Contacts of the helix formed by residues 538 - 544 (chain B) in PDB entry 1LQF
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 538 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B LYS 3.5 3.3 - - - +
537B LEU* 1.3 89.8 - - + +
539B LYS* 1.3 64.1 + - + +
541B LYS* 3.0 28.3 + - + +
542B ASN* 5.6 0.2 + - - -
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B LEU* 4.0 26.8 - - + +
538B PRO* 1.3 75.7 - - + +
540B ASN* 1.3 67.8 + - - +
541B LYS 3.4 0.6 + - - -
542B ASN* 3.8 13.0 + - - -
543B ARG* 4.6 2.4 + - - -
563B ASP 4.2 14.3 + - - -
564B ASN* 3.5 36.0 + - - +
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Residues in contact with ASN 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B VAL* 2.7 30.7 + - - +
535B ALA 3.8 10.3 - - - +
537B LEU* 3.0 21.5 + - - +
539B LYS* 1.3 80.2 - - - +
541B LYS* 1.3 65.4 + - - +
542B ASN 3.2 2.9 - - - -
543B ARG* 3.1 16.4 + - - +
544B ASN* 3.0 17.5 + - - -
564B ASN* 2.9 29.9 + - - +
566B TYR* 3.3 37.2 - - + +
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Residues in contact with LYS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B ALA 5.3 0.7 - - - -
536B LYS 6.1 1.1 - - - +
537B LEU 3.4 5.3 + - - +
538B PRO* 3.0 23.0 + - + +
539B LYS 3.4 0.4 - - - -
540B ASN* 1.3 79.8 - - - +
542B ASN* 1.3 59.9 + - - +
543B ARG 3.5 0.2 + - - -
544B ASN* 3.7 20.7 + - - +
547B ARG* 4.8 16.5 - - - +
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Residues in contact with ASN 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B PRO 4.9 0.2 + - - -
539B LYS 3.8 13.9 + - - -
541B LYS* 1.3 73.1 - - - +
543B ARG* 1.3 73.8 + - - +
544B ASN 3.3 3.4 - - - -
588B LEU* 3.5 9.6 - - - +
590B ASN* 3.3 32.7 + - - +
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Residues in contact with ARG 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B LYS 4.6 3.0 + - - -
540B ASN* 3.1 17.5 + - - +
542B ASN* 1.3 93.1 - - - +
544B ASN* 1.3 61.0 + - - +
559B LEU* 4.2 3.4 - - - +
561B GLN* 4.9 4.0 + - - -
564B ASN* 3.4 50.3 + - - +
566B TYR* 2.8 52.8 + - + -
567B ILE* 5.5 2.0 - - - +
568B ASN* 4.3 5.5 + - - +
585B GLN* 3.0 20.1 + - - -
588B LEU* 3.5 7.1 - - - +
590B ASN* 4.4 8.5 - - - +
591B THR* 4.2 12.9 + - - +
594B HIS* 3.2 34.0 + - + -
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Residues in contact with ASN 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B ALA* 3.1 25.1 + - - +
536B LYS* 5.8 4.6 - - - +
540B ASN 3.0 23.0 + - - -
541B LYS* 3.7 15.9 + - - +
542B ASN* 3.3 1.6 - - - -
543B ARG* 1.3 79.5 - - - +
545B ARG* 1.3 63.9 + - - +
546B TYR* 3.4 18.9 + - - +
547B ARG* 5.6 0.9 - - - -
549B VAL 4.3 2.6 - - - +
550B SER* 5.5 1.3 - - - -
566B TYR* 2.4 30.8 + - - -
568B ASN* 2.7 17.7 + - - +
585B GLN* 3.7 2.7 - - - -
588B LEU* 3.8 5.2 - - - +
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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