Contacts of the helix formed by residues 208 - 220 (chain A) in PDB entry 1HBX
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 SER 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A PRO* 2.6 34.8 + - - +
207A THR* 1.3 93.5 - - - +
209A GLU* 1.3 60.3 + - - +
210A THR* 3.9 6.1 + - - -
211A GLY* 3.1 15.2 + - - -
212A LYS* 3.1 20.3 + - - +
214B LEU* 4.2 8.9 - - - +
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A THR 4.4 2.4 - - - +
208A SER* 1.3 70.6 - - - +
210A THR* 1.3 67.2 + - - +
211A GLY 3.1 1.6 - - - -
212A LYS* 3.5 31.5 + - - +
213A ALA* 3.1 26.2 + - - +
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Residues in contact with THR 210 (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 SER* 3.4 6.0 + - - -
209A GLU* 1.3 79.7 + - - +
211A GLY* 1.3 62.3 + - - +
213A ALA* 3.5 6.0 - - - +
214A LEU* 3.3 20.4 + - - +
210B THR* 4.7 19.0 - - + +
214B LEU* 4.6 13.4 - - + +
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Residues in contact with GLY 211 (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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205A MET 3.7 19.3 - - - -
208A SER* 3.1 17.9 + - - -
209A GLU 3.1 0.4 - - - -
210A THR* 1.3 75.3 - - - +
212A LYS* 1.3 59.0 + - - +
213A ALA 2.9 1.8 - - - -
214A LEU* 2.6 26.8 + - - +
215A ILE* 2.9 12.2 + - - +
205B MET* 6.0 0.2 - - - -
214B LEU* 3.7 15.2 - - - +
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Residues in contact with LYS 212 (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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205A MET 4.3 2.2 + - - -
206A ILE 3.0 25.3 + - - +
207A THR* 3.3 11.0 - - - +
208A SER 3.1 10.5 + - - +
209A GLU* 3.5 37.0 + - - +
211A GLY* 1.3 72.7 - - - +
213A ALA* 1.3 62.6 + - - +
215A ILE* 3.4 10.9 + - - +
216A GLN* 3.1 37.7 + - - +
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Residues in contact with ALA 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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209A GLU 3.1 20.3 + - - +
210A THR* 3.5 8.3 - - - +
211A GLY 2.7 1.0 + - - -
212A LYS* 1.3 77.1 - - - +
214A LEU* 1.3 62.2 + - - +
216A GLN* 3.1 8.7 + - - +
217A THR* 3.1 25.1 + - - -
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Residues in contact with LEU 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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210A THR 3.3 9.5 + - - +
211A GLY* 2.6 13.8 + - - +
213A ALA* 1.3 76.3 - - - +
215A ILE* 1.3 57.4 + - - +
217A THR* 3.2 13.0 + - + -
218A CYS* 2.9 34.6 + - - +
204B PRO* 4.2 16.2 - - + +
205B MET* 3.5 29.8 - - + -
208B SER* 4.8 3.6 - - - +
210B THR* 4.1 17.7 - - + -
211B GLY* 3.7 33.0 - - - +
214B LEU* 4.4 8.7 - - + -
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Residues in contact with ILE 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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186A LEU* 3.6 29.6 - - + -
194A VAL* 5.2 4.7 - - + -
205A MET 3.7 18.4 - - - +
206A ILE* 3.9 18.6 - - + +
211A GLY 2.9 11.4 + - - +
212A LYS* 3.7 11.4 - - - +
214A LEU* 1.3 75.0 - - - +
216A GLN* 1.3 64.8 + - - +
218A CYS* 3.5 5.6 + - - +
219A LEU* 2.9 51.8 + - + +
202B LEU* 4.9 2.2 - - + -
205B MET* 3.3 24.5 - - + -
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Residues in contact with GLN 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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194A VAL* 5.8 0.9 - - - +
212A LYS* 3.1 27.4 + - - +
213A ALA* 3.4 11.0 - - - +
215A ILE* 1.3 81.5 - - - +
217A THR* 1.3 68.7 + - - +
219A LEU* 3.6 9.3 - - - +
220A ASN* 2.7 45.1 + - - +
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Residues in contact with THR 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 ALA 3.1 12.5 + - - -
214A LEU* 3.4 17.5 - - + -
216A GLN* 1.3 76.4 - - - +
218A CYS* 1.3 71.6 + - - +
220A ASN* 2.9 7.6 + - - +
221A SER* 2.8 21.4 + - - -
204B PRO* 6.3 1.8 - - + -
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Residues in contact with CYS 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 LEU* 2.9 17.3 + - - +
215A ILE 3.6 0.9 - - - +
217A THR* 1.3 84.8 - - - +
219A LEU* 1.3 58.9 - - - +
221A SER* 2.8 25.4 + - - -
201B LYS* 3.1 32.4 - - - +
202B LEU* 3.3 26.9 - - + -
204B PRO* 3.4 33.0 - - - -
205B MET* 3.7 14.1 - - - -
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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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186A LEU* 4.8 1.6 - - + -
188A ALA* 4.0 18.2 - - + -
192A GLY 5.5 0.9 - - - +
194A VAL* 3.3 35.2 - - + -
215A ILE* 2.9 34.1 + - + +
216A GLN* 4.0 9.9 - - - +
218A CYS* 1.3 76.5 - - - +
220A ASN* 1.3 63.7 + - - +
221A SER 3.6 0.3 + - - -
182B GLN* 4.0 13.7 - - + -
201B LYS* 3.9 20.3 + - - +
202B LEU* 3.9 30.7 - - + -
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Residues in contact with ASN 220 (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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216A GLN* 2.7 47.8 + - - +
217A THR* 3.4 4.9 - - - +
219A LEU* 1.3 75.2 - - - +
221A SER* 1.3 67.5 + - - +
222A PRO* 3.5 3.3 - - - +
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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