Contacts of the strand formed by residues 246 - 250 (chain E) in PDB entry 5IJ7
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 LEU 246 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E MET* 4.3 5.4 - - + -
239E SER 3.1 6.1 - - - +
240E CYS* 3.7 15.5 - - + -
244E HIS 4.6 3.8 - - - +
245E SER* 1.3 75.0 - - - +
247E LYS* 1.3 60.7 + - - +
285E PHE* 4.2 2.8 - - - +
286E SER* 3.4 2.8 - - - -
287E THR* 3.0 35.0 + - + +
288E ARG* 6.2 0.2 - - - -
290E ILE* 4.1 14.4 - - + +
291E HIS* 4.1 22.0 - - - +
295E VAL* 4.1 7.9 - - + -
298E VAL* 3.6 30.5 - - + -
307E SER* 3.7 17.3 - - - +
317E TRP* 3.8 31.6 - - + -
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Residues in contact with LYS 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E GLU* 3.2 23.3 + - - +
220E GLY 3.5 21.9 + - - -
221E HIS* 3.7 29.8 - - + +
222E ARG* 6.2 0.2 - - - +
238E MET* 3.3 8.6 - - - +
239E SER* 2.8 43.7 + - - +
243E ASP* 4.1 2.2 + - - -
245E SER* 3.7 14.1 + - - +
246E LEU* 1.3 74.6 - - - +
248E LEU* 1.3 59.4 + - - +
249E TRP* 3.6 29.6 - - + +
283E PRO* 3.9 8.3 - - + -
285E PHE 3.5 5.2 - - - +
286E SER* 2.9 34.0 + - - +
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Residues in contact with LEU 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E LYS* 3.7 17.7 - - + -
237E ILE 3.4 15.9 - - - +
238E MET* 3.8 13.0 - - + -
247E LYS* 1.3 71.3 - - - +
249E TRP* 1.3 58.2 + - - +
250E ARG* 4.0 32.3 - - + +
283E PRO* 3.4 4.9 - - - +
284E ASP* 2.6 40.5 + - + -
285E PHE* 2.9 30.2 + - + -
300E TRP* 3.5 30.7 - - + -
319E PRO* 5.4 0.7 - - + -
326E ILE* 4.3 16.6 - - + -
329E ILE* 5.2 1.6 - - + -
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Residues in contact with TRP 249 (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 LEU* 4.1 15.5 - - + +
215E PHE* 3.6 52.9 - + + -
216E GLY 4.0 0.2 - - - -
220E GLY* 3.8 23.3 - - - -
221E HIS* 4.3 3.6 - + - -
236E LYS* 3.5 1.5 - - - -
237E ILE* 2.8 58.8 + - + +
239E SER* 2.8 27.8 + - - -
247E LYS* 3.6 38.3 - - + +
248E LEU* 1.3 72.0 - - - +
250E ARG* 1.3 61.9 + - - +
251E ILE* 3.7 1.7 + - - +
280E ILE* 3.5 28.3 - - + -
282E PHE 4.0 2.5 - - - -
283E PRO* 3.8 29.2 - - + -
284E ASP* 3.9 3.8 - - - -
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Residues in contact with ARG 250 (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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215E PHE* 5.0 2.1 - - - -
235E GLU 3.9 3.6 - - - -
236E LYS* 4.1 15.5 - - + +
248E LEU* 4.0 17.4 - - + +
249E TRP* 1.3 72.5 - - - +
251E ILE* 1.3 64.9 + - - +
252E ASN* 3.5 18.2 - - - +
253E SER* 4.1 13.5 + - - -
256E MET* 3.7 12.8 - - - +
284E ASP* 3.0 50.5 + - + +
326E ILE* 2.6 33.5 + - - +
327E ASP* 3.7 21.9 + - - +
329E ILE* 3.1 26.1 + - - +
330E LYS 5.6 0.2 - - - -
331E PRO* 5.7 1.8 - - - +
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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