Contacts of the strand formed by residues 429 - 434 (chain A) in PDB entry 1LB6
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 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A GLY* 1.3 74.8 - - - -
430A ILE* 1.3 71.9 + - - +
431A ARG 4.3 0.2 - - - -
449A ILE* 3.3 31.0 - - + -
450A MET 3.3 10.8 - - - +
451A ASP* 2.8 23.6 + - - +
498A GLU 3.8 0.9 - - - +
499A VAL* 3.6 1.2 - - - +
500A SER* 2.9 40.7 + - - +
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Residues in contact with ILE 430 (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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389A LEU* 4.8 4.0 - - + -
411A VAL* 4.2 24.2 - - + -
426A PHE* 4.4 20.4 - - + -
428A GLY 5.3 0.4 - - - +
429A THR* 1.3 80.3 - - - +
431A ARG* 1.3 62.6 + - - +
432A LEU* 3.8 15.7 + - + +
448A GLU 4.0 0.3 - - - +
449A ILE* 3.5 3.8 - - - -
450A MET* 2.9 59.4 + - + +
452A ALA* 5.8 1.3 - - + -
459A PHE* 4.5 12.1 - - + -
497A CYS* 3.6 29.6 - - - -
498A GLU 3.4 4.5 - - - +
499A VAL* 4.3 16.8 - - + -
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Residues in contact with ARG 431 (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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430A ILE* 1.3 72.0 - - - +
432A LEU* 1.3 63.1 + - - +
433A THR* 3.8 4.2 + - - +
447A GLU* 2.7 53.4 + - - +
448A GLU 3.6 3.1 - - - +
449A ILE* 3.8 34.1 - - + +
496A ARG* 3.4 11.2 + - - +
497A CYS* 3.4 6.2 - - - -
498A GLU* 2.8 61.0 + - + +
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Residues in contact with LEU 432 (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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391A MET* 4.0 26.9 - - + -
409A LEU* 3.9 33.9 - - + +
411A VAL* 4.0 18.6 - - + -
430A ILE* 3.8 7.4 + - + +
431A ARG* 1.3 72.7 - - - +
433A THR* 1.3 61.2 + - - +
447A GLU* 3.0 19.6 - - - +
448A GLU 2.9 19.3 + - - +
450A MET* 3.8 24.0 - - + -
473A TYR* 4.1 22.2 - - + -
476A PHE* 3.4 10.7 - - + -
496A ARG 3.5 0.9 - - - +
497A CYS* 4.1 14.8 - - + -
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Residues in contact with THR 433 (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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431A ARG* 3.8 8.7 - - - +
432A LEU* 1.3 74.5 - - - +
434A ILE* 1.3 64.9 + - - +
435A LEU* 3.7 15.9 + - + -
445A ASN* 3.4 33.7 - - + +
446A HIS 3.4 2.7 - - - +
447A GLU* 2.5 34.6 + - + +
476A PHE* 4.5 1.1 - - - -
495A VAL* 3.3 6.3 - - - +
496A ARG* 2.7 57.0 + - - +
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Residues in contact with ILE 434 (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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393A LEU* 5.4 0.9 - - + -
407A ILE* 4.2 23.8 - - + -
409A LEU* 5.2 2.0 - - + -
433A THR* 1.3 73.8 - - - +
435A LEU* 1.3 63.3 + - - +
436A ASP 3.7 0.2 + - - -
445A ASN* 3.8 1.2 - - - +
446A HIS 2.8 34.8 + - - +
476A PHE* 3.6 29.1 - - + -
477A MET* 3.8 26.7 - - - -
487A PHE* 3.5 23.7 - - + -
493A LEU* 3.9 29.2 - - + -
494A LEU 3.5 4.0 - - - +
495A VAL* 4.4 16.8 - - + -
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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