Contacts of the helix formed by residues 211 - 223 (chain A) in PDB entry 6BQG
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ILE* 3.7 30.5 - - + +
199A LYS* 3.5 27.7 + - + +
209A LEU* 3.8 5.9 - - + +
210A ASN* 1.3 77.6 - - - +
212A PRO* 1.3 65.8 - - - +
213A ASN* 2.9 28.3 + - - +
214A PHE* 3.1 28.7 + - + +
215A VAL* 3.3 16.0 + - - +
1201A ERM 5.1 0.9 - - - -
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Residues in contact with PRO 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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199A LYS* 6.0 0.9 - - - +
210A ASN 3.5 11.0 - - - +
211A ASP* 1.3 83.8 - - - +
213A ASN* 1.3 71.7 + - - +
215A VAL* 3.3 2.9 + - + +
216A LEU* 3.1 32.3 + - + +
335A VAL* 3.7 30.6 - - + +
1201A ERM 5.2 4.0 - - + -
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Residues in contact with ASN 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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211A ASP* 2.9 13.5 + - - +
212A PRO* 1.3 84.7 - - - +
214A PHE* 1.3 64.4 + - - +
216A LEU* 3.3 10.7 + - - +
217A ILE* 2.9 40.3 + - + +
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Residues in contact with PHE 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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135A VAL* 4.2 12.1 - - + -
185A VAL* 3.9 6.1 - - + -
188A PRO* 3.7 38.4 - - + -
189A ILE* 3.6 32.1 - - + -
192A ILE* 4.2 17.0 - - + -
209A LEU* 3.8 32.3 - - + -
211A ASP* 3.1 16.8 + - + +
213A ASN* 1.3 78.1 - - - +
215A VAL* 1.3 60.3 + - + +
217A ILE* 3.2 8.4 + - + +
218A GLY* 2.6 43.1 + - - -
1201A ERM 4.2 24.0 - + - -
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Residues in contact with VAL 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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209A LEU* 4.2 19.7 - - + -
211A ASP 3.3 15.2 + - - +
212A PRO* 3.6 7.0 - - + +
213A ASN 3.3 0.4 - - - -
214A PHE* 1.3 81.1 - - + +
216A LEU* 1.3 64.1 + - - +
219A SER* 2.9 31.6 + - - +
331A ASN* 3.0 39.9 - - - +
332A ILE* 5.5 0.4 - - - -
335A VAL* 3.9 19.3 - - + -
1201A ERM 4.0 30.5 - - + -
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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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212A PRO* 3.1 24.2 + - + +
213A ASN* 3.6 12.6 - - - +
215A VAL* 1.3 78.3 - - - +
217A ILE* 1.3 65.9 + - + +
219A SER* 3.8 1.4 - - - -
220A PHE* 2.9 25.7 + - - +
332A ILE* 4.2 18.8 - - + +
335A VAL* 4.0 25.8 - - + -
336A LEU* 4.3 25.8 - - + +
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Residues in contact with ILE 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 ASN* 2.9 33.2 + - + +
214A PHE* 3.8 5.2 - - + +
216A LEU* 1.3 75.7 - - + +
218A GLY* 1.3 65.6 + - - +
220A PHE* 2.9 7.3 + - - -
221A VAL* 2.9 42.8 + - + +
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Residues in contact with GLY 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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185A VAL* 4.8 4.3 - - - -
214A PHE* 2.6 30.5 + - - -
217A ILE* 1.3 74.4 - - - +
219A SER* 1.3 56.1 + - - +
221A VAL* 3.9 7.6 - - - -
222A ALA* 2.8 36.0 + - - +
1201A ERM 3.6 18.8 - - - -
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Residues in contact with SER 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 VAL 2.9 24.6 + - - -
218A GLY* 1.3 74.1 - - - +
220A PHE* 1.3 64.8 + - - +
223A PHE* 3.2 19.2 + - - +
224A PHE* 3.2 14.5 - - - -
328A PHE* 3.5 28.3 - - - -
331A ASN* 3.4 20.4 + - - +
332A ILE* 3.6 25.0 - - - +
1201A ERM 3.9 4.7 - - - -
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Residues in contact with PHE 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 LEU 2.9 18.8 + - - +
217A ILE* 3.5 5.2 - - + +
219A SER* 1.3 76.5 - - - +
221A VAL* 1.3 71.0 + - + +
224A PHE* 3.4 22.3 + + + +
225A ILE* 3.0 55.1 + - + +
332A ILE* 5.0 2.2 - - + +
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Residues in contact with VAL 221 (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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143A MET* 5.1 2.6 - - - +
181A ILE* 6.2 0.2 - - - +
185A VAL* 4.5 18.7 - - + +
217A ILE* 2.9 35.2 + - + +
218A GLY* 3.6 10.8 - - - +
220A PHE* 1.3 93.5 - - + +
222A ALA* 1.3 64.4 + - - +
223A PHE 3.4 0.2 - - - -
225A ILE* 4.0 17.7 - - + +
226A PRO* 3.3 19.1 - - - +
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Residues in contact with ALA 222 (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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139A THR* 3.9 16.2 - - + +
142A ILE* 3.6 19.5 - - - +
143A MET* 4.7 4.1 - - - +
185A VAL* 4.0 12.6 - - + -
218A GLY 2.8 19.2 + - - +
221A VAL* 1.3 77.9 - - - +
223A PHE* 1.3 60.3 + - + +
226A PRO* 3.4 13.7 - - - +
328A PHE* 5.0 0.9 - - + -
1201A ERM 3.5 29.4 - - + +
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Residues in contact with PHE 223 (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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142A ILE* 4.5 4.0 - - + -
219A SER 3.2 9.5 + - - +
221A VAL 3.4 0.4 - - - -
222A ALA* 1.3 80.6 - - - +
224A PHE* 1.3 75.7 + + - +
225A ILE 3.4 1.6 - - - -
226A PRO* 3.4 5.0 - - - +
227A LEU* 2.6 62.0 + - + +
320A PHE* 3.7 24.0 - + - -
324A TRP* 3.4 24.5 - - + -
325A CYS* 3.8 34.5 - - - -
328A PHE* 3.3 51.8 - + + -
329A ILE* 5.4 1.6 - - + -
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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