Contacts of the strand formed by residues 273 - 286 (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 PRO 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A GLY 3.9 4.0 - - - +
272A GLN* 1.3 107.7 - - + +
274A ALA* 1.3 61.3 + - - +
275A LEU 4.2 0.2 - - - -
428A GLU 3.7 7.4 - - - +
429A ILE* 3.9 9.9 - - - +
472A GLU* 4.7 20.0 - - + +
473A LEU 3.5 10.5 - - - +
474A LEU* 4.0 9.0 - - + -
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Residues in contact with ALA 274 (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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228A ILE* 3.8 11.4 - - + -
272A GLN 3.9 0.4 + - - -
273A PRO* 1.3 74.1 - - - +
275A LEU* 1.3 59.9 + - - +
276A VAL 3.9 0.5 + - - -
427A LEU* 3.8 24.2 - - + -
428A GLU 3.3 5.6 - - - +
429A ILE* 3.6 19.3 - - + -
471A ASP 3.7 0.5 - - - +
472A GLU* 3.5 3.0 - - - -
473A LEU* 2.6 53.6 + - + +
474A LEU 4.5 0.2 - - - +
475A CYS 4.6 0.9 - - - +
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Residues in contact with LEU 275 (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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273A PRO 4.2 0.4 - - - -
274A ALA* 1.3 73.2 - - - +
276A VAL* 1.3 67.6 + - - +
277A THR* 3.2 6.4 + - - +
427A LEU* 3.3 2.2 - - - -
428A GLU* 2.7 61.3 + - + +
470A GLY* 3.1 37.2 - - - +
471A ASP 3.3 6.5 - - - +
472A GLU* 4.2 13.0 - - + +
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Residues in contact with VAL 276 (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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275A LEU* 1.3 72.8 - - - +
277A THR* 1.3 60.2 + - - +
278A SER 3.6 21.3 - - - +
279A TYR* 4.5 0.7 - - + -
425A ILE* 4.2 7.2 - - + -
426A GLU 3.7 6.3 - - - +
427A LEU* 3.5 13.2 - - + -
467A VAL* 4.3 15.9 - - + -
468A ALA 3.3 30.3 - - - +
469A LYS* 3.3 5.4 - - - +
470A GLY* 2.7 28.9 + - - -
471A ASP* 3.1 9.6 + - + +
473A LEU* 3.0 34.3 - - + -
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.2 10.3 + - - -
276A VAL* 1.3 71.7 - - - +
278A SER* 1.4 73.4 + - - +
426A GLU* 2.9 54.3 + - + +
427A LEU* 4.1 6.5 - - - +
428A GLU* 5.3 8.3 - - - -
469A LYS* 3.6 18.6 - - - +
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 3.6 10.4 - - - +
277A THR* 1.4 85.0 - - - +
279A TYR* 1.3 61.2 + - - +
280A ASN* 4.5 11.4 + - - -
424A VAL* 5.0 1.7 + - - +
425A ILE* 3.7 1.7 - - - -
426A GLU* 3.1 50.6 + - - +
469A LYS* 4.6 4.3 - - - -
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Residues in contact with TYR 279 (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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276A VAL* 4.5 4.0 - - + -
278A SER* 1.3 75.1 - - - +
280A ASN* 1.4 77.4 + - - +
281A ASP* 4.4 22.4 + - + +
421A ARG* 5.4 1.6 + - - -
423A CYS* 3.1 33.8 - - - -
424A VAL 3.5 2.7 - - - -
425A ILE* 3.3 24.9 - - + -
464A LEU 5.0 0.9 + - - -
465A PRO 3.8 9.9 + - - -
466A VAL* 3.7 28.0 - - + +
467A VAL* 3.0 35.9 - - + +
468A ALA* 4.4 8.1 - - - -
469A LYS* 4.6 4.2 - - - +
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Residues in contact with ASN 280 (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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278A SER* 4.5 12.6 + - - -
279A TYR* 1.4 85.6 + - - +
281A ASP* 1.3 60.8 + - - +
282A LYS* 4.0 14.6 - - + +
422A LYS 4.3 0.2 - - - -
423A CYS* 3.2 11.2 - - - -
424A VAL* 3.0 45.7 + - + +
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Residues in contact with ASP 281 (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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279A TYR* 4.4 21.3 + - + +
280A ASN* 1.3 75.1 - - - +
282A LYS* 1.3 64.1 + - - +
283A ARG* 3.3 18.5 + - - -
421A ARG* 3.1 39.5 + - - +
422A LYS 3.5 8.5 - - - +
423A CYS* 4.5 1.2 - - - +
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Residues in contact with LYS 282 (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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280A ASN* 4.7 12.0 - - + +
281A ASP* 1.3 78.0 - - - +
283A ARG* 1.3 76.9 + - - +
284A GLU* 4.1 5.6 + - + +
421A ARG* 3.6 2.7 - - - -
422A LYS* 2.8 86.4 + - + +
424A VAL* 2.9 37.4 - - - +
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Residues in contact with ARG 283 (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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281A ASP 3.3 19.1 + - - -
282A LYS* 1.3 86.2 - - - +
284A GLU* 1.3 60.9 + - - +
419A VAL* 4.0 17.3 - - + -
420A PHE 3.2 9.0 - - - +
421A ARG* 4.4 8.5 - - + +
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Residues in contact with GLU 284 (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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282A LYS* 4.1 6.4 - - + +
283A ARG* 1.3 74.2 - - - +
285A SER* 1.3 61.0 + - - +
286A GLU* 6.3 0.7 - - + -
419A VAL* 3.5 3.3 - - - +
420A PHE* 2.6 63.3 + - + +
422A LYS* 3.6 25.5 - - + +
439A ARG* 3.1 31.2 + - - -
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Residues in contact with SER 285 (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* 1.3 79.4 - - - +
286A GLU* 1.4 62.3 + - - +
287A SER 4.2 0.5 + - - -
417A ASP* 4.1 20.0 + - - -
418A ALA 3.1 11.2 - - - -
419A VAL* 4.4 10.8 - - - -
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Residues in contact with GLU 286 (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* 4.3 0.9 + - + -
285A SER* 1.4 73.8 - - - +
287A SER* 1.3 62.0 + - - +
417A ASP* 3.0 5.1 - - - +
418A ALA* 2.7 33.4 + - + +
420A PHE* 2.8 34.2 - - + -
446A TRP* 3.1 17.8 + - - +
447A ARG* 2.7 30.3 + - - -
458A GLU* 3.0 21.2 - - - +
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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