Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 2BEW
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 ILE 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA* 3.7 43.5 - - + +
172A VAL* 3.7 5.8 - - + +
175A ALA* 4.0 6.7 - - + -
186A VAL* 4.3 0.2 - - - -
187A VAL* 3.3 14.4 - - + +
189A CYS* 4.3 2.5 - - + -
208A ALA* 3.8 25.4 - - + -
213A CYS* 3.0 18.6 + - + +
214A PRO* 1.3 74.8 - - - +
216A ILE* 1.3 75.9 + - - +
217A PHE* 3.7 22.2 - - + -
272A ALA* 4.2 3.6 - - - +
277A GLN 4.2 0.9 - - - +
278A PRO* 3.2 10.8 - - + +
279A PHE 3.0 23.9 + - - +
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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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103A LEU* 4.5 9.0 - - + -
186A VAL* 3.9 15.9 - - + -
187A VAL 2.9 5.6 + - - +
188A ILE* 3.3 20.0 - - + +
189A CYS 2.9 26.0 + - - -
215A ILE* 1.3 78.7 - - - +
217A PHE* 1.3 72.2 + - - +
218A PHE* 4.5 1.8 - - + +
265A THR* 4.0 18.2 - - + +
268A ALA* 4.1 16.2 - - + +
269A ARG* 3.7 34.8 - - + +
272A ALA* 4.7 1.8 - - + -
279A PHE* 3.5 7.2 - - + +
281A ILE* 3.9 23.8 - - + -
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Residues in contact with PHE 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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168A ILE* 3.7 26.7 - - + -
172A VAL* 3.7 6.5 - - + -
189A CYS* 3.6 11.4 - - + -
191A PHE* 3.9 11.0 - + + -
204A GLY 3.6 20.6 - - - -
205A PHE* 3.8 30.1 - + + -
208A ALA* 3.6 23.8 - - + -
215A ILE* 3.7 20.0 - - + -
216A ILE* 1.3 74.2 - - - +
218A PHE* 1.3 60.2 + - - +
219A CYS 4.0 0.9 - - - -
248A ILE* 4.2 11.4 - - + -
278A PRO* 4.1 12.6 - - + -
279A PHE 2.9 16.9 + - - +
280A LEU* 3.4 19.1 - - + +
281A ILE 2.9 27.2 + - - +
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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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95A THR* 4.0 20.0 - - - -
99A SER* 3.7 17.0 - - - -
188A ILE* 4.2 24.5 - - + -
189A CYS 2.8 11.6 + - - +
190A TYR* 3.2 31.3 - + + +
191A PHE* 3.0 28.6 + - - +
216A ILE* 4.6 0.7 - - + -
217A PHE* 1.3 74.3 - - - +
219A CYS* 1.3 63.0 + - - +
220A ARG* 3.8 6.9 + - + -
261A VAL* 3.9 18.6 - - + -
265A THR* 3.8 11.7 - - - -
281A ILE* 3.5 27.1 - - + -
283A ALA* 3.6 32.3 - - + -
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Residues in contact with CYS 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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191A PHE* 3.2 23.3 - - + -
192A GLY 3.9 22.4 - - - -
193A GLU* 3.9 7.0 - - - -
217A PHE 4.0 1.0 - - - -
218A PHE* 1.3 74.8 - - - +
220A ARG* 1.3 64.8 + - - +
221A ASN* 3.5 2.9 + - - -
239A ILE* 3.9 37.7 - - + -
280A LEU* 4.7 0.9 - - + -
281A ILE 2.8 14.2 + - - +
282A GLU* 3.5 8.6 - - - -
283A ALA* 2.8 30.3 + - - +
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Residues in contact with ARG 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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92A GLU* 2.8 43.1 + - - +
95A THR* 4.0 21.5 - - + +
96A HIS* 4.4 3.6 - - - -
112A GLN* 3.6 21.4 - - - +
114A ARG* 3.4 26.5 + - - +
115A GLU* 2.9 34.6 + - - +
190A TYR* 5.1 5.4 - - + +
191A PHE 2.9 11.9 + - - +
192A GLY* 3.3 10.0 - - - +
193A GLU* 3.3 21.8 + - - +
218A PHE* 3.8 14.1 + - + -
219A CYS* 1.3 71.5 - - - +
221A ASN* 1.3 58.9 + - - +
222A ASN* 3.6 5.2 + - - +
283A ALA* 3.8 6.5 - - - -
285A THR* 4.7 2.7 - - + -
601A THW 2.8 30.9 + - - -
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Residues in contact with ASN 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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193A GLU* 3.6 25.0 - - + +
219A CYS* 3.5 2.5 + - - -
220A ARG* 1.3 71.0 - - - +
222A ASN* 1.3 60.2 + - - +
223A GLY* 3.4 10.9 + - - -
230A THR* 3.8 6.1 - - - +
234A TYR* 3.0 24.9 + - - -
238A GLY* 4.7 0.6 - - - -
282A GLU* 2.8 32.8 + - + +
283A ALA 2.9 14.5 + - - +
284A MET* 3.7 24.1 - - - +
285A THR* 2.9 27.7 + - - +
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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