Contacts of the strand formed by residues 585 - 589 (chain B) in PDB entry 1LRX
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 ILE 585 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B TYR* 3.8 20.9 - - + -
577B TRP 3.6 3.6 - - - -
578B VAL* 3.6 14.6 - - + -
583B HIS 4.4 4.0 - - - +
584B SER* 1.3 73.8 + - - +
586B SER* 1.3 64.0 + - - +
587B SER 4.2 0.2 - - - -
597B THR 3.7 1.4 - - - +
598B ILE* 3.3 0.7 - - - -
599B LEU* 2.8 53.4 + - + +
611B LEU* 3.6 27.6 - - + -
618B VAL* 3.9 14.4 - - + +
620B TRP* 3.4 46.2 - - + -
631B ALA* 5.0 0.2 - - + -
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Residues in contact with SER 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B GLU* 3.8 10.5 + - - -
559B ASN* 4.4 3.1 + - - -
575B LEU 3.5 0.7 - - - +
576B TYR* 3.4 3.7 - - - -
577B TRP* 2.8 65.9 + - - -
579B ASP* 4.1 7.4 + - - -
584B SER* 3.0 20.4 + - - -
585B ILE* 1.3 72.2 + - - +
587B SER* 1.3 62.1 + - - +
595B ARG* 4.6 2.7 - - - -
597B THR 3.4 3.1 - - - -
598B ILE* 3.4 17.0 - - - +
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Residues in contact with SER 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B ARG* 4.9 8.1 - - - -
575B LEU 3.3 5.8 - - - -
576B TYR* 3.4 42.1 + - - -
585B ILE 4.2 0.4 - - - -
586B SER* 1.3 71.3 - - - +
588B ILE* 1.3 56.8 + - - +
595B ARG* 3.1 3.5 - - - +
596B LYS* 2.8 37.2 + - - +
597B THR* 2.9 35.8 + - - -
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Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ILE* 3.9 12.8 - - + -
544B LYS* 4.1 8.3 - - - +
556B VAL* 3.7 22.0 - - + -
558B GLU* 3.8 22.0 - - - +
574B ARG* 3.2 4.6 - - - -
575B LEU* 2.8 57.0 + - + +
577B TRP* 3.6 34.5 - - + +
587B SER* 1.3 75.6 - - - +
589B ASP* 1.3 61.1 + - - +
593B GLY 3.1 26.7 - - - +
594B ASN 3.4 5.8 - - - +
595B ARG* 4.0 2.0 - - - +
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Residues in contact with ASP 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B GLY 3.4 8.0 - - - +
574B ARG* 3.3 26.9 + - + +
587B SER 4.1 1.6 + - - -
588B ILE* 1.3 74.6 - - - +
590B VAL* 1.3 59.6 + - - +
591B ASN* 3.0 42.7 + - - +
592B GLY* 3.0 8.3 + - - +
593B GLY* 3.0 26.0 + - - -
594B ASN 3.0 9.1 + - - +
596B LYS* 3.5 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
------------------------------------------------------------
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