Contacts of the strand formed by residues 313 - 319 (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 ALA 313 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E HIS* 4.5 2.3 + - - -
307E SER 4.0 0.2 - - - +
308E LYS* 3.5 15.2 - - - +
309E SER 4.3 3.6 + - - +
311E GLU* 3.3 11.6 + - + +
312E ASN* 1.3 78.9 - - - +
314E ILE* 1.4 59.8 + - - +
315E VAL* 3.9 9.7 + - + +
341E ARG* 3.8 20.0 - - + -
342E PHE 3.2 9.4 - - - +
343E ASP* 3.6 18.8 - - - +
344E TYR* 3.2 15.7 + - - -
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Residues in contact with ILE 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E LEU* 3.9 30.5 - - + -
307E SER 3.5 14.6 - - - +
308E LYS* 4.0 7.0 - - + -
313E ALA* 1.4 71.2 - - - +
315E VAL* 1.3 61.2 + - - +
341E ARG* 3.2 4.7 - - - +
342E PHE* 2.8 44.7 + - + -
344E TYR* 3.8 10.5 - - + +
354E PHE* 3.9 34.3 - - + -
363E LEU* 4.0 10.8 - - + -
365E LEU* 3.8 22.2 - - + -
375E TRP* 3.9 21.8 - - + -
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Residues in contact with VAL 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E ILE* 3.7 26.5 - - + +
291E HIS* 3.6 29.6 - - + +
305E ILE 3.4 4.0 - - - +
306E LEU* 3.4 2.2 - - - -
307E SER 2.8 29.8 + - - -
311E GLU* 5.5 1.3 - - - +
313E ALA* 4.5 9.6 - - + +
314E ILE* 1.3 75.9 - - - +
316E CYS* 1.3 63.5 + - - +
317E TRP* 3.6 5.5 - - + -
338E ILE* 3.9 31.0 - - + -
340E GLY 3.8 3.4 - - - +
341E ARG* 4.3 12.1 - - + -
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Residues in contact with CYS 316 (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* 3.5 37.2 - - + -
301E LEU* 4.5 2.7 - - - -
304E LEU* 4.1 20.6 - - - -
305E ILE 3.3 9.2 - - - -
306E LEU* 3.8 19.7 - - + -
314E ILE 4.0 1.2 + - - -
315E VAL* 1.3 70.9 - - - +
317E TRP* 1.3 64.4 + - - +
338E ILE* 3.7 1.9 - - - -
339E LEU* 2.8 25.8 + - - -
340E GLY 2.8 23.1 + - - +
342E PHE* 4.4 7.4 - - + -
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Residues in contact with TRP 317 (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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238E MET* 4.6 7.6 - - + -
246E LEU* 3.8 26.9 - - + -
285E PHE* 3.8 20.4 - + - -
287E THR* 3.8 14.8 - - + -
290E ILE* 3.6 39.0 - - + +
304E LEU* 3.7 3.5 - - - +
305E ILE* 2.8 72.1 + - + +
307E SER* 3.1 18.2 + - - -
315E VAL* 3.6 12.8 - - + -
316E CYS* 1.3 77.0 - - - +
318E LYS* 1.3 83.1 + - - +
319E PRO* 3.7 17.7 - - + -
336E VAL* 4.0 7.9 - - + -
337E THR 3.2 13.9 - - - +
338E ILE* 4.0 10.1 - - + -
339E LEU* 4.1 6.1 - - - +
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Residues in contact with LYS 318 (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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41A MET* 3.4 35.2 - - + -
303E ASP 4.7 5.2 - - - +
304E LEU* 4.0 17.5 - - + -
305E ILE* 4.5 0.4 - - - -
317E TRP* 1.3 83.8 - - - +
319E PRO* 1.4 87.8 + - + +
321E LYS 2.8 20.9 + - - +
322E MET* 3.2 18.8 - - - +
324E ASP 2.7 28.4 + - - -
326E ILE 5.9 0.4 - - - +
329E ILE* 5.0 0.2 - - - +
336E VAL* 3.6 3.1 - - - -
337E THR* 2.9 42.5 + - - +
339E LEU* 4.3 3.8 - - + -
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Residues in contact with PRO 319 (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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238E MET* 4.6 4.7 - - + -
248E LEU* 5.4 0.7 - - + -
285E PHE* 3.6 47.1 - - + -
303E ASP 4.8 1.3 - - - +
305E ILE* 3.7 19.7 - - + -
317E TRP* 3.7 5.6 - - + -
318E LYS* 1.4 108.7 + - + +
320E GLY* 1.3 58.0 + - - +
326E ILE* 3.5 26.0 - - + -
329E ILE* 3.4 23.9 - - + +
335E ASN 4.1 0.4 - - - +
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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
------------------------------------------------------------
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