Contacts of the strand formed by residues 424 - 428 (chain E) in PDB entry 5LS6
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 424 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E PHE* 3.9 19.7 - - + -
111E LEU* 3.6 19.5 - - + -
126E CYS* 3.5 34.5 - - + -
418E PHE* 3.5 11.6 - - - -
419E SER* 3.3 28.1 + - - +
422E SER 3.7 2.3 - - - +
423E SER* 1.3 87.3 + - - +
425E LEU* 1.3 68.7 + - - +
426E ILE* 4.1 4.3 - - + -
436E ARG* 3.8 34.8 - - + +
437E TRP 3.8 2.5 - - - -
438E ASP* 3.7 17.0 - - - +
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Residues in contact with LEU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E PHE* 3.8 26.0 - - + -
378E ALA* 4.1 2.9 - - + -
386E LEU* 4.7 15.5 - - + -
388E VAL* 3.6 30.5 - - + -
404E LEU* 5.1 2.5 - - + -
416E THR* 4.0 18.6 - - + -
417E SER 3.7 8.7 - - - +
418E PHE* 3.9 22.0 - - + -
424E ILE* 1.3 75.2 - - - +
426E ILE* 1.3 73.6 + - - +
435E TRP 3.5 2.9 - - - +
437E TRP* 3.0 43.3 + - + +
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Residues in contact with ILE 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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99E VAL* 3.9 26.5 - - + -
101E PHE* 3.4 24.5 - - + -
113E PHE* 3.3 33.0 - - + -
126E CYS* 4.4 1.8 - - - -
132E ILE* 4.5 2.0 - - + -
416E THR* 3.4 2.9 - - - -
417E SER* 2.9 37.5 + - - +
424E ILE* 4.1 6.7 - - + -
425E LEU* 1.3 77.0 - - - +
427E ALA* 1.3 64.8 + - - +
428E VAL* 4.3 0.7 - - + -
434E ILE* 3.6 24.9 - - + -
435E TRP 3.3 1.8 - - - +
436E ARG* 3.9 28.7 - - + -
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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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386E LEU* 3.7 26.9 - - + -
413E ILE* 3.7 22.4 - - + -
415E GLN 3.6 7.0 - - - -
416E THR* 4.2 6.1 - - + -
425E LEU* 5.0 0.4 - - + +
426E ILE* 1.3 75.7 - - - +
428E VAL* 1.3 62.9 + - - +
434E ILE* 3.8 0.2 - - - -
435E TRP* 2.9 44.7 + - + +
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Residues in contact with VAL 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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96E LEU* 3.3 49.4 - - + +
98E GLY 4.1 5.8 - - - +
99E VAL* 3.8 33.7 - - + -
115E THR* 4.2 5.4 - - + -
413E ILE* 3.3 9.4 - - - +
414E ARG* 3.2 21.5 + - - -
415E GLN 3.2 19.6 + - - +
426E ILE* 4.3 0.4 - - + -
427E ALA* 1.3 78.6 - - - +
429E CYS* 1.3 61.6 + - - +
433E SER 3.7 3.4 - - - -
434E ILE* 4.0 16.8 - - + -
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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