Contacts of the helix formed by residues 205 - 221 (chain A) in PDB entry 3BMW
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ASN 3.0 27.3 + - - -
174A GLY 3.5 16.0 + - - +
175A TYR* 3.8 14.6 - - - -
202A ASN* 3.1 21.7 + - - +
203A GLN 3.5 1.8 - - - +
204A GLN* 1.3 78.5 - - - +
206A SER* 1.3 58.6 + - - +
207A THR* 2.9 35.2 + - - -
208A ILE* 3.0 14.1 + - + +
209A ASP 2.9 24.6 + - - -
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLN 3.3 4.2 + - - -
205A ASN* 1.3 73.0 + - - +
207A THR* 1.3 62.1 + - - +
209A ASP* 3.9 4.8 - - - +
210A SER* 3.0 34.7 + - - -
673A SER* 4.1 24.7 - - - -
674A THR* 3.4 21.5 + - - +
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Residues in contact with THR 207 (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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165A LEU* 4.9 18.4 - - + -
175A TYR* 3.9 28.5 + - + +
205A ASN* 2.9 11.3 + - - -
206A SER* 1.3 81.3 + - - +
208A ILE* 1.3 58.8 + - + +
210A SER* 3.5 4.4 + - - -
211A TYR* 2.9 30.9 + - + +
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.0 23.8 - - + -
165A LEU* 4.6 8.5 - - + -
175A TYR* 3.6 47.6 - - + +
201A LEU* 4.3 16.4 - - + -
202A ASN 3.4 27.6 - - - +
203A GLN* 4.1 5.6 - - - -
205A ASN* 3.0 7.1 + - + +
207A THR* 1.3 74.6 - - - +
209A ASP* 1.3 65.2 + - - +
211A TYR* 3.5 5.2 - - + +
212A LEU* 2.9 45.3 + - + +
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Residues in contact with ASP 209 (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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203A GLN 3.4 19.0 + - - +
205A ASN 2.9 8.9 + - - +
206A SER 3.9 3.1 - - - +
208A ILE* 1.3 75.8 - - - +
210A SER* 1.3 65.1 + - - +
212A LEU* 3.4 2.1 + - - +
213A LYS* 2.9 55.7 + - - +
239A TRP* 2.7 29.8 + - - +
242A ASN* 3.1 14.7 + - - -
672A SER 4.5 8.1 - - - +
673A SER* 5.2 0.3 - - - -
674A THR* 3.6 26.6 + - + +
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Residues in contact with SER 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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206A SER 3.0 19.1 + - - -
207A THR* 3.8 5.2 - - - -
209A ASP* 1.3 80.7 + - - +
211A TYR* 1.3 57.9 + - - +
213A LYS* 3.4 8.4 + - - +
214A SER* 2.9 30.1 + - - -
672A SER 5.2 4.9 + - - -
673A SER* 5.1 7.6 + - - -
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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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105A ASP* 3.5 1.9 + - - -
106A PHE* 2.9 50.8 + + + -
107A LYS* 3.9 14.6 - - + +
158A LEU* 3.6 21.3 - - + +
159A TYR 2.7 21.8 + - - -
160A ASP* 3.6 45.1 - - + -
165A LEU* 4.2 11.9 - - + -
201A LEU* 6.2 0.2 - - + -
207A THR* 2.9 21.4 + - + +
208A ILE* 3.2 8.7 + - + +
210A SER* 1.3 76.3 - - - +
212A LEU* 1.3 70.0 + - + +
214A SER* 3.3 6.9 + - - -
215A ALA* 2.8 27.9 + - - +
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Residues in contact with LEU 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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106A PHE* 4.5 19.5 - - + -
137A PHE* 4.6 4.8 - - + -
139A PRO* 3.9 28.9 - - + +
201A LEU* 4.7 5.6 - - + -
203A GLN* 3.9 10.5 - - + -
208A ILE* 2.9 36.1 + - + +
209A ASP 4.0 2.7 - - - +
211A TYR* 1.3 91.6 - - + +
213A LYS* 1.3 66.0 + - - +
215A ALA* 3.7 2.4 - - - +
216A ILE* 3.0 20.6 + - - +
239A TRP* 3.7 34.1 - - + -
243A PHE* 3.6 16.3 - - + -
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 2.9 51.6 + - - +
210A SER* 3.7 7.4 - - - +
212A LEU* 1.3 77.3 - - - +
214A SER* 1.3 61.5 + - - +
216A ILE* 3.4 12.3 - - - +
217A LYS* 3.3 32.9 + - - +
242A ASN* 2.8 34.1 + - - +
243A PHE* 4.2 11.4 - - + +
246A SER* 3.6 33.7 - - - +
583A GLN 4.4 6.7 + - - -
584A ILE* 5.1 2.6 - - - +
585A CYS 5.4 0.2 - - - +
672A SER 4.5 9.7 + - - -
