Contacts of the strand formed by residues 377 - 382 (chain E) in PDB entry 5FXY
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 ILE 377 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E PHE* 5.4 1.4 - - - +
322E GLN* 6.1 0.2 - - - +
336E SER* 3.8 23.8 + - - +
337E GLY* 3.1 26.7 + - - +
339E ASP 4.2 3.1 + - - +
340E ARG 3.5 26.2 - - - +
341E ARG 4.1 2.2 - - - +
342E LEU* 3.7 32.5 - - + +
370E HIS* 5.0 0.4 - - + -
373E HIS* 3.9 23.1 - - + -
375E ALA 4.0 6.3 - - - +
376E LYS* 1.3 74.3 + - - +
378E SER* 1.3 62.7 + - - +
379E ASP 3.9 13.2 - - - +
392E SER* 4.3 10.8 - - - -
393E VAL 3.2 17.5 - - - +
394E SER* 4.1 1.1 - - - +
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Residues in contact with SER 378 (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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44E SER 3.7 12.0 + - - -
45E LEU* 3.7 41.7 - - - +
129E ARG* 5.5 3.8 + - - -
181E TYR* 6.1 2.0 - - - -
321E PHE* 5.2 6.9 - - - +
322E GLN* 4.8 8.1 - - - +
336E SER* 5.3 0.4 - - - -
376E LYS* 3.5 11.6 + - - +
377E ILE* 1.3 74.5 - - - +
379E ASP* 1.3 62.8 + - - +
393E VAL 3.1 7.4 + - - -
394E SER 4.1 0.3 - - - -
395E GLU* 3.7 27.7 + - - +
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Residues in contact with ASP 379 (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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45E LEU 3.4 15.9 - - - +
46E THR* 3.6 11.1 + - - -
47E ALA* 3.2 23.4 + - - +
129E ARG* 4.9 5.5 + - - +
131E ARG* 3.0 21.4 + - - -
322E GLN* 2.7 35.3 + - - -
336E SER* 5.0 0.2 - - - -
377E ILE* 3.6 4.8 - - - +
378E SER* 1.3 82.9 - - - +
380E PHE* 1.3 83.1 + - - +
392E SER* 3.7 0.2 - - - -
393E VAL* 3.1 30.8 + - + +
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Residues in contact with PHE 380 (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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47E ALA* 4.0 5.8 - - - +
131E ARG* 5.5 0.2 + - - -
322E GLN* 3.6 22.9 - - + -
324E GLN* 3.7 29.0 + - + +
334E ALA* 3.6 43.5 - - + -
335E SER* 4.1 1.8 - - - -
336E SER* 3.3 33.0 - - - -
342E LEU* 3.5 10.5 - - + -
377E ILE* 4.9 0.4 - - + -
379E ASP* 1.3 89.3 + - - +
381E SER* 1.3 67.3 + - - +
382E TRP* 3.7 15.5 - + - -
390E ILE* 3.6 17.5 - - + -
391E CYS 3.2 14.1 - - - +
392E SER* 3.7 16.2 - - - -
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Residues in contact with SER 381 (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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47E ALA* 3.5 19.1 - - - -
48E GLN* 3.6 18.2 - - - +
49E TRP* 3.0 23.9 + - - +
324E GLN* 5.2 4.0 - - - -
380E PHE* 1.3 84.4 - - - +
382E TRP* 1.3 69.3 + - - +
390E ILE* 3.6 1.3 - - - -
391E CYS* 2.9 32.0 + - - -
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Residues in contact with TRP 382 (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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49E TRP* 3.2 10.8 - - - +
324E GLN* 3.3 32.9 + - + +
325E TRP 3.5 15.0 + - - -
326E SER* 3.8 23.8 - - - -
327E PRO* 3.3 24.8 - - + +
328E HIS* 6.2 0.4 - - - -
332E ILE* 3.7 25.4 - - + -
333E LEU 4.2 0.7 - - - -
334E ALA* 3.6 26.9 - - + -
344E VAL* 4.0 9.4 - - + -
380E PHE* 3.7 12.5 - + - -
381E SER* 1.3 77.4 + - - +
383E ASN* 1.3 63.9 + - - +
384E PRO* 3.5 6.2 - - - +
388E TRP* 4.1 33.7 - + - -
389E VAL 3.7 8.5 - - - -
390E ILE* 3.7 32.3 - - + +
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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