Contacts of the helix formed by residues 526 - 538 (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 ALA 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.5 26.9 - - + +
294A LEU* 5.3 0.9 - - - -
313A LEU* 4.6 14.2 - - - +
330A ARG* 4.3 21.5 - - - +
524A THR* 3.3 2.6 - - + +
525A GLU* 1.3 82.8 - - + +
527A THR* 1.3 66.8 + - + +
528A ARG 3.8 0.2 + - - -
529A ALA* 4.5 4.9 + - - +
530A GLY* 4.6 3.8 + - - -
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Residues in contact with THR 527 (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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165A ARG* 5.5 8.0 + - - +
169A ASP* 6.2 0.4 - - - +
198A VAL* 5.8 0.5 - - - +
523A GLY* 3.7 6.2 - - - -
524A THR* 2.8 40.4 + - - +
526A ALA* 1.3 79.2 - - + +
528A ARG* 1.3 65.8 + - - +
529A ALA 3.3 2.2 - - - -
530A GLY* 2.8 14.6 + - - +
531A ILE* 2.9 22.6 + - - +
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Residues in contact with ARG 528 (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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295A SER* 3.8 31.9 + - - +
298A GLN* 5.0 3.3 + - - +
332A ASP* 5.7 1.6 - - - +
497A LEU* 4.0 23.6 - - + +
500A MET* 3.9 28.2 - - - +
501A THR* 4.3 9.3 + - - +
520A ASP* 3.0 42.6 + - - -
522A LEU 2.7 39.5 + - - +
523A GLY* 3.7 13.2 - - - -
524A THR 3.2 20.4 + - - +
525A GLU* 4.2 9.5 + - - +
526A ALA 3.7 1.4 - - - -
527A THR* 1.3 77.0 + - - +
529A ALA* 1.3 63.7 + - - +
531A ILE* 3.0 19.6 + - + +
532A ILE* 3.1 18.2 + - - +
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Residues in contact with ALA 529 (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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298A GLN* 4.0 9.8 - - - +
309A ALA* 3.6 20.5 - - + +
310A GLN* 3.6 36.5 + - + +
313A LEU* 4.9 13.2 - - + -
525A GLU 5.3 1.2 + - - -
526A ALA 4.5 3.9 + - - +
527A THR 3.3 1.0 - - - -
528A ARG* 1.3 78.1 - - - +
530A GLY* 1.3 63.8 + - - +
532A ILE* 3.2 5.9 + - - +
533A GLU* 3.1 26.1 + - - +
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Residues in contact with GLY 530 (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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310A GLN* 5.7 1.6 - - - -
526A ALA 4.6 2.6 + - - -
527A THR* 2.8 9.8 + - - -
529A ALA* 1.3 80.5 - - - +
531A ILE* 1.3 61.5 + - - +
533A GLU* 3.1 9.2 + - - +
534A LEU* 2.9 23.5 + - - +
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Residues in contact with ILE 531 (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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198A VAL* 2.9 39.9 - - + -
199A GLN* 3.7 32.5 - - + +
202A VAL* 4.1 18.2 - - + -
500A MET* 5.2 2.5 - - - -
523A GLY* 4.3 3.1 - - - -
527A THR* 2.9 34.0 + - - +
528A ARG* 3.0 17.0 + - + +
530A GLY* 1.3 76.2 - - - +
532A ILE* 1.3 63.4 + - + +
534A LEU* 3.2 7.7 + - - +
535A LEU* 3.2 23.4 + - + +
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Residues in contact with ILE 532 (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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202A VAL* 5.2 1.3 - - + -
308A SER* 5.7 4.3 - - - +
309A ALA* 4.3 14.6 - - + -
493A ASP* 5.4 7.2 - - + +
496A LEU* 4.3 20.4 - - + -
497A LEU* 4.0 17.0 - - + +
500A MET* 3.5 33.0 - - + -
528A ARG 3.1 13.3 + - - +
529A ALA* 3.6 4.9 - - - +
531A ILE* 1.3 76.3 - - - +
533A GLU* 1.3 67.5 + - + +
535A LEU* 3.3 17.1 + - - +
536A PHE* 3.0 45.5 + - + -
541A LEU* 5.1 2.0 - - + -
548A ILE* 5.1 3.4 - - + -
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Residues in contact with GLU 533 (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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308A SER* 3.5 15.8 + - - -
310A GLN* 3.3 37.1 - - + +
529A ALA 3.1 15.9 + - - +
530A GLY* 3.1 8.9 + - - +
532A ILE* 1.3 81.6 - - + +
534A LEU* 1.3 62.3 + - - +
536A PHE* 3.1 28.8 + - - +
537A LYS* 3.1 12.5 + - - +
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Residues in contact with LEU 534 (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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194A SER* 5.0 0.7 - - - +
199A GLN* 3.6 26.7 - - + +
530A GLY 2.9 15.8 + - - +
531A ILE* 3.7 7.2 - - - +
533A GLU* 1.3 73.9 - - - +
535A LEU* 1.3 68.6 + - + +
537A LYS* 3.0 15.5 + - + +
538A ARG* 2.9 66.0 + - + +
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Residues in contact with LEU 535 (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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199A GLN* 3.8 44.9 - - + +
200A THR* 6.4 0.4 - - + -
202A VAL* 3.8 21.5 - - + -
203A LEU* 3.9 18.8 - - + +
531A ILE* 3.2 15.5 + - + +
532A ILE* 3.7 5.4 - - - +
533A GLU 3.3 0.2 - - - -
534A LEU* 1.3 78.8 - - + +
536A PHE* 1.3 63.6 + - - +
538A ARG* 3.4 4.9 + - + +
539A SER 3.3 2.4 + - - -
540A PHE* 3.0 45.8 + - + -
541A LEU* 3.5 34.6 + - + -
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Residues in contact with PHE 536 (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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493A ASP* 5.3 2.0 - - - -
532A ILE* 3.0 49.3 + - + -
533A GLU* 3.1 20.9 + - - +
535A LEU* 1.3 74.5 - - - +
537A LYS* 1.3 67.2 + - - +
539A SER* 2.9 16.3 + - - -
541A LEU* 3.4 43.0 - - + +
542A THR* 4.0 12.1 - - - -
543A LYS* 4.7 11.4 - - + -
548A ILE* 4.1 29.6 - - + -
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Residues in contact with LYS 537 (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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533A GLU 3.1 10.6 + - - +
534A LEU* 3.0 20.9 + - + +
536A PHE* 1.3 76.8 - - - +
538A ARG* 1.3 67.7 + - - +
539A SER* 3.0 1.8 + - - -
620A PRO* 3.6 17.2 - - - +
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Residues in contact with ARG 538 (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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189A TYR* 4.1 8.8 + - - -
192A VAL* 3.9 30.4 - - - +
194A SER* 2.7 30.9 + - - -
534A LEU* 2.9 52.0 + - + +
535A LEU* 3.6 2.5 - - + +
536A PHE 3.2 0.2 - - - -
537A LYS* 1.3 81.2 - - - +
539A SER* 1.3 66.6 + - - +
540A PHE* 2.9 42.6 + - + -
620A PRO* 3.2 12.2 - - - +
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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