Contacts of the strand formed by residues 336 - 343 (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 VAL 336 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285E PHE* 3.6 17.5 - - + -
287E THR* 3.5 27.8 - - + +
289E ASP* 4.3 19.5 - - + +
290E ILE* 3.7 30.7 - - + -
317E TRP* 4.0 6.3 - - + -
318E LYS 3.6 4.0 - - - +
320E GLY 3.4 8.7 - - - -
334E SER 5.5 2.0 - - - +
335E ASN* 1.3 80.5 + - - +
337E THR* 1.3 58.8 + - - +
338E ILE* 4.2 8.9 + - + +
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Residues in contact with THR 337 (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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34A ARG* 4.2 10.5 - - - +
317E TRP* 3.2 4.4 - - - -
318E LYS* 2.9 44.1 + - + -
320E GLY 2.7 21.6 + - - -
321E LYS* 3.2 3.3 - - - -
322E MET* 3.1 55.8 + - + +
336E VAL* 1.3 71.7 + - - +
338E ILE* 1.3 63.5 + - - +
339E LEU* 3.5 9.5 + - + +
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Residues in contact with ILE 338 (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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34A ARG* 2.5 33.2 + - - +
289E ASP 4.4 11.4 - - - +
290E ILE* 4.2 20.4 - - + +
315E VAL* 3.9 31.9 - - + -
316E CYS 3.8 2.7 - - - -
317E TRP* 4.0 6.3 - - + -
336E VAL* 4.6 8.3 - - + +
337E THR* 1.3 71.9 - - - +
339E LEU* 1.3 58.3 + - - +
340E GLY* 3.9 14.8 - - - +
341E ARG* 5.7 1.8 - - + -
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Residues in contact with LEU 339 (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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34A ARG* 4.9 0.7 + - - -
38A VAL* 3.5 31.9 - - + +
41A MET* 3.7 33.4 - - + -
42A PHE* 3.9 26.2 - - + -
304E LEU* 3.8 39.0 - - + -
316E CYS* 2.8 16.7 + - - +
317E TRP* 4.5 4.9 - - - -
318E LYS* 4.3 3.1 - - + -
322E MET* 3.9 5.2 - - - -
337E THR* 3.5 27.6 + - + +
338E ILE* 1.3 72.7 - - - +
340E GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 340 (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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42A PHE* 5.8 2.0 - - - -
315E VAL* 3.7 4.3 - - - +
316E CYS* 2.8 36.1 + - - +
338E ILE* 3.5 8.9 - - - +
339E LEU* 1.3 80.2 - - - +
341E ARG* 1.3 59.1 + - - +
342E PHE* 5.6 0.9 - - - -
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Residues in contact with ARG 341 (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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313E ALA* 3.8 13.5 - - + -
314E ILE 3.2 13.2 - - - +
315E VAL* 4.3 11.9 - - + -
338E ILE* 5.7 1.6 - - + -
340E GLY* 1.3 74.0 - - - +
342E PHE* 1.3 67.6 + - - +
343E ASP* 2.9 42.6 + - - +
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Residues in contact with PHE 342 (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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42A PHE* 5.5 10.5 - + - -
301E LEU* 5.8 0.7 - - + -
306E LEU* 3.8 22.2 - - + -
313E ALA* 3.2 4.9 - - - -
314E ILE* 2.8 57.2 + - + +
316E CYS* 4.4 11.9 - - + -
340E GLY 5.7 0.4 - - - -
341E ARG* 1.3 76.0 - - - +
343E ASP* 1.3 61.3 + - - +
344E TYR* 3.4 6.0 - - - -
363E LEU* 4.4 5.6 - - + -
375E TRP* 3.6 46.7 - + + +
376E ASP 5.4 1.6 - - - -
377E LEU* 3.6 28.7 - - + -
379E VAL* 5.1 15.0 - - + -
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Residues in contact with ASP 343 (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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312E ASN 3.9 5.1 - - - +
313E ALA* 3.6 8.7 - - - +
341E ARG* 2.9 49.7 + - - +
342E PHE* 1.3 73.4 - - - +
344E TYR* 1.3 63.2 + - - +
373E TYR* 5.1 0.7 - - - -
375E TRP* 3.5 16.0 + - - +
387E CYS* 5.1 3.5 - - - -
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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