 - - - +
195D GLY* 3.1 27.9 + - - -
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Residues in contact with MET 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ILE 5.3 1.6 - - - +
164C CYS* 3.5 37.2 - - - +
165C ARG* 4.9 12.1 - - + -
169C VAL* 3.3 34.3 - - + +
170C THR* 3.8 2.9 - - - -
171C LEU 3.6 17.5 + - - -
190C VAL* 2.8 28.3 + - + +
191C ALA 3.7 5.6 - - - +
192C LYS 3.1 0.6 - - - -
193C ALA* 1.3 77.3 - - - +
195C GLY* 1.3 58.3 + - - +
196C ALA 3.6 0.2 - - - -
170D THR* 3.7 23.8 - - - +
171D LEU* 4.0 20.0 - - + -
193D ALA 3.6 3.4 - - - -
194D MET* 3.7 19.7 - - - +
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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
------------------------------------------------------------
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