Contacts of the strand formed by residues 213 - 224 (chain E) in PDB entry 4BEI
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 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205E THR* 3.9 29.2 - - + +
206E ALA 3.7 2.7 - - - -
207E VAL* 4.5 4.3 - - + +
211E GLY 4.1 7.2 - - - +
212E LEU* 1.3 77.4 - - - +
214E ILE* 1.3 57.6 + - - +
77F TRP* 3.2 8.5 + - - -
79F SER* 2.6 48.2 + - - +
80F ILE 4.6 7.0 - - - +
81F LYS* 3.9 20.0 - - + -
87F TYR* 3.9 36.1 - - + -
88F PHE 5.3 0.2 - - - +
132F SER* 5.4 4.9 - - - -
134F GLN* 2.9 15.5 + - - +
1272F O4B 4.4 14.8 - - - -
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Residues in contact with ILE 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E THR* 3.2 3.1 - - - -
206E ALA* 2.7 50.6 + - + +
212E LEU* 4.3 15.0 - - + -
213E ILE* 1.3 73.5 - - - +
215E PRO* 1.3 81.9 - - + +
216E VAL* 3.6 0.3 - - - +
236E ILE* 4.7 10.1 - - + -
242E TYR* 3.9 34.5 - - + +
247E TYR* 3.7 30.7 - - + -
77F TRP* 3.5 33.4 - - + +
79F SER* 4.8 0.2 - - - -
101F GLN* 4.9 2.7 - - + +
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Residues in contact with PRO 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E MET 4.0 5.2 - - - +
205E THR* 4.6 1.8 - - + -
213E ILE 3.4 3.1 - - - +
214E ILE* 1.3 94.0 - - + +
216E VAL* 1.3 60.0 - - - +
217E ASN 5.1 2.5 - - - +
218E ALA* 5.6 1.1 - - - +
236E ILE* 5.6 0.5 - - - +
77F TRP* 3.4 40.6 - - + -
78F LEU 4.5 3.6 - - - +
79F SER* 3.7 11.0 - - - +
89F PRO* 3.8 28.0 - - + -
91F LYS* 6.2 2.7 - - + -
101F GLN* 3.9 15.7 - - - +
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Residues in contact with VAL 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E PHE* 5.6 0.7 - - + -
204E MET* 2.9 39.8 + - + +
205E THR 3.7 2.9 - - - +
206E ALA* 3.6 34.8 - - + +
214E ILE 3.2 3.3 + - - +
215E PRO* 1.3 76.0 - - - +
217E ASN* 1.3 60.0 - - - +
234E ARG* 2.9 39.4 + - + +
235E GLY 4.5 5.8 - - - +
236E ILE* 4.0 33.7 - - + -
249E ILE* 4.9 5.2 - - + -
97F ASP* 4.6 0.4 - - - -
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Residues in contact with ASN 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E PHE* 3.7 14.9 - - + -
203E TRP* 3.5 0.5 - - - +
204E MET* 2.9 49.4 + - + +
215E PRO 5.3 0.4 - - - -
216E VAL* 1.3 77.6 - - - +
218E ALA* 1.3 91.4 + - - +
220E GLU* 3.1 16.6 + - - +
232E LYS* 3.0 37.2 - - - +
234E ARG* 3.6 15.7 - - - +
89F PRO* 3.4 8.7 - - - +
97F ASP* 3.5 6.6 - - - +
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Residues in contact with ALA 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E PHE 3.4 3.8 - - - +
215E PRO* 5.6 2.5 - - - +
216E VAL 4.4 0.2 - - - -
217E ASN* 1.3 92.0 + - - +
219E ARG* 1.3 65.9 + - - +
220E GLU* 3.2 4.2 + - - +
89F PRO* 4.1 7.0 - - - -
91F LYS* 3.5 35.2 - - + +
93F VAL* 4.0 14.4 - - + +
97F ASP* 2.7 27.6 + - + +
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Residues in contact with ARG 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 3.8 22.5 + - - +
202E PHE 3.5 3.8 - - - -
203E TRP* 3.6 31.1 - - + -
218E ALA* 1.3 70.6 - - - +
220E GLU* 1.3 59.7 + - - +
221E LYS* 4.3 1.2 + - - +
88F PHE* 3.4 36.1 - - - -
89F PRO* 2.8 26.4 + - + +
90F ALA* 2.9 24.7 + - - +
91F LYS 3.0 13.1 + - - +
92F ALA* 3.3 15.2 - - + +
93F VAL 2.9 28.8 + - - +
118F PHE* 4.1 4.8 - - - +
119F TRP* 2.4 37.6 + - - +
121F PRO* 3.5 20.0 - - - +
124F MET* 5.3 2.0 - - - +
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Residues in contact with GLU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E VAL 3.9 0.5 - - - +
201E GLU* 3.2 4.9 - - - +
202E PHE* 2.8 47.5 + - + +
217E ASN* 3.1 16.0 - - - +
218E ALA 3.7 10.1 - - - +
219E ARG* 1.3 72.0 - - - +
221E LYS* 1.3 62.2 + - - +
222E TRP* 2.7 30.8 + - + +
230E TYR* 2.5 25.2 + - - -
232E LYS* 3.2 9.7 + - - -
93F VAL* 3.6 15.0 - - + -
95F GLY 3.5 20.5 - - - +
97F ASP 2.7 22.7 + - - -
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Residues in contact with LYS 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E VAL 3.5 4.5 - - - +
201E GLU* 4.0 14.5 + - - +
219E ARG 5.6 1.1 - - - +
220E GLU* 1.3 74.4 - - - +
222E TRP* 1.3 75.2 + - - +
256E ILE* 3.8 20.2 - - + -
93F VAL 4.2 6.9 + - - +
94F VAL* 4.0 12.8 - - - +
121F PRO* 5.6 3.0 - - - +
123F TYR* 3.5 27.6 + - - +
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Residues in contact with TRP 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E LEU* 5.9 0.7 - - + -
198E ALA 3.5 1.7 - - - +
199E ASN* 3.5 6.0 - - - +
200E VAL* 2.8 51.6 + - + +
202E PHE* 5.3 4.7 - - + -
220E GLU* 2.7 36.6 + - + +
221E LYS* 1.3 85.6 - - - +
223E VAL* 1.3 73.3 + - - +
224E ILE* 3.8 12.8 - - + -
230E TYR* 3.6 40.5 - + + -
256E ILE* 5.2 1.0 - - - +
94F VAL 4.5 4.9 - - - -
95F GLY* 3.6 23.8 - - - -
96F VAL* 3.8 15.0 - - + -
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Residues in contact with VAL 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E GLU* 3.5 39.5 - - + +
198E ALA 3.6 3.6 - - - +
199E ASN* 3.3 19.1 - - - +
222E TRP* 1.3 82.8 - - - +
224E ILE* 1.3 63.6 + - - +
225E ALA* 4.0 3.1 + - - +
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Residues in contact with ILE 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E LEU* 4.4 9.9 - - + -
190E LEU* 4.2 17.7 - - + +
192E ASN* 2.8 33.8 + - + +
197E GLU* 4.4 2.0 - - - -
198E ALA* 2.9 30.6 + - + +
200E VAL* 4.1 22.2 - - + -
222E TRP* 4.2 13.7 - - + -
223E VAL* 1.3 75.0 - - - +
225E ALA* 1.3 66.0 + - - +
228E ASP* 3.6 31.9 - - + +
229E THR 4.4 1.8 - - - +
230E TYR* 4.1 28.0 - - + +
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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