Contacts of the strand formed by residues 416 - 422 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B PRO* 3.4 1.0 - - - +
413B LYS 2.8 42.2 + - - +
414B ASP* 3.1 16.8 + - + +
415B ASN* 1.3 85.7 - - - +
417B LEU* 1.3 60.0 + - - +
418B TRP* 3.5 26.5 - - + +
459B TYR* 3.5 42.4 - - + -
460B LEU 5.6 2.5 - - - +
492B LEU* 4.1 6.0 - - - +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ALA* 4.0 8.1 - - + -
411B PHE* 3.7 30.7 - - - +
412B PRO* 3.9 6.3 - - + -
416B MET* 1.3 70.2 - - - +
418B TRP* 1.3 61.4 + - - +
459B TYR* 4.3 1.9 - - - +
460B LEU* 3.3 37.1 + - + +
464B LEU* 4.2 24.5 - - + +
470B TYR* 5.0 4.7 - - + -
472B ILE* 3.7 31.4 - - + -
490B ALA* 4.1 15.5 - - + +
491B TYR 4.0 23.6 - - - +
492B LEU* 4.2 10.3 - - + +
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Residues in contact with TRP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ALA* 3.1 7.1 - - - +
411B PHE* 2.8 67.2 + + + +
413B LYS* 3.8 31.9 + - + +
416B MET* 3.5 25.3 + - + +
417B LEU* 1.3 71.9 - - - +
419B VAL* 1.3 58.6 + - - +
457B ARG* 3.5 39.5 - - + -
458B THR* 3.4 18.8 - - - -
459B TYR* 3.7 38.5 - + + +
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 3.6 24.5 - - + -
409B LYS 3.5 5.6 - - - +
410B ALA* 4.2 2.9 - - + -
417B LEU 3.8 1.1 + - - +
418B TRP* 1.3 78.4 - - - +
420B GLU* 1.3 66.2 + - - +
421B TRP* 3.9 15.2 - - + -
433B LEU* 4.1 9.0 - - + -
457B ARG* 3.4 1.1 - - - +
458B THR 2.6 36.1 + - - +
460B LEU* 4.0 22.4 - - + -
472B ILE* 3.7 35.7 - - + -
474B VAL* 4.0 10.8 - - + -
488B ILE* 5.8 0.9 - - + -
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ASP 3.7 1.1 - - - +
408B LEU* 3.2 4.7 - - - +
409B LYS* 3.0 56.5 + - + +
411B PHE* 3.0 33.2 - - + -
419B VAL* 1.3 78.4 - - - +
421B TRP* 1.3 68.1 + - - +
456B HIS 3.3 13.9 - - - +
457B ARG* 3.4 31.9 + - + +
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Residues in contact with TRP 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B VAL* 4.0 18.8 - - + -
406B MET 3.5 10.1 - - - +
407B ASP 3.5 9.4 - - - +
408B LEU* 3.8 20.6 - - + -
419B VAL* 3.9 25.4 - - + -
420B GLU* 1.3 85.2 - - - +
422B THR* 1.3 79.3 + - - +
423B THR 3.7 2.2 + - - +
424B PRO* 4.6 0.4 - - + -
431B TYR* 3.2 48.4 + + + -
433B LEU* 4.2 22.9 - - + -
451B GLU* 5.1 0.2 - - + -
455B VAL* 3.6 35.9 + - + -
456B HIS* 3.0 24.9 + - - +
458B THR* 4.5 2.9 - - + -
474B VAL* 4.1 14.4 - - + -
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Residues in contact with THR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B MET* 2.9 26.8 + - + +
407B ASP* 2.7 32.1 + - - +
421B TRP* 1.3 78.1 - - - +
423B THR* 1.3 75.0 + - - +
424B PRO* 3.0 13.1 - - + +
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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