Contacts of the helix formed by residues 200 - 212 (chain Z) in PDB entry 5LN3
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 ALA 200 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155Z GLY* 6.3 0.2 - - - -
195Z ASN* 3.0 22.2 + - + +
198Z HIS* 3.2 12.2 - - + +
199Z ASN* 1.4 75.2 - - - +
201Z GLU* 1.4 61.4 + - - +
202Z HIS* 3.4 3.8 - - - +
203Z GLU* 3.3 30.5 + - + +
204Z ALA* 3.2 15.9 + - - +
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Residues in contact with GLU 201 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Z ASN 5.1 0.7 - - - -
196Z MET* 5.9 1.6 - - - +
199Z ASN* 3.1 17.6 - - - +
200Z ALA* 1.4 73.9 - - - +
202Z HIS* 1.3 62.6 + - + +
204Z ALA* 3.3 8.1 + - - +
205Z CYS* 2.9 34.6 + - - +
232Z TYR* 3.2 60.4 + - + +
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Residues in contact with HIS 202 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Z ARG* 5.8 5.8 - - - -
200Z ALA* 3.4 1.3 - - - +
201Z GLU* 1.3 80.4 - - + +
203Z GLU* 1.3 67.8 + - + +
205Z CYS* 3.2 26.8 - - - -
206Z ASP* 2.8 22.1 + - + +
236Z CYS* 4.7 13.9 - - - -
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Residues in contact with GLU 203 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Z GLY* 4.6 11.3 - - - +
156Z HIS 4.2 15.7 - - - +
157Z GLU* 5.2 1.4 - - - -
159Z VAL* 5.8 0.2 - - - -
160Z ARG* 3.6 35.5 + - + +
195Z ASN* 3.6 30.4 + - - +
200Z ALA* 3.3 24.1 + - + +
202Z HIS* 1.3 80.7 - - + +
204Z ALA* 1.3 63.2 + - - +
206Z ASP* 3.1 27.4 - - - +
207Z LEU* 3.3 11.3 + - + +
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Residues in contact with ALA 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Z VAL* 4.2 22.0 - - + +
195Z ASN* 4.2 17.0 - - + +
196Z MET* 4.7 15.5 - - + +
200Z ALA 3.2 11.1 + - - +
201Z GLU* 3.3 11.4 + - - +
203Z GLU* 1.3 78.5 - - - +
205Z CYS* 1.4 55.4 + - - +
207Z LEU* 3.2 9.1 + - - +
208Z LEU* 3.1 32.0 + - + +
229Z VAL* 5.5 4.5 - - + -
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Residues in contact with CYS 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Z GLU 2.9 17.0 + - - +
202Z HIS* 3.2 32.1 - - - -
204Z ALA* 1.4 73.1 - - - +
206Z ASP* 1.4 58.6 + - - +
208Z LEU* 3.3 16.1 - - + +
209Z MET* 3.1 29.1 + - - +
229Z VAL* 5.5 4.0 - - + +
232Z TYR* 4.8 9.2 - - + -
233Z LEU* 3.6 28.1 - - + +
236Z CYS* 3.9 26.7 - - - -
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Residues in contact with ASP 206 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Z ARG* 3.3 35.5 + - - +
202Z HIS* 2.8 25.9 - - + +
203Z GLU* 3.1 24.0 - - - +
205Z CYS* 1.4 78.2 - - - +
207Z LEU* 1.3 74.7 + - - +
209Z MET* 3.0 29.5 + - - +
210Z GLU* 3.1 31.6 + - + +
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Residues in contact with LEU 207 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Z ARG* 4.4 14.1 - - + +
163Z ALA* 4.2 10.5 - - + +
164Z GLY* 3.7 35.2 - - - +
167Z ALA* 5.9 1.1 - - + -
188Z VAL* 5.3 4.3 - - + +
191Z ILE* 3.9 29.6 - - + -
192Z VAL* 4.5 19.5 - - + +
195Z ASN* 4.2 10.3 - - - +
203Z GLU 3.3 9.8 + - - +
204Z ALA* 3.2 10.8 + - - +
206Z ASP* 1.3 86.6 + - - +
208Z LEU* 1.3 55.3 + - - +
210Z GLU* 3.2 12.1 + - + +
211Z ILE* 2.9 32.8 + - - +
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Residues in contact with LEU 208 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Z VAL* 4.1 12.1 - - + -
196Z MET* 4.9 4.3 - - + -
204Z ALA 3.1 14.4 + - - +
205Z CYS* 3.3 13.7 - - - +
206Z ASP 3.3 0.2 - - - -
207Z LEU* 1.3 73.0 - - - +
209Z MET* 1.3 65.8 + - - +
211Z ILE* 3.6 23.7 - - + +
212Z GLU* 4.0 3.1 + - - -
213Z GLN 4.4 5.5 - - - +
216Z MET* 4.7 2.5 - - + -
217Z LEU* 3.9 36.8 - - + +
220Z ASP* 3.5 24.9 - - - +
229Z VAL* 4.3 20.4 - - + -
233Z LEU* 3.7 25.7 - - + +
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Residues in contact with MET 209 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205Z CYS 3.1 16.3 + - - +
206Z ASP* 3.0 21.6 + - - +
208Z LEU* 1.3 78.9 - - - +
210Z GLU* 1.4 60.9 + - + +
212Z GLU* 3.7 13.7 + - - +
233Z LEU* 3.9 15.2 - - + +
236Z CYS* 4.5 23.6 - - - +
237Z VAL* 4.6 15.3 - - + -
240Z VAL* 5.5 3.4 - - + -
241Z PRO* 3.9 34.8 - - + -
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Residues in contact with GLU 210 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Z ARG* 5.3 4.3 + - - +
164Z GLY* 3.5 25.6 - - - -
167Z ALA* 4.9 6.1 - - + -
168Z LYS* 3.6 32.0 - - + +
171Z GLN* 2.7 29.9 + - - +
206Z ASP* 3.1 35.8 + - + +
207Z LEU* 3.6 13.8 - - + +
209Z MET* 1.4 71.8 - - + +
211Z ILE* 1.4 64.0 + - - +
212Z GLU* 3.1 7.0 + - - +
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Residues in contact with ILE 211 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Z ALA* 4.0 26.2 - - + +
170Z TRP* 5.1 3.4 - - + -
171Z GLN* 4.5 2.6 - - - +
180Z GLN* 4.9 2.0 - - - +
185Z LEU* 3.9 24.0 - - + -
188Z VAL* 4.0 16.6 - - + -
207Z LEU 2.9 16.4 + - - +
208Z LEU* 3.6 18.4 - - + +
210Z GLU* 1.4 74.0 - - - +
212Z GLU* 1.4 78.9 - - - +
213Z GLN* 3.2 39.1 + - - +
216Z MET* 3.7 24.2 - - + -
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Residues in contact with GLU 212 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170Z TRP* 4.4 9.2 - - - -
171Z GLN* 3.9 29.4 - - + +
208Z LEU 4.0 1.3 + - - -
209Z MET 3.7 14.1 + - - +
210Z GLU 3.1 11.5 + - - +
211Z ILE* 1.4 92.7 - - - +
213Z GLN* 1.3 79.3 + - - +
214Z VAL* 5.9 0.4 - - - -
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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