Contacts of the strand formed by residues 416 - 422 (chain A) in PDB entry 3L5J
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 MET 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A PRO* 3.4 1.9 - - - +
413A LYS 2.8 38.4 + - - +
414A ASP* 2.9 28.8 + - + +
415A ASN* 1.3 82.7 - - - +
417A LEU* 1.3 60.9 + - - +
418A TRP* 3.0 42.7 + - + +
459A TYR* 4.5 28.0 - - + -
460A LEU 5.7 1.6 - - - +
464A LEU* 5.4 2.0 - - - -
492A LEU* 3.6 3.8 - - - -
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Residues in contact with LEU 417 (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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410A ALA* 5.0 0.2 - - + -
411A PHE 3.8 9.4 - - - +
412A PRO* 3.7 20.4 - - + -
416A MET* 1.3 70.6 - - - +
418A TRP* 1.3 62.7 + - - +
419A VAL 3.9 0.2 + - - -
459A TYR* 3.4 1.7 - - - +
460A LEU* 3.1 37.5 + - + +
464A LEU* 3.9 22.9 - - + +
470A TYR* 4.6 13.0 - - + -
472A ILE* 3.9 27.8 - - + -
490A ALA* 4.4 18.2 - - + +
491A TYR 3.4 23.6 - - - +
492A LEU* 3.6 19.0 - - + +
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Residues in contact with TRP 418 (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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410A ALA* 3.1 6.2 - - - +
411A PHE* 2.9 63.5 + + + +
413A LYS* 3.7 33.9 + - + +
416A MET* 3.0 48.7 - - + +
417A LEU* 1.3 75.0 - - - +
419A VAL* 1.3 60.1 + - - +
457A ARG* 3.9 34.1 - - + -
458A THR* 3.4 25.6 - - - -
459A TYR* 3.8 26.9 - + + +
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Residues in contact with VAL 419 (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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408A LEU* 3.7 17.9 - - + -
409A LYS 3.5 2.5 - - - +
410A ALA* 4.0 4.7 - - + -
417A LEU 3.9 0.8 + - - +
418A TRP* 1.3 79.2 - - - +
420A GLU* 1.3 64.1 + - - +
421A TRP* 3.6 25.0 - - + -
433A LEU* 4.1 9.0 - - + -
457A ARG* 3.6 0.3 - - - -
458A THR* 2.6 44.4 + - - +
460A LEU* 4.1 14.6 - - + -
472A ILE* 3.7 38.4 - - + -
474A VAL* 3.9 9.9 - - + -
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Residues in contact with GLU 420 (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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407A ASP 4.5 0.2 - - - -
408A LEU* 3.6 0.9 - - - +
409A LYS* 3.0 54.5 + - + +
411A PHE* 3.2 31.8 - - + -
419A VAL* 1.3 76.2 - - - +
421A TRP* 1.3 66.4 + - - +
456A HIS* 3.4 14.7 + - - +
457A ARG* 3.4 29.3 - - + +
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Residues in contact with TRP 421 (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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405A VAL* 3.9 23.1 - - + -
406A MET 3.6 11.2 - - - +
407A ASP* 4.0 4.9 - - - -
408A LEU* 4.2 9.0 - - + -
419A VAL* 3.6 33.4 - - + -
420A GLU* 1.3 81.7 - - - +
422A THR* 1.3 78.3 + - - +
423A THR 3.6 2.8 + - - -
431A TYR* 3.2 48.1 + + + -
433A LEU* 4.2 18.2 - - + -
455A VAL* 3.5 20.6 - - + -
456A HIS* 3.0 38.1 + - - +
458A THR* 4.2 10.3 - - + -
474A VAL* 4.0 23.8 - - + -
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Residues in contact with THR 422 (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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406A MET* 2.7 34.6 + - + +
407A ASP* 2.6 32.6 + - - +
421A TRP* 1.3 79.3 - - - +
423A THR* 1.3 75.3 + - + +
424A PRO* 3.2 12.1 - - + +
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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