Contacts of the strand formed by residues 493 - 500 (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 LEU 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A TRP 3.5 2.3 - - - +
356A LYS* 3.6 0.2 - - - -
357A ILE* 2.8 39.8 + - + +
360A PHE* 3.8 32.7 - - + +
393A LEU* 4.2 14.8 - - + -
407A ILE* 4.8 4.3 - - + -
434A ILE* 3.9 32.8 - - + -
482A LEU* 4.1 12.8 - - + -
487A PHE* 3.9 9.9 - - + +
488A ILE* 3.5 24.6 - - + +
492A THR* 1.3 76.4 - - - +
494A LEU* 1.3 62.3 + - - +
495A VAL* 4.1 20.6 - - + -
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Residues in contact with LEU 494 (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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354A ILE* 4.5 10.1 - - + -
355A TRP 3.5 1.8 - - - +
356A LYS* 3.5 37.5 - - + -
434A ILE* 3.5 5.7 - - - +
435A LEU* 2.9 57.4 + - + +
437A GLN* 3.5 40.4 - - + +
487A PHE 4.6 0.6 + - - -
492A THR* 4.2 7.4 - - + -
493A LEU* 1.3 80.3 - - - +
495A VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 495 (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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353A TYR 3.8 0.9 - - - +
354A ILE* 3.6 2.5 - - - +
355A TRP* 2.7 56.6 + - + +
357A ILE* 4.0 26.5 - - + -
391A MET* 3.7 25.6 - - - +
393A LEU* 4.5 6.1 - - + -
409A LEU* 3.9 21.5 - - + -
433A THR 3.3 8.3 - - - +
434A ILE* 4.4 8.5 - - + -
435A LEU* 5.3 0.2 - - - -
493A LEU* 4.2 15.3 - - + -
494A LEU* 1.3 78.6 - - - +
496A ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 496 (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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352A ILE* 3.4 41.4 - - + +
353A TYR 3.5 4.5 - - - +
354A ILE* 3.6 25.1 - - + +
431A ARG* 3.4 16.7 + - - +
432A LEU* 3.5 2.4 - - - +
433A THR* 2.7 48.8 + - - +
435A LEU* 4.2 24.0 - - + -
494A LEU 4.2 0.2 + - - -
495A VAL* 1.3 78.7 - - - +
497A CYS* 1.3 64.1 + - - +
498A GLU* 3.0 32.3 + - - +
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Residues in contact with CYS 497 (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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351A GLY 3.7 1.6 - - - +
352A ILE* 3.3 3.3 - - - -
353A TYR* 2.9 32.9 + - - +
380A PHE* 3.9 24.5 - - + -
389A LEU* 5.3 1.8 - - - -
391A MET* 3.7 27.1 - - + -
411A VAL* 4.7 6.1 - - - -
430A ILE* 3.6 28.0 - - - -
431A ARG 3.4 2.9 - - - -
432A LEU* 4.1 6.7 - - + -
496A ARG* 1.3 76.7 - - - +
498A GLU* 1.3 58.4 + - - +
499A VAL* 4.0 11.7 - - - +
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Residues in contact with GLU 498 (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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350A ASN* 2.9 34.3 + - + +
351A GLY 3.5 3.1 - - - -
352A ILE* 3.5 19.8 - - + +
429A THR 3.8 0.9 - - - +
430A ILE* 3.4 3.6 - - - -
431A ARG* 2.8 62.0 + - + +
496A ARG* 3.0 39.0 + - - +
497A CYS* 1.3 73.0 - - - +
499A VAL* 1.3 63.3 + - - +
500A SER* 4.2 0.4 + - - -
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Residues in contact with VAL 499 (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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350A ASN* 3.2 21.8 - - - +
351A GLY 2.9 23.1 + - - +
380A PHE* 5.0 3.1 - - + -
382A THR* 4.0 20.3 - - + -
389A LEU* 3.9 24.9 - - + -
426A PHE* 3.5 36.6 - - + -
429A THR 3.6 4.7 - - - +
430A ILE* 4.3 7.4 - - + -
497A CYS* 4.0 16.4 - - - +
498A GLU* 1.3 77.2 - - - +
500A SER* 1.3 63.1 + - - +
501A THR* 4.2 8.9 + - - +
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Residues in contact with SER 500 (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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350A ASN* 3.3 28.3 + - - -
428A GLY* 3.2 5.7 - - - -
429A THR* 2.9 41.5 + - - +
498A GLU* 4.2 1.1 + - - -
499A VAL* 1.3 76.0 - - - +
501A THR* 1.3 61.9 + - - +
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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