Contacts of the helix formed by residues 430 - 439 (chain A) in PDB entry 5LLU
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 THR 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A GLU* 2.9 23.5 + - - +
416A ALA* 3.8 20.7 - - - +
419A GLY 4.6 2.9 - - - +
420A ALA* 3.8 32.3 - - - +
421A ALA 5.3 0.4 - - - +
426A ALA* 2.7 23.1 + - + +
427A GLY* 3.4 1.4 + - - -
429A VAL* 1.4 78.3 - - + +
431A MET* 1.3 57.8 + - - +
432A VAL 3.1 6.5 + - - -
433A ILE* 3.4 31.1 + - + +
434A VAL 4.1 1.0 + - - -
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Residues in contact with MET 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A TYR* 4.1 22.4 - - - -
386A GLU* 3.3 21.8 - - - +
389A ALA* 3.6 43.1 - - + +
390A ALA 4.8 1.1 - - - +
393A ILE* 5.0 5.8 - - + -
427A GLY 3.5 6.6 + - - +
428A LEU* 3.4 18.2 - - - +
429A VAL 3.3 0.8 - - - -
430A THR* 1.3 74.8 - - - +
432A VAL* 1.3 57.2 + - - +
433A ILE 3.3 0.2 - - - -
434A VAL* 3.4 12.1 - - + +
435A LEU* 3.0 43.6 + - + +
445A ILE* 3.8 31.6 - - + -
448A ILE* 4.7 8.7 - - + -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU 5.8 0.4 - - - -
172A VAL* 3.8 28.0 - - + +
175A CYS* 5.0 8.3 - - - -
428A LEU 4.8 0.2 - - - +
429A VAL* 3.3 22.7 - - + +
430A THR 3.1 0.2 - - - -
431A MET* 1.3 77.0 - - - +
433A ILE* 1.3 58.9 + - + +
435A LEU 3.5 0.2 + - - -
436A THR* 2.7 36.4 + - - -
442A THR* 3.8 24.6 - - + +
445A ILE* 3.8 18.4 - - + -
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.8 17.7 - - + +
175A CYS* 3.8 34.3 - - + -
176A PHE* 4.6 25.6 - - + -
412A THR* 4.3 27.8 - - + +
415A ALA* 5.4 4.0 - - + -
416A ALA* 4.7 8.3 - - + +
429A VAL 5.0 0.7 - - - +
430A THR* 3.4 27.5 + - + +
431A MET 3.3 0.4 - - - -
432A VAL* 1.3 78.8 - - + +
434A VAL* 1.4 57.0 + - - +
436A THR* 4.1 1.2 - - - -
437A ALA* 3.2 30.0 + - - +
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLU* 3.6 25.8 - - + +
390A ALA* 4.1 17.7 - - + +
409A ILE* 3.8 31.7 - - + +
412A THR* 3.4 24.5 - - - +
413A ALA* 3.9 17.5 - - + +
416A ALA* 5.2 0.9 - - + -
430A THR 4.1 1.5 + - - +
431A MET* 3.4 22.4 - - + +
433A ILE* 1.4 78.5 - - - +
435A LEU* 1.4 59.9 + - + +
437A ALA* 4.0 1.7 + - - +
438A VAL* 3.4 21.7 + - - +
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ALA* 4.2 17.3 - - + -
393A ILE* 3.7 33.2 - - + -
431A MET* 3.0 26.4 + - + +
432A VAL 4.0 2.7 - - - +
433A ILE 3.3 0.2 - - - -
434A VAL* 1.4 76.1 - - + +
436A THR* 1.3 59.2 + - - +
437A ALA 3.3 0.4 - - - -
438A VAL* 3.4 2.6 - - - +
439A GLY 3.0 8.1 + - - -
440A LEU* 2.9 50.4 + - + +
441A PRO 3.5 19.5 - - - +
442A THR* 3.8 16.2 - - + -
444A ASP* 5.0 0.7 - - + -
445A ILE* 3.9 25.4 - - + +
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Residues in contact with THR 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.5 30.1 - - + +
432A VAL 2.7 22.5 + - - -
433A ILE 4.3 2.5 - - - -
435A LEU* 1.3 73.3 - - - +
437A ALA* 1.4 64.0 + - - +
439A GLY* 3.5 11.6 + - - +
440A LEU 4.4 4.0 - - - -
442A THR* 3.4 15.9 - - - +
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Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A GLN* 6.0 0.5 - - - +
408A THR* 4.9 15.1 + - - +
409A ILE* 6.3 0.2 - - - -
412A THR* 3.7 32.8 - - + +
433A ILE 3.2 18.5 + - - +
434A VAL 4.0 2.2 - - - +
435A LEU 3.3 0.2 - - - -
436A THR* 1.4 77.8 - - - +
438A VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ALA* 5.6 1.8 - - + -
405A GLN* 4.5 16.2 - - + +
406A ILE* 6.1 0.4 - - + -
408A THR* 4.7 6.2 + - - +
409A ILE* 3.8 37.2 - - + -
434A VAL 3.4 12.8 + - - +
435A LEU* 3.4 13.9 - - + +
437A ALA* 1.3 78.4 - - - +
439A GLY* 1.3 59.2 + - - +
440A LEU* 3.7 29.4 - - + -
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Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A LEU 3.0 6.2 + - - -
436A THR* 3.5 9.4 + - - -
437A ALA 3.5 2.0 - - - -
438A VAL* 1.3 78.8 - - - +
440A LEU* 1.3 65.6 + - - +
441A PRO* 3.9 1.2 - - - +
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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