Contacts of the helix formed by residues 421 - 429 (chain E) in PDB entry 5U8T
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 421 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271E TRP* 3.5 21.8 - - + -
274E ILE* 3.3 33.9 - - + -
275E LEU* 3.7 7.3 - - + +
278E THR* 3.9 12.1 - - + +
409E PHE* 2.9 15.2 + - + +
419E ILE 3.7 1.0 + - - -
420E SER* 1.3 70.6 - - - +
422E SER* 1.3 65.8 + - - +
424E PHE* 3.0 3.8 + - - +
425E VAL* 2.9 25.5 + - - +
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Residues in contact with SER 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E THR* 3.6 18.9 - - - +
281E ASP* 5.6 0.7 - - - -
323E ASP* 4.2 15.5 + - - +
324E TYR 4.9 7.5 + - - -
406E ARG* 5.3 14.6 - - - -
409E PHE 4.8 0.4 + - - -
420E SER* 3.6 15.1 - - - -
421E ALA* 1.3 76.3 - - - +
423E GLU* 1.3 67.1 + - - +
425E VAL* 3.4 5.6 - - - +
426E GLU* 3.0 24.9 - - - +
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Residues in contact with GLU 423 (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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324E TYR 4.2 8.5 + - - +
326E LEU 3.7 12.7 - - - +
328E LEU* 3.0 26.0 + - + +
329E LEU* 3.0 42.1 + - - +
330E ARG* 4.2 10.2 + - + +
331E HIS* 6.0 2.7 - - + +
419E ILE* 3.9 9.9 - - + -
420E SER* 3.5 30.5 + - - +
421E ALA 3.1 0.4 - - - -
422E SER* 1.3 77.2 + - - +
424E PHE* 1.3 62.6 + - - +
425E VAL 3.0 6.3 + - - -
426E GLU* 3.0 24.6 + - - +
427E ALA* 4.2 1.9 + - - +
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Residues in contact with PHE 424 (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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271E TRP* 4.0 16.8 - + + -
275E LEU* 3.4 39.0 - - + -
411E ARG* 6.0 2.9 - - - -
419E ILE* 3.7 19.7 - - + +
420E SER 3.0 9.7 + - - +
421E ALA 3.0 7.7 + - - +
423E GLU* 1.3 78.5 - - - +
425E VAL* 1.3 62.2 - - - +
427E ALA* 3.9 5.5 + - - +
428E LEU* 3.3 34.1 + - + +
483E ALA 3.4 21.8 - - - -
484E LEU* 4.5 11.4 - - + -
486E ASP* 5.5 5.2 - - - -
492E LEU* 3.5 39.0 - - + +
496E ILE* 6.0 1.1 - - + -
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Residues in contact with VAL 425 (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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36E ILE* 5.0 3.8 - - + +
275E LEU* 4.3 10.8 - - + +
278E THR* 3.8 35.9 - - + +
279E SER* 4.1 19.7 - - - +
282E ILE* 5.9 4.3 - - + -
421E ALA 2.9 17.4 + - - +
422E SER 3.4 10.3 - - - +
424E PHE* 1.3 77.4 - - - +
426E GLU* 1.3 80.6 + - - +
428E LEU* 3.0 31.1 + - + +
429E THR* 3.3 17.1 + - + +
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Residues in contact with GLU 426 (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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282E ILE* 4.4 20.9 - - - +
327E PHE* 3.7 35.4 - - + -
328E LEU* 4.7 6.5 - - + +
422E SER 3.0 19.5 - - - +
423E GLU* 3.0 16.7 + - - +
425E VAL* 1.3 90.7 - - - +
427E ALA* 1.3 57.6 + - - +
429E THR* 2.4 38.3 + - - +
430E ALA* 3.0 6.3 + - - +
499E ALA* 4.6 11.5 - - + +
502E LEU* 5.2 0.2 - - - +
503E GLN* 5.5 0.3 - - - +
547E ARG* 5.1 10.6 + - - +
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Residues in contact with ALA 427 (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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423E GLU 4.2 2.3 + - - +
424E PHE* 3.9 4.6 + - - +
425E VAL 3.4 0.6 - - - -
426E GLU* 1.3 75.8 - - - +
428E LEU* 1.3 64.8 + - - +
430E ALA* 3.0 16.8 + - - +
431E LEU* 3.1 17.0 - - + +
492E LEU* 4.1 15.7 - - + +
495E GLY 3.4 9.4 - - - +
496E ILE* 3.4 44.9 - - + +
499E ALA* 5.0 1.7 - - + +
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Residues in contact with LEU 428 (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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36E ILE* 5.0 20.0 - - + -
39E LEU* 6.0 3.1 - - + -
40E CYS* 5.9 2.5 - - - -
275E LEU* 4.8 11.4 - - + +
424E PHE* 3.3 47.6 - - + +
425E VAL* 3.0 21.2 + - + +
427E ALA* 1.3 78.4 - - - +
429E THR* 1.3 59.3 + - + +
430E ALA 3.2 0.9 + - - -
431E LEU* 3.5 6.1 + - - -
432E LEU* 3.2 20.3 - - - +
480E SER* 3.3 35.5 + - - +
483E ALA* 4.2 16.4 - - + +
484E LEU* 4.5 7.0 - - + +
492E LEU* 5.4 2.2 - - + +
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Residues in contact with THR 429 (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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36E ILE* 3.6 28.5 - - + -
425E VAL* 3.4 23.6 - - + +
426E GLU* 2.4 28.8 + - - +
428E LEU* 1.3 74.6 - - - +
430E ALA* 1.3 52.5 + - - +
431E LEU 3.5 0.2 - - - -
432E LEU* 3.4 17.2 - - + +
433E GLU* 2.6 29.1 - - - +
543E LEU* 4.8 4.9 - - + +
547E ARG* 3.9 28.7 + - - -
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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