Contacts of the strand formed by residues 296 - 307 (chain E) in PDB entry 3EI4
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 THR 296 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226E PHE* 5.7 3.6 - - - -
244E LYS* 3.2 33.9 + - - +
287E LYS* 4.2 1.7 - - - -
288E GLU* 2.9 56.8 + - + +
290E GLN* 3.4 25.8 - - - +
294E THR 3.4 2.4 + - - -
295E VAL* 1.3 74.7 - - - +
297E LEU* 1.3 61.9 + - - +
298E LYS* 5.6 0.2 - - - -
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Residues in contact with LEU 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E PHE* 4.6 18.9 - - + -
239E TYR* 3.7 38.6 - - + -
244E LYS* 5.2 11.5 - - + +
246E LEU* 4.0 20.0 - - + +
285E LEU* 3.8 20.9 - - + -
286E GLU 3.6 19.1 - - - +
287E LYS* 5.3 0.2 - - - +
296E THR* 1.3 80.9 + - - +
298E LYS* 1.3 62.3 + - - +
299E ASP 3.4 20.6 - - - +
300E LEU* 3.5 24.9 - - + -
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Residues in contact with LYS 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E LEU* 3.3 16.3 - - - +
286E GLU* 2.8 36.5 + - + +
287E LYS 5.3 1.8 - - - +
288E GLU* 3.6 43.0 + - + +
296E THR* 3.5 2.4 + - - -
297E LEU* 1.3 73.6 - - - +
299E ASP* 1.3 67.1 + - + +
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Residues in contact with ASP 299 (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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246E LEU* 3.8 17.6 - - - +
248E ILE* 4.5 8.0 - - - +
285E LEU 3.8 0.2 - - - -
286E GLU* 2.9 45.2 + - + +
297E LEU* 3.4 11.3 - - - +
298E LYS* 1.3 90.7 - - + +
300E LEU* 1.3 84.1 + - - +
301E ARG* 4.9 3.3 - - - +
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Residues in contact with LEU 300 (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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230E ILE* 5.0 2.9 - - + -
237E ILE* 3.6 35.9 - - + +
238E THR 4.3 1.1 - - - -
239E TYR* 4.1 12.1 - - + +
246E LEU* 4.0 20.8 - - + +
247E ALA* 4.5 0.7 - - - -
248E ILE* 3.4 35.8 - - + +
283E LEU* 5.2 6.5 - - + -
284E LEU 3.5 4.9 - - - +
285E LEU* 3.8 20.0 - - + -
286E GLU* 4.9 0.4 - - - -
297E LEU* 3.5 31.9 - - + -
299E ASP* 1.3 92.6 + - - +
301E ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 301 (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 ILE* 4.2 3.1 - - - -
282E MET 3.7 0.5 - - - +
283E LEU* 3.7 1.3 - - - +
284E LEU* 2.8 70.7 + - + +
286E GLU* 3.6 20.4 + - - +
299E ASP* 4.9 4.3 - - - +
300E LEU* 1.3 76.7 - - - +
302E VAL* 1.3 75.0 + - - +
303E GLU* 5.5 8.3 - - - +
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Residues in contact with VAL 302 (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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237E ILE* 3.6 20.2 - - + -
248E ILE* 3.7 6.9 - - + +
250E PRO* 3.6 35.0 - - + +
253E ILE* 5.2 4.0 - - + -
273E LEU* 4.5 8.1 - - + -
281E PHE* 3.9 28.0 - - + -
282E MET 3.3 16.2 - - - +
283E LEU* 4.0 12.3 - - + +
301E ARG* 1.3 87.0 - - - +
303E GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 303 (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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281E PHE* 4.0 3.6 - - - -
282E MET* 2.9 35.5 + - + +
301E ARG* 5.5 10.3 - - - +
302E VAL* 1.3 76.0 - - - +
304E LEU* 1.3 76.8 + - - +
305E LEU* 3.4 22.2 + - + +
346E TYR* 3.2 30.0 + - - -
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Residues in contact with LEU 304 (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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252E ILE* 4.9 16.5 - - + +
279E ARG* 3.8 34.5 - - + +
280E LEU 3.8 0.7 - - - +
281E PHE* 3.5 25.2 - - + -
303E GLU* 1.3 84.4 - - - +
305E LEU* 1.3 61.4 + - - +
306E GLY* 3.8 20.9 - - - +
344E GLY 4.9 8.2 - - - +
346E TYR* 4.2 5.7 - - - -
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Residues in contact with LEU 305 (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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272E LEU* 4.0 16.8 - - + -
280E LEU* 2.8 14.7 + - + +
281E PHE 4.0 4.5 - - - -
282E MET* 3.6 40.8 - - + +
303E GLU* 3.5 35.9 - - - +
304E LEU* 1.3 77.2 - - - +
306E GLY* 1.3 57.6 + - - +
336E LEU* 4.2 15.5 - - + -
337E ASN 5.8 1.1 - - - +
344E GLY 3.8 3.2 - - - +
346E TYR* 3.0 51.0 + - + +
347E VAL* 3.4 15.1 - - + +
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Residues in contact with GLY 306 (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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279E ARG* 3.8 2.7 - - - +
280E LEU* 2.8 30.0 + - - +
304E LEU* 3.6 18.3 - - - +
305E LEU* 1.3 81.0 - - - +
307E GLU* 1.3 59.9 + - - -
344E GLY 5.1 2.2 - - - -
345E SER* 5.2 5.2 - - - -
346E TYR 5.2 0.2 - - - -
347E VAL* 3.8 9.2 - - - +
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Residues in contact with GLU 307 (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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277E GLU 4.7 2.6 - - - +
278E GLY 3.2 14.3 - - - +
279E ARG* 4.7 5.4 - - + -
306E GLY* 1.3 72.1 - - - -
308E THR* 1.3 58.1 - - - +
345E SER* 5.7 0.6 + - - -
347E VAL* 4.5 13.6 - - - +
383E LYS* 3.2 37.9 + - - +
753E ARG* 4.2 14.6 + - - -
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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