Contacts of the strand formed by residues 416 - 422 (chain B) in PDB entry 5MJ6
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 LYS 416 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B LEU* 5.3 2.3 - - + +
329B SER 2.7 30.3 + - - +
330B ASN 3.4 16.1 + - - -
331B MET* 3.8 14.8 + - - +
332B PRO* 3.8 20.8 - - + +
376B THR* 4.4 0.9 - - - -
377B LEU* 3.9 13.5 - - + +
379B SER* 5.7 0.2 - - - +
412B TYR* 2.9 22.9 + - - -
414B LEU* 3.2 6.5 - - - +
415B LYS* 1.3 81.9 - - - +
417B LEU* 1.3 62.1 + - - +
418B ASP* 2.8 36.2 + - - +
434B GLY* 3.3 20.3 + - - -
435B LEU* 4.5 1.2 - - - +
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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
----------------------------------------------------------
376B THR* 4.4 7.0 - - + -
377B LEU 3.2 8.7 + - - -
378B VAL* 3.5 10.6 - - + +
379B SER 3.1 23.6 + - - +
397B THR* 4.4 9.4 - - + -
401B LEU* 4.1 31.2 - - + -
412B TYR* 3.5 31.9 - - + +
416B LYS* 1.3 74.9 - - - +
418B ASP* 1.3 63.8 + - - +
419B LEU* 4.1 10.8 + - + +
434B GLY* 3.8 2.0 - - - -
436B LEU* 3.9 29.6 - - + -
466B LEU* 4.0 21.3 - - + -
469B GLN* 4.4 1.3 - - - +
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 4.0 12.5 - - - +
379B SER* 3.4 22.2 + - - +
381B TYR* 3.8 24.2 + - + -
416B LYS* 2.8 39.9 + - - +
417B LEU* 1.3 79.1 + - - +
419B LEU* 1.3 58.7 + - - +
420B VAL* 4.8 0.4 - - + -
434B GLY 2.8 15.7 + - - +
435B LEU* 4.0 14.1 - - + -
436B LEU* 2.7 35.3 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B VAL* 5.0 0.9 - - + -
379B SER 3.0 8.2 + - - +
380B ILE* 3.3 25.1 - - + +
381B TYR* 2.8 31.4 + - - +
397B THR* 3.3 40.8 - - + +
417B LEU* 4.2 19.3 - - + +
418B ASP* 1.3 78.4 - - - +
420B VAL* 1.3 55.9 + - - +
436B LEU* 3.3 17.5 - - + -
438B PHE* 3.7 31.9 - - + -
443B LEU* 4.2 13.5 - - + -
462B ILE* 4.2 9.6 - - + -
466B LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 4.9 0.7 - - + -
328B LEU* 4.0 7.9 - - + -
362B ILE* 3.9 11.4 - - + -
366B MET* 3.9 22.2 - - - -
381B TYR* 3.7 22.9 - - + +
382B ALA* 5.2 0.4 - - - +
418B ASP* 4.8 0.2 - - + -
419B LEU* 1.3 76.8 - - - +
421B ALA* 1.3 63.8 + - - +
422B ILE* 3.4 26.0 + - + +
435B LEU* 3.7 30.1 - - + -
436B LEU 2.7 13.0 + - - +
437B THR* 3.5 2.3 - - + -
438B PHE* 2.9 28.1 + - - -
443B LEU* 4.2 3.4 - - - -
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Residues in contact with ALA 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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289B PHE* 5.7 0.5 - - - -
381B TYR 3.1 17.6 + - - +
382B ALA* 4.3 14.9 - - + +
383B VAL* 4.7 2.4 + - - +
420B VAL* 1.3 74.7 - - - +
422B ILE* 1.3 62.2 + - - +
423B PRO* 3.6 6.9 - - - +
438B PHE 3.7 5.4 - - - -
440B GLU* 4.1 18.1 - - + +
443B LEU* 4.1 19.2 - - + +
444B LEU* 4.2 26.9 - - + -
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Residues in contact with ILE 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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275B TYR* 3.9 8.1 - - - +
277B PHE* 3.8 11.4 - - + -
289B PHE* 3.6 24.0 - - + -
291B ALA* 4.2 8.3 - - + -
362B ILE* 4.1 13.2 - - + -
420B VAL* 3.7 26.7 - - + +
421B ALA* 1.3 70.8 - - - +
423B PRO* 1.3 73.1 - - + +
424B ASP 3.4 25.2 + - - +
425B PHE* 4.1 12.1 - - + +
437B THR* 4.2 16.2 - - - -
438B PHE 2.9 19.5 + - - +
439B ARG* 3.9 3.1 - - - -
440B GLU* 3.4 20.4 + - - -
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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