Contacts of the strand formed by residues 422 - 428 (chain A) in PDB entry 5LG1
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 VAL 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A GLU 4.3 0.2 - - - +
383A SER* 3.6 22.5 - - - -
384A ASN* 3.8 16.8 + - - +
420A GLY 4.1 6.1 - - - +
421A ASN* 1.3 75.7 - - - +
423A PHE* 1.3 65.6 + - - +
424A SER* 4.5 3.4 + - - +
440A SER* 3.9 30.3 - - - +
441A LEU 3.8 5.2 - - - +
442A SER* 3.8 15.9 - - - +
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Residues in contact with PHE 423 (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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365A LEU* 3.6 24.0 - - + -
381A TRP* 4.6 10.1 - - + -
382A GLU 3.7 2.9 - - - +
383A SER* 3.8 16.4 - - - -
388A GLU* 4.1 4.5 - - + -
410A LEU* 3.9 14.8 - - + -
412A VAL* 3.9 23.6 - - + -
416A ARG* 3.9 42.0 - - + -
417A TRP* 4.1 19.3 - + - -
421A ASN* 3.9 29.6 - - + -
422A VAL* 1.3 72.4 - - - +
424A SER* 1.3 61.8 + - - +
440A SER* 3.3 2.9 - - - -
441A LEU* 2.7 51.7 + - + +
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Residues in contact with SER 424 (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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380A GLU 3.8 0.2 - - - +
381A TRP* 3.3 13.6 - - - -
382A GLU* 3.0 41.6 + - - +
383A SER* 6.0 0.3 - - - -
422A VAL* 4.5 5.0 + - - +
423A PHE* 1.3 73.9 - - - +
425A CYS* 1.3 61.1 + - - +
426A SER 3.9 0.6 + - - -
438A GLN* 3.2 32.5 + - - -
439A LYS 3.3 4.7 - - - -
440A SER* 3.2 19.8 + - - -
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Residues in contact with CYS 425 (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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348A VAL* 4.4 2.3 - - + +
350A THR* 4.4 6.3 - - + +
367A CYS* 2.0 52.7 - - + -
379A VAL* 3.9 22.0 - - - -
380A GLU 3.6 3.6 - - - -
381A TRP* 4.2 13.9 - - + -
424A SER* 1.3 71.3 - - - +
426A SER* 1.3 61.4 + - - +
427A VAL* 3.8 10.8 + - - +
438A GLN* 3.4 4.7 - - - -
439A LYS* 2.9 33.6 + - - +
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Residues in contact with SER 426 (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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378A ALA 3.8 0.9 - - - +
379A VAL* 3.2 7.1 - - - +
380A GLU* 2.6 56.2 + - - +
382A GLU* 3.3 21.3 + - - +
424A SER 3.9 0.2 + - - -
425A CYS* 1.3 72.0 - - - +
427A VAL* 1.3 60.9 + - - +
428A MET* 5.3 2.9 - - - -
436A TYR* 3.1 34.8 + - - -
437A THR 3.6 5.2 - - - -
438A GLN* 4.2 4.4 - - - +
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Residues in contact with VAL 427 (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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346A PRO* 4.4 2.7 - - + -
348A VAL* 3.7 23.1 - - + -
369A VAL* 3.8 25.1 - - + -
377A ILE* 3.7 30.3 - - + -
378A ALA 3.5 3.1 - - - +
379A VAL* 4.2 4.5 - - + -
425A CYS* 3.8 14.1 + - - +
426A SER* 1.3 78.9 - - - +
428A MET* 1.3 66.0 + - - +
432A LEU* 3.6 15.4 - - + +
436A TYR* 3.5 3.8 - - - -
437A THR* 3.0 42.1 + - + +
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Residues in contact with MET 428 (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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248A LYS* 3.5 52.0 - - + +
251A LEU* 3.4 16.4 - - + +
252A MET* 3.6 29.8 - - + +
377A ILE* 3.4 6.0 - - - +
378A ALA* 2.8 42.6 + - + +
380A GLU* 5.1 9.6 - - - +
426A SER* 5.3 2.9 - - - -
427A VAL* 1.3 78.0 - - - +
429A HIS* 1.3 59.9 + - - +
435A HIS 3.3 17.0 - - - +
436A TYR* 3.6 22.2 - - + -
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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