Contacts of the strand formed by residues 433 - 443 (chain A) in PDB entry 1LMU
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 LYS 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A TRP* 3.4 9.7 - - - -
241A GLN* 2.9 51.5 + - + +
243A SER* 5.9 6.9 - - - -
426A GLU* 6.1 2.2 - - + +
427A LEU 3.7 7.0 - - - +
428A GLU* 5.1 8.3 - - + +
431A LYS* 3.3 23.5 + - - +
432A GLY* 1.3 73.2 - - - -
434A PHE* 1.3 60.0 + - - +
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Residues in contact with PHE 434 (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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224A VAL* 4.0 8.5 - - + -
226A ALA* 3.9 10.8 - - + -
238A ALA* 3.6 22.9 - - + -
239A ILE 3.3 3.4 - - - -
240A TRP* 3.2 52.9 - + + -
241A GLN* 2.9 8.2 - - - +
265A VAL* 4.0 13.2 - - + -
269A ILE* 3.1 25.1 - - + -
426A GLU* 3.3 1.7 - - - +
427A LEU* 2.7 40.4 + - + +
429A ILE* 3.2 34.5 - - + -
432A GLY* 3.4 14.1 - - - -
433A LYS* 1.3 72.5 - - - +
435A VAL* 1.4 64.5 + - - +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ALA* 3.2 3.7 - - - -
239A ILE* 2.7 37.1 + - + +
241A GLN* 2.7 45.5 - - + +
424A VAL* 5.1 0.4 - - + -
425A ILE 3.4 5.4 - - - +
426A GLU* 3.5 26.7 - - + +
433A LYS* 5.8 0.2 - - + -
434A PHE* 1.4 77.6 - - - +
436A ALA* 1.4 60.7 + - - +
437A LYS* 3.8 27.4 - - + +
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Residues in contact with ALA 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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236A PHE* 3.9 13.5 - - + -
237A THR 3.3 25.6 - - - +
238A ALA* 4.2 1.6 - - + -
239A ILE* 5.6 2.5 - - - -
423A CYS 3.6 0.5 - - - +
424A VAL* 3.3 5.5 - - - +
425A ILE 2.8 35.9 + - - +
435A VAL* 1.4 74.1 - - - +
437A LYS* 1.4 63.5 + - - +
464A LEU* 3.6 23.3 - - + +
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Residues in contact with LYS 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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422A LYS* 4.6 15.9 - - - +
423A CYS 3.3 4.9 - - - -
424A VAL* 3.1 45.7 - - + +
435A VAL* 3.8 32.5 - - + +
436A ALA* 1.4 74.4 - - - +
438A ALA* 1.4 64.9 + - - +
439A ARG* 6.0 1.1 - - + -
461A GLY* 4.1 12.4 - - - -
462A THR 4.2 3.8 + - - +
464A LEU* 5.2 2.2 - - - +
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Residues in contact with ALA 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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421A ARG 3.3 2.2 - - - +
422A LYS* 3.3 5.4 - - - +
423A CYS* 3.0 35.1 + - + +
437A LYS* 1.4 74.2 - - - +
439A ARG* 1.3 65.1 + - - +
440A PHE* 5.5 2.2 - - + -
460A ASP 3.5 9.6 - - - +
461A GLY 4.6 0.2 - - - -
462A THR 3.2 32.3 - - - +
463A PRO* 4.3 7.0 - - + -
464A LEU* 4.5 8.3 - - + +
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Residues in contact with ARG 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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284A GLU* 3.1 27.5 + - - -
420A PHE* 5.2 11.2 - - + +
421A ARG 3.3 4.3 - - - +
422A LYS* 3.3 46.6 - - + +
437A LYS* 6.0 1.1 - - + -
438A ALA* 1.3 74.7 - - - +
440A PHE* 1.3 63.1 + - - +
458A GLU* 4.3 19.8 + - + +
459A ASN* 3.3 6.8 - - - +
460A ASP* 3.0 35.0 + - - +
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Residues in contact with PHE 440 (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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420A PHE* 3.3 8.0 - - - -
421A ARG* 2.8 53.3 + - - +
438A ALA* 5.5 2.9 - - + -
439A ARG* 1.3 76.1 - - - +
441A LEU* 1.4 79.2 + - + +
442A ALA* 3.1 8.2 + - - -
459A ASN* 4.0 24.5 - - + +
463A PRO* 6.4 3.1 - - + -
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Residues in contact with LEU 441 (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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419A VAL 3.7 2.5 - - - +
420A PHE* 3.0 37.2 - - + -
440A PHE* 1.4 91.5 - - + +
442A ALA* 1.3 63.1 + - - +
443A GLU 3.5 20.2 - - - +
444A ALA* 4.3 7.4 - - - +
447A ARG* 3.3 28.3 - - + -
455A ARG* 3.7 31.4 - - + +
456A ASP* 5.3 0.7 - - - -
458A GLU* 4.7 0.7 - - + -
459A ASN* 4.4 25.5 - - - +
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Residues in contact with ALA 442 (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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419A VAL* 2.8 20.8 + - + +
421A ARG* 3.7 32.8 - - + +
440A PHE* 3.1 9.9 + - - -
441A LEU* 1.3 74.6 - - - +
443A GLU* 1.3 60.4 + - + +
444A ALA 4.2 0.6 + - - -
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Residues in contact with GLU 443 (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 PRO* 5.5 9.3 - - + +
417A ASP 4.3 5.6 - - - +
418A ALA* 3.2 2.9 - - - +
419A VAL* 2.7 55.5 + - + +
441A LEU* 4.0 3.2 - - - +
442A ALA* 1.3 81.6 - - + +
444A ALA* 1.3 66.9 + - - +
445A GLY* 4.2 10.5 - - - +
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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