Contacts of the helix formed by residues 212 - 221 (chain O) in PDB entry 4WNC
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 212 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124O PRO* 6.6 0.2 - - - -
211O THR* 1.3 73.4 + - - +
213O ALA* 1.3 58.1 + - - +
214O ALA 3.3 2.0 - - - -
215O LYS* 3.2 17.2 + - - +
216O ALA* 2.9 29.9 + - - +
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Residues in contact with ALA 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124O PRO* 6.5 1.1 - - - -
151O SER* 3.7 6.5 - - - +
153O THR* 3.7 33.2 - - + -
154O THR* 3.1 30.3 + - - +
157O LEU* 5.0 1.3 - - + -
175O MET* 4.9 0.7 - - + -
211O THR* 3.1 19.7 + - + +
212O GLY* 1.3 78.6 - - - +
214O ALA* 1.3 62.6 + - - +
216O ALA* 3.3 2.2 + - - -
217O VAL* 3.3 19.3 + - - +
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Residues in contact with ALA 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157O LEU* 3.8 25.3 - - + +
175O MET* 4.1 14.9 - - + +
211O THR 4.8 1.2 + - - -
212O GLY 3.3 0.6 - - - -
213O ALA* 1.3 75.2 - - - +
215O LYS* 1.3 66.7 + - - +
217O VAL* 3.2 17.7 + - - +
218O GLY 3.9 0.9 + - - -
228O LEU* 3.5 16.9 - - + +
229O THR* 3.5 35.4 - - - +
230O GLY* 3.8 2.5 - - - +
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Residues in contact with LYS 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211O THR 5.5 0.2 + - - -
212O GLY* 3.2 16.4 + - - +
214O ALA* 1.3 80.9 - - - +
216O ALA* 1.3 55.8 + - - +
218O GLY* 3.0 22.2 + - - -
219O LYS* 3.9 11.0 + - - +
225O ASN* 5.3 3.4 - - - +
226O GLY* 5.7 5.9 + - - +
228O LEU 3.6 14.9 + - - +
229O THR* 4.3 21.2 + - - +
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Residues in contact with ALA 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124O PRO* 6.1 3.1 - - + -
130O MET* 3.6 28.2 - - + +
154O THR* 3.7 17.0 - - + +
212O GLY 2.9 16.6 + - - +
213O ALA* 3.5 7.2 - - - +
214O ALA 3.2 0.4 - - - -
215O LYS* 1.3 72.1 - - - +
217O VAL* 1.3 60.3 + - - +
218O GLY 3.0 2.0 - - - -
219O LYS* 2.8 27.9 + - - +
220O VAL* 3.3 13.0 + - - +
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Residues in contact with VAL 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154O THR* 4.3 8.1 - - + -
157O LEU* 3.6 32.5 - - + -
158O ALA* 4.2 12.6 - - + +
161O ALA* 4.1 9.6 - - + -
213O ALA 3.3 15.5 + - - +
214O ALA 3.2 9.3 + - - +
216O ALA* 1.3 76.1 - - - +
218O GLY* 1.3 57.4 + - - +
219O LYS 3.1 0.2 - - - -
220O VAL* 3.2 7.9 + - - +
221O ILE* 2.8 50.5 + - + +
224O LEU* 4.2 3.4 - - + -
228O LEU* 3.6 21.3 - - + -
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Residues in contact with GLY 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214O ALA 3.9 1.4 + - - -
215O LYS 3.0 14.1 + - - -
217O VAL* 1.3 79.2 - - - +
219O LYS* 1.3 58.4 + - - +
221O ILE 3.4 18.4 - - - +
222O PRO* 3.5 11.4 - - - +
224O LEU* 3.8 8.4 + - - +
225O ASN* 3.6 35.4 - - - +
226O GLY 5.1 0.2 - - - -
228O LEU* 5.1 0.6 - - - +
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Residues in contact with LYS 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O SER 5.2 6.3 - - - -
126O ALA 5.4 6.8 + - - -
128O ALA 6.1 0.4 - - - +
130O MET* 3.7 32.3 - - + +
136O ASN* 4.8 2.8 + - - -
215O LYS* 3.9 9.9 + - - +
216O ALA* 2.8 16.9 + - - +
218O GLY* 1.3 80.7 - - - +
220O VAL* 1.3 64.9 + - + +
221O ILE 3.3 0.9 - - - -
222O PRO* 4.2 11.0 - - - +
225O ASN* 5.5 3.4 - - - +
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Residues in contact with VAL 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O MET* 3.9 32.3 - - + +
132O VAL* 4.0 20.6 - - + -
135O VAL* 4.1 7.6 - - + +
136O ASN* 3.6 34.8 - - - +
150O ALA* 5.4 0.2 - - + -
154O THR* 4.9 4.9 - - + -
158O ALA* 3.9 27.6 - - + -
216O ALA 3.3 6.5 + - - +
217O VAL* 3.2 15.0 + - - +
219O LYS* 1.3 79.7 - - + +
221O ILE* 1.3 69.0 + - + +
222O PRO* 3.6 7.0 - - - +
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Residues in contact with ILE 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135O VAL* 3.6 16.4 - - + -
158O ALA* 3.7 11.7 - - - +
161O ALA 4.2 0.2 - - - -
162O LYS* 3.7 37.2 - - + +
165O HIS* 4.6 13.5 - - + -
217O VAL* 2.8 21.7 + - + +
218O GLY 3.4 9.1 - - - +
220O VAL* 1.3 81.9 - - + +
222O PRO* 1.3 63.0 - - + +
223O GLU* 4.3 6.5 - - + +
224O LEU* 2.8 53.0 + - + +
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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