Contacts of the strand formed by residues 220 - 226 (chain E) in PDB entry 3EBL
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 GLY 220 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192E VAL 3.8 0.2 + - - -
193E PHE* 3.1 19.8 - - - +
194E LEU 2.9 24.8 + - - -
218E VAL* 3.1 6.1 + - - +
219E CYS* 1.3 81.3 - - - +
221E ASN* 1.3 65.6 + - - +
286E ALA* 4.0 3.6 - - - -
287E LYS 3.1 13.5 - - - -
347E PHE* 3.9 6.1 - - - -
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Residues in contact with ASN 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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194E LEU* 3.2 22.4 - - - +
204E ALA 4.3 4.1 + - - -
205E HIS* 4.3 6.3 - - - +
208E ALA* 3.2 31.6 - - - +
218E VAL* 3.8 5.9 - - - +
220E GLY* 1.3 79.5 - - - +
222E ILE* 1.3 60.2 + - - +
223E LEU* 4.0 14.8 - - + +
285E PHE* 3.6 17.8 - - - -
286E ALA* 4.1 6.0 - - - +
287E LYS 2.7 12.4 + - - +
288E SER* 3.5 11.1 + - - +
289E LEU* 2.7 35.0 + - - +
305E TYR* 4.9 2.4 + - - -
347E PHE* 4.0 1.4 - - - -
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Residues in contact with ILE 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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116E ILE* 5.1 6.5 - - + -
141E PHE* 5.4 2.9 - - + -
193E PHE* 4.3 14.6 - - + -
194E LEU 2.9 9.3 + - - -
195E SER* 3.2 42.5 + - - +
196E GLY 3.2 4.9 + - - +
221E ASN* 1.3 76.0 - - - +
223E LEU* 1.3 61.3 + - - +
224E LEU* 4.1 6.6 + - + +
289E LEU* 3.4 11.7 - - + -
291E ILE* 4.2 8.7 - - + -
344E ILE* 4.0 35.9 - - + -
347E PHE* 3.8 22.0 - - + -
348E LEU* 3.9 32.1 - - + -
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Residues in contact with LEU 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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196E GLY 3.7 2.9 - - - +
201E GLY* 3.8 22.7 - - - +
204E ALA* 3.8 17.3 - - + -
205E HIS* 4.7 2.5 - - + +
221E ASN* 4.2 14.4 - - + +
222E ILE* 1.3 87.5 - - - +
224E LEU* 1.3 59.3 + - - +
225E ASN 3.9 0.2 - - - -
226E ALA* 3.8 28.4 + - + -
228E PHE* 4.7 1.6 - - + -
288E SER* 5.9 1.1 - - - +
289E LEU 2.9 15.2 + - - +
290E ILE* 3.6 14.0 - - + +
291E ILE* 2.7 36.1 + - - +
305E TYR* 3.8 36.1 - - + +
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Residues in contact with LEU 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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118E PHE* 5.0 3.8 - - + -
137E LEU* 5.1 5.2 - - + -
141E PHE* 4.3 22.2 - - + -
195E SER* 4.5 11.2 - - - +
196E GLY 3.1 17.4 + - - +
197E ASP* 3.0 35.4 - - + +
198E SER 3.0 1.0 + - - -
222E ILE* 4.6 6.3 - - + -
223E LEU* 1.3 75.4 - - - +
225E ASN* 1.3 70.7 - - - +
226E ALA 3.1 0.2 + - - -
291E ILE* 3.7 29.8 - - + -
329E TYR* 3.8 37.0 - - + -
340E VAL* 4.1 11.7 - - + -
341E MET* 6.1 0.4 - - + -
344E ILE* 4.6 4.0 - - + -
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Residues in contact with ASN 225 (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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198E SER* 3.1 16.4 + - - +
224E LEU* 1.3 73.9 - - - +
226E ALA* 1.3 68.2 + - - +
227E MET* 4.3 0.5 - - - -
291E ILE 2.9 18.2 + - - +
292E VAL* 3.6 1.0 - - - -
293E SER* 2.8 49.4 + - - -
296E ASP* 3.5 21.9 + - - +
302E GLN* 3.0 13.1 + - - +
326E VAL* 3.8 21.6 - - + +
327E GLY 4.2 0.2 - - - +
328E PHE* 4.5 2.8 - - - -
329E TYR* 3.8 20.6 + - + +
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Residues in contact with ALA 226 (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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198E SER 3.7 7.4 - - - -
201E GLY* 4.0 11.9 - - - -
223E LEU* 3.8 29.7 + - + -
224E LEU 3.1 5.3 + - - +
225E ASN* 1.3 77.4 - - - +
227E MET* 1.3 61.9 + - - +
228E PHE* 3.6 28.0 + - + -
290E ILE* 5.9 3.5 - - + +
298E THR* 4.4 2.9 + - - -
302E GLN* 3.5 26.6 + - + +
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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