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Residues in contact with SER 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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107A LYS* 3.3 24.8 + - - -
210A SER 2.9 18.3 + - - -
211A TYR* 3.6 4.9 - - - -
213A LYS* 1.3 75.9 - - - +
215A ALA* 1.3 63.5 + - - +
217A LYS* 3.2 12.6 + - - +
218A VAL* 3.1 23.0 + - - +
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Residues in contact with ALA 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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106A PHE* 3.7 33.9 - - + +
107A LYS* 3.9 18.3 - - + +
137A PHE* 4.2 6.3 - - + -
211A TYR* 2.8 19.5 + - + +
212A LEU* 3.7 8.1 - - - +
213A LYS 3.3 0.2 - - - -
214A SER* 1.3 77.0 - - - +
216A ILE* 1.3 62.2 + - - +
218A VAL* 3.1 13.4 + - - +
219A TRP* 3.1 19.9 + - - -
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Residues in contact with ILE 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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135A ILE* 4.5 2.7 - - + -
137A PHE* 3.9 36.5 - - + -
212A LEU 3.0 16.3 + - - +
213A LYS* 3.4 13.5 - - - +
215A ALA* 1.3 76.5 - - - +
217A LYS* 1.3 63.3 + - + +
219A TRP* 3.1 13.8 + - + -
220A LEU* 2.9 30.1 + - + +
224A ILE* 4.6 1.1 - - + -
227A ILE* 3.8 35.4 - - + -
243A PHE* 3.8 17.7 - - + -
246A SER* 5.6 1.8 - - - +
247A ILE* 3.8 27.4 - - + +
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Residues in contact with LYS 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 LYS* 3.3 21.0 + - - +
214A SER* 3.2 12.5 + - - +
215A ALA 3.1 0.6 - - - -
216A ILE* 1.3 77.1 - - + +
218A VAL* 1.3 64.6 + - - +
220A LEU* 3.8 9.5 - - + +
221A ASP* 2.9 31.7 + - - +
246A SER* 3.6 28.1 + - - -
247A ILE* 6.2 0.2 - - - -
250A TYR* 3.7 54.2 - - + +
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Residues in contact with VAL 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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107A LYS* 4.1 31.4 - - + +
116A PHE* 4.0 30.5 - - + -
214A SER* 3.1 15.4 + - - +
215A ALA* 3.1 11.2 + - - +
217A LYS* 1.3 75.3 - - - +
219A TRP* 1.3 69.6 + - + +
221A ASP* 3.3 7.5 + - - +
222A MET* 3.2 22.6 + - + +
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Residues in contact with TRP 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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54A TRP* 4.8 0.2 - + - -
79A PRO* 3.5 40.6 - - + -
80A VAL* 3.6 17.2 - - + +
106A PHE 2.9 21.6 + - - -
108A ARG 3.7 20.4 - - - -
109A THR* 3.9 8.7 - - + -
116A PHE* 3.6 30.7 - + - -
119A PHE* 3.9 35.0 - + - -
135A ILE* 3.8 19.5 - - + -
137A PHE* 4.1 13.0 - + - -
215A ALA 3.1 24.9 - - - -
216A ILE* 3.1 8.8 + - + +
218A VAL* 1.3 80.9 - - + +
220A LEU* 1.3 63.9 + - - +
221A ASP 3.2 0.4 - - - -
222A MET* 3.0 18.3 + - + +
223A GLY 3.4 4.5 + - - -
224A ILE* 3.5 15.6 - - + +
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Residues in contact with LEU 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 ILE* 2.9 24.3 + - + +
217A LYS* 3.8 11.0 - - + +
219A TRP* 1.3 75.8 - - - +
221A ASP* 1.3 58.9 + - - +
223A GLY* 3.0 9.9 + - - -
224A ILE* 3.9 17.9 - - + +
227A ILE* 4.7 1.3 - - + -
247A ILE* 4.1 31.9 - - + -
250A TYR* 4.0 26.7 - - + -
251A ARG* 2.8 55.4 + - - +
253A VAL* 3.9 26.5 - - + -
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Residues in contact with ASP 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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217A LYS* 2.9 21.6 + - - +
218A VAL* 3.6 8.4 - - - +
220A LEU* 1.3 75.5 - - - +
222A MET* 1.3 62.3 + - - +
223A GLY* 3.2 1.9 + - - -
250A TYR* 2.8 36.7 + - - -
251A ARG* 5.8 0.5 + - - -
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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