Contacts of the strand formed by residues 409 - 419 (chain A) in PDB entry 5LXX
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 LEU 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.7 20.0 - - + -
35A ILE* 4.3 14.8 - - + -
37A MET* 3.3 33.7 - - + -
42A ILE* 4.3 13.0 - - + -
65A VAL* 4.4 6.1 - - + -
66A ILE 3.4 4.0 - - - +
68A GLY 4.0 0.9 - - - +
102A THR* 4.5 1.0 - - - +
401A ILE* 3.4 39.5 - - + -
407A ALA* 4.5 1.1 - - - -
408A ASP* 1.3 85.8 - - - +
410A VAL* 1.3 71.3 + - - +
411A ILE* 6.3 0.2 - - + -
446A VAL* 3.6 0.5 - - - +
447A ILE* 2.8 45.4 + - + +
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Residues in contact with VAL 410 (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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65A VAL* 3.3 4.0 - - - -
66A ILE* 2.9 47.6 + - + +
68A GLY* 4.0 11.4 - - - -
100A GLY* 3.4 32.8 - - - +
409A LEU* 1.3 83.7 - - - +
411A ILE* 1.3 76.1 + - - +
412A TRP* 3.6 15.9 + - + +
443A PRO* 3.8 19.3 - - + -
445A VAL 3.3 10.3 - - - +
446A VAL* 4.3 9.6 - - + -
447A ILE* 6.5 0.2 - - - -
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Residues in contact with ILE 411 (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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19A ILE* 4.2 21.3 - - + -
58A ILE* 3.9 27.8 - - + -
59A GLU 5.5 0.2 - - - +
60A ALA* 4.3 10.3 - - + -
63A ARG* 3.8 32.3 - - + -
64A MET 3.3 10.5 - - - +
65A VAL* 4.3 15.5 - - + -
409A LEU* 6.3 0.2 - - + -
410A VAL* 1.3 75.9 - - - +
412A TRP* 1.3 56.1 + - - +
444A LEU* 2.8 39.8 + - + +
445A VAL* 2.9 36.3 + - + +
447A ILE* 5.7 1.1 - - + +
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Residues in contact with TRP 412 (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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63A ARG* 4.4 7.4 - - - +
64A MET* 2.9 54.6 + - + +
66A ILE* 4.4 23.1 - - + -
99A GLY 4.1 2.7 - - - -
100A GLY* 5.1 0.4 - - - -
362A MET* 3.6 35.4 - - + -
363A SER* 3.7 11.4 - - - -
366A TRP* 3.4 40.1 - + + -
380A PHE* 4.1 7.4 - + - -
410A VAL* 3.6 11.0 + - + -
411A ILE* 1.3 73.3 - - - +
413A ASP* 1.3 63.8 + - - +
414A PRO* 3.4 20.0 - - + +
441A GLY* 3.6 17.7 - - - -
442A SER 3.6 21.3 - - - -
443A PRO* 3.6 24.9 - - + -
444A LEU* 4.6 2.8 - - - +
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Residues in contact with ASP 413 (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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63A ARG* 4.4 13.4 + - - +
411A ILE 4.1 0.6 + - - -
412A TRP* 1.3 74.0 + - - +
414A PRO* 1.3 64.9 - - - +
415A ASP* 2.9 21.0 + - - +
416A SER* 3.1 26.0 + - - +
441A GLY* 3.3 2.6 - - - -
442A SER* 2.8 39.7 + - - +
444A LEU* 3.6 30.5 - - + +
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Residues in contact with PRO 414 (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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63A ARG* 5.3 5.8 - - + +
64A MET* 4.1 17.5 - - + +
366A TRP* 3.2 44.4 + - + +
412A TRP* 3.4 15.9 - - + +
413A ASP* 1.3 86.6 - - - +
415A ASP* 1.3 75.7 + - - +
440A ARG* 2.9 24.9 + - - +
441A GLY* 4.4 0.7 - - - -
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Residues in contact with ASP 415 (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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413A ASP* 2.9 7.4 + - - +
414A PRO* 1.3 94.2 - - - +
416A SER* 1.3 67.7 + - - +
417A VAL* 3.6 9.7 + - - +
440A ARG* 3.1 31.5 + - - +
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Residues in contact with SER 416 (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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413A ASP* 3.1 24.1 + - - -
415A ASP* 1.3 78.8 - - - +
417A VAL* 1.3 58.0 + - - +
418A LYS* 4.3 11.8 - - - +
440A ARG* 3.1 5.2 - - - -
441A GLY 2.9 24.9 + - - -
442A SER* 2.6 42.4 + - - -
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Residues in contact with VAL 417 (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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415A ASP 3.6 7.6 + - - +
416A SER* 1.3 77.5 - - - +
418A LYS* 1.3 69.6 + - - +
438A GLU* 3.7 37.7 - - + +
439A CYS 3.4 10.3 - - - +
440A ARG* 4.4 16.8 - - + -
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Residues in contact with LYS 418 (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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416A SER* 4.6 8.5 - - - +
417A VAL* 1.3 82.1 - - - +
419A THR* 1.3 67.5 + - - +
420A ILE* 3.6 2.9 + - + +
437A MET 3.4 0.9 - - - +
438A GLU* 4.4 3.8 - - - -
439A CYS* 2.8 35.1 + - + +
441A GLY 6.0 0.2 - - - +
442A SER* 3.5 37.5 + - - +
443A PRO* 4.6 8.1 + - - +
444A LEU* 6.4 0.2 - - - +
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Residues in contact with THR 419 (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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418A LYS* 1.3 76.4 - - - +
420A ILE* 1.3 74.8 + - - +
421A SER* 3.6 9.0 + - - -
424A THR* 4.3 8.3 + - - -
435A GLU* 5.8 0.4 - - - +
436A GLY* 3.9 19.7 - - - +
437A MET 3.2 5.8 - - - +
438A GLU* 2.4 31.1 + - - +
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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