Contacts of the helix formed by residues 210 - 220 (chain A) in PDB entry 3Q29
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 ASP 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ASN* 3.3 12.6 - - - -
153A GLN* 3.7 14.6 - - + -
208A ASP 3.3 3.8 + - - +
209A THR* 1.3 75.2 - - - +
211A TYR* 1.3 65.9 + - - +
212A SER* 3.4 8.1 + - - -
213A ILE* 2.9 38.4 + - - +
214A ALA* 3.1 25.1 + - - +
391A SO4 3.0 16.5 + - - +
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Residues in contact with TYR 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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15A ASP* 4.7 13.4 - - + +
151A ASN* 3.4 19.5 - - + +
157A PHE* 4.0 20.4 - + - -
210A ASP* 1.3 72.7 - - - +
212A SER* 1.3 58.6 + - - +
214A ALA* 3.9 2.2 - - - +
215A GLU* 3.0 52.8 + - + +
228A ASN* 3.3 35.3 + - - -
231A TRP* 3.0 32.0 + + - -
232A ALA* 3.7 6.6 - - - +
391A SO4 2.7 23.7 + - - +
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Residues in contact with SER 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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210A ASP* 3.4 9.7 + - - -
211A TYR* 1.3 83.4 - - - +
213A ILE* 1.3 60.9 + - - +
215A GLU* 3.4 6.6 + - - +
216A ALA* 3.0 32.1 + - - +
391A SO4 4.4 0.6 + - - -
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Residues in contact with ILE 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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149A MET* 3.6 13.5 - - + -
208A ASP* 4.3 9.2 - - + +
209A THR* 4.3 9.9 - - + +
210A ASP* 2.9 37.3 + - - +
212A SER* 1.3 78.6 - - - +
214A ALA* 1.3 63.4 + - - +
217A ALA* 3.1 10.7 + - - +
396A GOL 2.7 46.9 + - - +
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Residues in contact with ALA 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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149A MET* 3.5 21.5 - - - +
150A PHE* 3.5 33.7 - - - +
151A ASN 4.0 1.3 - - - +
209A THR* 4.0 4.0 - - + +
210A ASP 3.1 18.1 + - - +
211A TYR* 4.0 2.9 - - - +
213A ILE* 1.3 76.1 - - - +
215A GLU* 1.3 63.5 + - - +
217A ALA* 3.4 1.7 + - - +
218A PHE* 3.0 24.9 + - - +
223A THR* 4.8 0.5 - - - +
226A THR* 4.3 6.9 + - - +
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Residues in contact with GLU 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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211A TYR* 3.0 47.9 + - + +
212A SER* 3.8 6.6 - - - +
214A ALA* 1.3 76.0 - - - +
216A ALA* 1.3 57.8 + - - +
218A PHE* 3.4 2.1 + - - -
219A ASN* 2.8 52.5 + - - +
226A THR* 5.6 2.2 - - - -
228A ASN* 5.4 7.6 - - - +
232A ALA* 4.6 9.6 - - + +
235A ASN* 3.0 35.5 + - - +
236A ILE* 6.1 0.4 - - + -
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Residues in contact with ALA 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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212A SER 3.0 15.8 + - - +
215A GLU* 1.3 73.6 - - - +
217A ALA* 1.3 60.2 + - - +
219A ASN* 4.7 3.8 - - - -
220A LYS* 2.9 49.7 + - + +
396A GOL 3.3 21.8 - - - +
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Residues in contact with ALA 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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149A MET* 3.5 21.3 - - - -
213A ILE 3.1 14.4 + - - +
214A ALA 3.6 3.1 - - - +
216A ALA* 1.3 77.7 - - - +
218A PHE* 1.3 61.4 + - - +
221A GLY 3.3 3.3 + - - -
222A GLU* 2.9 40.2 + - + +
223A THR* 3.9 6.5 - - + -
396A GOL 3.4 30.4 - - - +
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Residues in contact with PHE 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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117A ILE* 3.6 29.8 - - + -
118A TYR 3.5 22.2 - - - -
119A ASN* 3.5 12.1 + - + -
214A ALA 3.0 16.8 + - - +
215A GLU* 4.1 1.3 - - - +
217A ALA* 1.3 76.5 - - - +
219A ASN* 1.3 77.9 + - - +
220A LYS 3.1 0.2 - - - -
221A GLY* 3.2 14.0 + - - -
223A THR* 3.6 24.6 - - + +
224A ALA 3.4 24.0 - - - -
225A MET 3.8 16.2 - - - -
226A THR* 3.8 19.3 - - + -
236A ILE* 4.0 19.7 - - + -
241A VAL* 3.8 11.1 - - + +
243A TYR* 4.1 5.2 - - + -
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Residues in contact with ASN 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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215A GLU* 2.8 43.1 + - - +
216A ALA* 3.7 4.0 - - - +
218A PHE* 1.3 92.6 - - - +
220A LYS* 1.3 60.5 + - + +
221A GLY 3.5 0.4 - - - -
226A THR* 5.9 0.2 - - - +
235A ASN* 3.8 22.7 - - - +
236A ILE* 3.5 25.1 + - - +
239A SER* 3.3 32.2 - - - +
241A VAL* 3.5 8.1 - - - +
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Residues in contact with LYS 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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145A LYS* 5.2 1.7 + - - -
216A ALA* 2.9 33.5 + - + +
219A ASN* 1.3 80.5 - - + +
221A GLY* 1.3 62.5 + - - +
222A GLU* 3.4 22.4 + - + +
241A VAL* 5.0 1.6 - - - -
396A GOL 3.2 23.1 + - - +
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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