Contacts of the helix formed by residues 207 - 219 (chain A) in PDB entry 4BN4
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 ASN 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ILE 2.9 23.6 + - - +
151A PRO* 3.8 22.8 - - + +
152A SER* 2.9 33.9 + - - +
206A PRO* 1.3 74.8 - - - +
208A VAL* 1.4 70.9 + - + +
209A THR* 2.8 36.4 + - - -
210A HIS* 3.0 21.8 + - - +
211A TYR* 3.0 17.4 + - - -
387A VAL* 5.5 1.1 - - - -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN* 1.4 74.3 - - + +
209A THR* 1.3 59.2 + - - +
211A TYR 4.4 0.9 - - - +
212A PHE* 2.8 32.3 + - - +
367A VAL* 3.6 40.4 - - + -
370A VAL* 4.3 6.2 - - + +
371A GLU* 4.1 18.8 - - + +
383A MET* 3.7 11.2 - - + +
387A VAL* 3.7 36.3 - - + +
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.8 38.3 + - + -
207A ASN* 2.8 17.5 + - - -
208A VAL* 1.3 79.1 - - - +
210A HIS* 1.3 62.4 + - - +
212A PHE* 3.4 8.5 + - - +
213A LEU* 3.4 16.0 + - + +
318A LEU* 4.0 18.4 - - + -
366A VAL* 4.0 22.2 - - + +
367A VAL* 4.1 7.1 - - - +
370A VAL* 4.2 21.8 - - + +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.4 22.8 - - + +
149A SER* 3.4 16.5 + - - -
152A SER* 4.0 0.2 - - - -
206A PRO* 3.5 17.4 - - + +
207A ASN* 3.0 42.0 + - - +
209A THR* 1.3 76.7 - - - +
211A TYR* 1.3 59.5 + - - +
213A LEU* 3.0 14.1 + - + +
214A ARG* 3.0 22.9 + - - +
233A LEU* 3.6 32.3 - - + +
234A GLU* 4.1 7.9 - - + -
237A SER* 3.8 13.6 + - - +
239A ILE* 4.9 0.5 - - - +
1394A NA 3.0 25.5 - - - -
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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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206A PRO* 3.6 37.7 - - + +
207A ASN 3.0 25.9 + - - +
208A VAL 4.1 1.1 - - - +
210A HIS* 1.3 75.9 - - - +
212A PHE* 1.3 59.6 + - - +
214A ARG* 3.2 11.6 + - + +
215A LEU* 2.9 24.8 + - - +
236A VAL* 4.3 3.6 + - - +
237A SER* 3.5 32.0 - - - -
383A MET* 4.0 3.6 - - + -
386A LEU* 3.4 19.7 - - + +
387A VAL* 4.1 26.2 - - + -
390A GLU* 3.6 41.7 + - + +
391A THR* 3.5 26.8 - - + +
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Residues in contact with PHE 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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132A ILE* 5.3 2.7 - - + -
208A VAL 2.8 21.7 + - - +
209A THR 3.6 4.7 - - - +
211A TYR* 1.3 72.5 - - - +
213A LEU* 1.4 71.3 + - + +
215A LEU* 3.1 1.6 + - + +
216A LEU* 2.9 39.6 + - + +
316A LEU* 4.2 19.3 - - + -
318A LEU* 5.5 3.6 - - + -
343A ILE* 6.1 0.9 - - + -
370A VAL* 3.7 27.1 - - + -
373A LEU* 3.7 28.9 - - + -
374A VAL* 3.6 19.3 - - + -
377A LEU* 3.7 25.8 - - + -
379A TRP* 3.9 16.6 - + - -
383A MET* 3.6 16.7 - - + +
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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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142A VAL* 3.9 30.5 - - + -
144A VAL* 4.1 11.7 - - + -
148A ILE* 4.9 6.1 - - + -
209A THR 3.4 14.1 + - - +
210A HIS* 3.0 13.2 + - - +
212A PHE* 1.4 94.9 - - + +
214A ARG* 1.3 62.3 + - - +
216A LEU* 3.4 9.2 + - + +
217A HIS* 3.0 22.5 + - - +
222A LEU* 4.3 7.4 - - + +
225A LEU* 3.8 34.3 - - + -
234A GLU* 5.7 1.1 - - + -
239A ILE* 3.8 12.7 - - + +
316A LEU* 5.1 1.3 - - + -
318A LEU* 4.2 11.4 - - + -
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Residues in contact with ARG 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 HIS 3.0 12.2 + - - +
211A TYR* 3.2 14.6 + - + +
213A LEU* 1.3 76.2 - - - +
215A LEU* 1.3 56.2 + - - +
217A HIS* 3.2 7.7 - - - +
218A ASP* 2.9 55.1 + - - +
237A SER* 2.8 32.8 + - - +
238A GLY* 3.5 27.0 + - - -
239A ILE* 3.6 11.1 - - + +
386A LEU* 4.1 17.5 - - + +
390A GLU* 3.4 27.9 + - - -
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Residues in contact with LEU 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 2.9 13.5 + - - +
212A PHE* 3.1 7.2 + - - +
214A ARG* 1.3 75.0 - - - +
216A LEU* 1.3 64.6 + - - +
218A ASP* 3.1 10.7 + - + +
219A LYS* 2.9 39.8 + - + +
379A TRP* 3.8 23.8 - - + -
382A GLU* 3.5 40.2 - - + +
383A MET* 3.6 35.4 - - + +
386A LEU* 4.1 13.7 - - + -
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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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132A ILE* 4.3 12.6 - - + -
140A VAL* 4.1 30.1 - - + -
142A VAL* 4.3 8.3 - - + -
212A PHE* 2.9 25.6 + - + +
213A LEU* 3.6 12.3 - - + +
214A ARG 3.3 0.2 - - - -
215A LEU* 1.3 77.7 - - - +
217A HIS* 1.3 60.0 + - - +
219A LYS* 3.4 6.9 + - - +
221A LEU* 3.0 53.0 + - + +
222A LEU* 4.2 16.8 - - + +
316A LEU* 4.5 9.2 - - + -
379A TRP* 4.2 26.6 - - + -
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Residues in contact with HIS 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 3.0 12.8 + - - +
214A ARG* 3.2 19.1 - - - +
216A LEU* 1.3 73.5 - - - +
218A ASP* 1.3 83.5 + - - +
220A GLY* 2.9 20.6 + - - -
222A LEU* 3.8 22.9 - - + +
238A GLY 4.7 1.3 - - - -
239A ILE* 4.3 2.5 - - + -
240A PRO* 3.4 39.4 - - + +
243A LYS* 4.1 29.3 - - + +
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Residues in contact with ASP 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 ARG* 2.9 47.4 + - - +
215A LEU* 3.1 14.8 + - + +
217A HIS* 1.3 101.2 + - - +
219A LYS* 1.3 60.2 + - - +
220A GLY 3.3 1.1 + - - -
386A LEU* 5.2 4.3 - - - +
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Residues in contact with LYS 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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135A ARG* 4.0 21.1 + - - +
215A LEU* 2.9 28.6 + - + +
216A LEU* 3.8 5.4 - - - +
217A HIS 3.1 0.4 - - - -
218A ASP* 1.3 77.5 - - + +
220A GLY* 1.3 59.2 + - - +
221A LEU* 3.4 21.5 + - + +
379A TRP* 3.4 46.6 - - + +
382A GLU* 2.7 40.7 + - - +
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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