Contacts of the helix formed by residues 212 - 219 (chain A) in PDB entry 4B18
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 ILE 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.9 11.7 - - + -
178A LEU* 3.6 17.3 - - + -
190A VAL* 5.4 1.3 - - + -
193A LEU* 3.6 37.0 - - + +
207A VAL* 3.7 31.9 + - + +
208A LEU* 3.9 8.5 + - + -
210A CYS 3.6 1.6 - - - -
211A ASN* 1.3 76.2 - - - +
213A LEU* 1.3 58.2 + - - +
215A PRO* 3.3 5.5 - - - +
216A LEU* 2.8 54.6 + - + +
235A ALA* 5.5 2.9 - - + -
239A LEU* 3.7 29.4 - - + -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 5.1 6.0 - - + +
211A ASN* 4.5 0.4 - - - +
212A ILE* 1.3 77.6 - - + +
214A PRO* 1.3 66.6 - - + +
216A LEU* 2.9 5.1 + - + -
217A LEU* 2.6 55.3 + - + +
236A LEU* 3.9 28.0 - - + -
239A LEU* 4.2 12.1 - - + -
251A LYS 3.3 27.4 - - - +
252A VAL* 4.3 8.7 - - + +
254A PRO* 3.6 32.3 - - + -
255A CYS* 4.4 3.8 - - + +
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Residues in contact with PRO 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ASN* 3.3 27.1 - - - +
212A ILE 3.9 0.4 - - - -
213A LEU* 1.3 91.8 - - + +
215A PRO* 1.3 75.0 - - + +
217A LEU* 3.3 6.9 + - + +
218A GLN* 3.0 25.6 + - - +
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Residues in contact with PRO 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 4.1 16.2 - - + +
178A LEU* 4.0 23.0 - - + +
179A SER* 4.3 12.1 - - - +
211A ASN* 3.5 15.7 - - + +
212A ILE 3.3 10.5 - - - +
214A PRO* 1.3 102.7 - - + +
216A LEU* 1.3 62.2 + - - +
218A GLN* 3.5 17.3 - - + +
219A LEU* 3.6 12.5 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 4.0 4.1 - - + +
190A VAL* 3.3 33.4 - - + -
212A ILE* 2.8 33.2 + - + +
213A LEU* 2.9 5.5 + - + +
215A PRO* 1.3 78.2 - - - +
217A LEU* 1.3 54.5 + - - +
219A LEU* 2.8 43.1 + - + +
220A PHE* 4.1 7.5 + - + -
232A ALA* 4.1 15.9 - - + +
235A ALA* 4.8 1.6 - - + -
236A LEU* 3.9 26.9 - - + +
239A LEU* 3.5 32.3 - - + -
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 2.6 49.9 + - + +
214A PRO* 3.9 5.6 - - + +
216A LEU* 1.3 71.3 - - - +
218A GLN* 1.3 64.1 + - - +
219A LEU 2.8 2.1 + - - -
220A PHE* 3.0 34.3 + - + +
221A SER 4.2 1.4 + - - -
236A LEU* 4.6 5.2 - - + -
254A PRO* 3.8 25.6 - - + +
255A CYS* 3.8 22.4 - - + -
258A VAL* 3.8 27.7 - - + +
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Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A PRO 3.0 18.3 + - - +
215A PRO* 3.5 13.2 - - + +
217A LEU* 1.3 76.6 - - - +
219A LEU* 1.3 60.9 + - - +
220A PHE 3.2 0.7 + - - -
221A SER* 3.1 33.7 + - - +
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.8 25.4 - - + +
186A GLN* 3.5 30.3 - - + +
190A VAL* 4.3 8.7 - - + -
215A PRO 3.6 7.4 - - - +
216A LEU* 2.8 46.2 + - + +
218A GLN* 1.3 73.2 - - - +
220A PHE* 1.3 62.0 + - - +
221A SER 3.2 0.4 + - - -
222A LYS* 3.6 15.2 + - - +
228A MET* 3.3 43.3 - - + +
229A THR* 5.6 1.4 + - - -
232A ALA* 4.6 10.8 - - + -
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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