Contacts of the helix formed by residues 543 - 554 (chain A) in PDB entry 1LWZ
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 THR 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A ASP* 4.4 17.9 - - + +
542A MET* 1.3 78.6 - - - +
544A GLU* 1.3 57.4 + - - +
545A GLU* 3.0 16.2 - - - +
546A LYS* 2.7 49.3 + - + +
547A LEU* 2.7 33.6 + - - +
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Residues in contact with GLU 544 (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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489A THR* 6.1 1.1 - - - +
490A THR* 5.6 6.9 - - - +
542A MET 5.3 1.5 - - - +
543A THR* 1.3 77.4 - - - +
545A GLU* 1.3 61.4 + - - +
547A LEU* 3.0 16.7 + - + +
548A ALA* 3.3 20.4 + - - +
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Residues in contact with GLU 545 (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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543A THR* 3.0 19.4 + - - +
544A GLU* 1.3 80.8 + - - +
546A LYS* 1.3 88.0 + - + +
548A ALA* 3.2 10.7 + - - +
549A GLU* 3.2 18.7 + - - +
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Residues in contact with LYS 546 (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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523A LEU* 2.7 31.0 + - - -
524A ILE* 2.7 35.7 - - + +
525A THR* 4.5 4.0 - - - +
542A MET* 2.9 23.2 - - + +
543A THR* 2.7 42.2 + - + +
545A GLU* 1.3 95.2 + - + +
547A LEU* 1.4 64.5 + - - -
549A GLU* 3.0 10.2 + - - +
550A ALA* 2.9 21.8 + - - +
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Residues in contact with LEU 547 (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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489A THR 4.3 6.7 - - - +
490A THR* 2.8 49.4 - - - +
492A GLU* 4.9 14.1 - - + +
542A MET* 2.9 26.2 - - + +
543A THR 2.7 37.0 + - - +
544A GLU* 3.0 23.3 - - + +
545A GLU 3.3 0.2 - - - -
546A LYS* 1.4 72.1 - - - +
548A ALA* 1.3 62.2 + - - +
550A ALA* 3.1 16.2 + - - +
551A GLU* 3.1 13.0 + - - +
555A LEU* 5.2 0.9 - - - +
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Residues in contact with ALA 548 (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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544A GLU 3.3 9.0 + - - +
545A GLU* 3.2 12.5 + - - +
546A LYS 3.1 0.4 - - - -
547A LEU* 1.3 81.6 - - - +
549A GLU* 1.3 60.4 + - - +
551A GLU* 3.1 18.2 + - - +
552A ARG* 3.2 18.4 + - - +
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Residues in contact with GLU 549 (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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524A ILE* 5.8 6.5 - - + -
545A GLU 3.2 8.7 + - - +
546A LYS* 3.0 13.5 + - - +
548A ALA* 1.3 79.1 - - - +
550A ALA* 1.3 63.8 + - - +
552A ARG* 3.1 29.4 + - - +
553A VAL* 3.0 36.8 + - + +
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Residues in contact with ALA 550 (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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492A GLU* 4.5 2.7 - - - +
524A ILE* 6.1 1.6 - - + -
542A MET* 5.0 10.8 - - + -
546A LYS 2.9 11.9 + - - +
547A LEU* 3.2 13.7 - - - +
549A GLU* 1.3 78.4 - - - +
551A GLU* 1.3 53.5 + - - +
553A VAL* 4.6 4.7 - - - +
554A GLY* 2.6 39.9 + - - -
555A LEU* 3.5 22.2 - - + -
558A VAL* 4.7 15.7 - - + -
559A PHE* 5.2 0.7 - - + -
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Residues in contact with GLU 551 (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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547A LEU 3.1 11.0 + - - +
548A ALA* 3.1 12.7 + - - +
550A ALA* 1.3 79.1 - - - +
552A ARG* 1.3 62.9 + - - +
554A GLY* 3.5 8.4 + - - -
555A LEU* 4.6 17.1 - - - +
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Residues in contact with ARG 552 (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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548A ALA* 3.2 8.8 + - - +
549A GLU* 3.1 42.1 + - - +
551A GLU* 1.3 82.7 - - - +
553A VAL* 1.3 66.2 + - + +
554A GLY* 4.5 0.3 - - - -
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Residues in contact with VAL 553 (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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549A GLU* 3.0 32.5 + - + +
550A ALA* 4.1 4.3 - - - +
552A ARG* 1.3 80.6 - - + +
554A GLY* 1.3 55.1 + - - +
557A LYS* 2.7 45.5 - - + +
558A VAL* 4.4 15.0 - - + +
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Residues in contact with GLY 554 (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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550A ALA 2.6 17.8 + - - -
551A GLU* 3.9 7.6 - - - -
552A ARG 3.3 2.4 - - - -
553A VAL* 1.3 73.3 - - - +
555A LEU* 1.3 59.7 + - - -
556A HIS* 6.0 0.2 - - - -
557A LYS* 2.9 20.3 - - - +
558A VAL* 2.9 31.4 + - - +
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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