Contacts of the strand formed by residues 261 - 270 (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 ARG 261 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E GLU* 4.6 8.6 + - - +
161E LEU* 3.9 2.1 - - - +
203E TRP* 4.5 2.5 - - - -
252E GLN* 3.2 33.2 + - + +
253E VAL 3.4 9.9 - - - +
254E VAL* 3.9 23.1 - - + +
259E GLY 3.4 5.3 + - - +
260E GLU* 1.3 76.6 - - - +
262E VAL* 1.3 72.5 + - - +
263E GLU* 3.2 25.4 + - - +
84F GLU* 2.5 46.7 + - - +
85F GLY 3.9 2.4 + - - -
86F ILE* 3.4 24.7 - - - +
124F MET* 5.7 1.3 - - - -
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Residues in contact with VAL 262 (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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159E PRO* 3.7 26.7 - - + -
160E GLU 4.1 14.4 - - - +
161E LEU* 3.7 16.8 - - + -
166E ILE* 3.9 34.5 - - + -
252E GLN* 3.4 5.4 - - - +
253E VAL* 2.9 36.8 + - + +
261E ARG* 1.3 78.6 - - - +
263E GLU* 1.3 66.6 + - - +
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Residues in contact with GLU 263 (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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83E PRO* 5.8 2.9 - - - -
84E GLU 4.2 13.5 + - - -
85E GLY 4.8 0.9 + - - -
159E PRO* 3.5 18.7 - - - +
166E ILE* 5.8 1.8 - - - -
250E ASN* 3.0 18.6 - - - +
251E ALA 3.3 5.8 - - - +
252E GLN* 3.5 24.7 - - + +
261E ARG* 3.2 23.3 + - - +
262E VAL* 1.3 81.6 - - - +
264E GLN* 1.3 64.9 + - - +
265E SER* 5.0 0.7 - - - +
1272E O4B 3.6 17.0 - - - +
84F GLU 4.1 5.4 - - - +
85F GLY* 3.6 11.0 - - - +
87F TYR* 5.9 0.2 - - - -
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Residues in contact with GLN 264 (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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128E LYS* 5.8 5.7 - - - +
158E LEU* 5.0 4.4 - - - +
159E PRO* 3.7 21.8 - - + +
166E ILE* 3.6 17.7 - - + +
167E ASP* 4.2 1.8 - - - +
168E ILE* 3.4 52.5 + - + +
249E ILE 4.0 0.3 - - - +
250E ASN* 3.6 0.7 - - - +
251E ALA* 2.8 35.8 + - - +
263E GLU* 1.3 75.3 - - - +
265E SER* 1.3 73.5 + - - +
266E MET* 4.1 4.6 - - + +
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Residues in contact with SER 265 (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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248E THR* 4.3 4.5 - - - -
249E ILE 3.2 8.3 - - - -
250E ASN* 2.8 25.5 + - - -
263E GLU* 4.2 1.9 + - - +
264E GLN* 1.3 78.1 - - - +
266E MET* 1.3 70.6 + - - +
1272E O4B 3.1 44.3 + - - +
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Residues in contact with MET 266 (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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168E ILE* 3.7 46.0 - - + +
169E LYS* 5.2 0.2 - - - -
170E ASN* 4.0 16.6 - - + +
186E PHE* 4.0 27.4 - - + -
204E MET* 5.2 0.4 - - + -
248E THR* 3.5 3.8 - - - -
249E ILE* 2.6 64.3 + - + +
251E ALA 5.1 1.3 - - - +
264E GLN* 4.1 8.3 - - + +
265E SER* 1.3 85.6 - - - +
267E THR* 1.3 64.4 + - - +
268E VAL* 5.7 0.2 - - + -
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Residues in contact with THR 267 (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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170E ASN* 5.1 1.4 - - - +
175E ASN* 4.2 17.2 + - - +
246E GLU* 4.1 24.1 + - - +
247E TYR 3.4 8.7 + - - -
248E THR* 4.8 7.2 - - - -
266E MET* 1.3 79.1 - - - +
268E VAL* 1.3 70.0 + - - +
269E VAL* 5.0 4.7 - - - +
1272E O4B 5.0 16.8 - - - -
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Residues in contact with VAL 268 (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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170E ASN* 4.3 2.2 - - - +
174E ILE 4.2 14.1 - - - +
175E ASN 3.7 8.7 - - - +
176E SER* 4.3 7.9 - - - -
177E VAL* 4.7 2.0 - - + +
184E VAL* 4.4 11.0 - - + -
186E PHE* 4.1 15.7 - - + -
238E PHE* 3.7 35.4 - - + -
247E TYR* 2.7 47.7 + - - +
249E ILE* 4.0 18.2 - - + -
266E MET* 4.1 0.4 + - + -
267E THR* 1.3 81.6 - - - +
269E VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 269 (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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175E ASN* 3.1 15.8 + - + +
176E SER* 3.1 13.8 - - - -
177E VAL* 3.0 24.1 + - - -
245E GLY* 3.3 14.6 - - - +
246E GLU* 4.5 11.4 - - + +
267E THR* 5.0 6.7 - - - +
268E VAL* 1.3 78.3 - - - +
270E LYS* 1.3 70.4 + - - +
271E LYS* 4.2 14.1 - - + +
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Residues in contact with LYS 270 (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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177E VAL* 3.6 15.0 - - + -
178E GLU 4.0 13.2 - - - +
179E SER* 2.8 31.6 + - - +
181E GLY* 4.6 0.7 - - - -
238E PHE* 4.6 11.4 - - + -
239E ASP 3.3 21.1 - - - -
240E LYS* 3.0 8.4 + - - +
242E TYR* 2.6 37.2 + - + +
243E PRO 3.7 9.5 - - - +
244E ALA* 3.7 2.2 - - - +
245E GLY* 2.7 36.2 + - - +
247E TYR* 3.8 21.6 - - + -
268E VAL 4.1 0.6 + - - -
269E VAL* 1.3 74.0 - - - +
271E LYS* 1.3 71.0 + - - +
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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