Contacts of the strand formed by residues 416 - 422 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A LEU* 5.3 3.4 - - - -
329A SER 2.8 19.8 + - - +
330A ASN 2.6 32.8 + - - +
331A MET 3.7 4.3 + - - -
332A PRO* 4.0 31.9 - - + +
376A THR* 4.1 0.9 - - - -
377A LEU* 3.3 17.3 - - + +
412A TYR* 2.9 22.4 + - - -
414A LEU* 3.5 6.0 - - + +
415A LYS* 1.3 81.9 - - - +
417A LEU* 1.3 60.9 + - - +
418A ASP* 3.0 36.1 - - - +
434A GLY* 3.0 14.1 + - - -
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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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376A THR* 4.2 5.6 - - + -
377A LEU 2.7 11.2 + - - +
378A VAL* 3.4 5.8 - - + -
379A SER 2.9 26.9 + - - +
397A THR* 4.3 11.2 - - + -
401A LEU* 3.9 27.4 - - + -
412A TYR* 3.3 33.9 - - + +
416A LYS* 1.3 75.6 - - - +
418A ASP* 1.3 62.6 + - - +
419A LEU* 3.8 10.9 - - + +
434A GLY* 4.1 1.1 - - - -
436A LEU* 3.6 32.1 - - + -
466A LEU* 3.9 24.7 - - + -
469A GLN* 4.7 0.2 - - - +
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Residues in contact with ASP 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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328A LEU* 3.6 14.2 - - - +
377A LEU* 4.8 1.6 - - - +
379A SER* 3.4 18.0 - - - -
381A TYR* 3.3 26.7 + - + -
416A LYS* 3.0 30.2 - - - +
417A LEU* 1.3 78.0 + - - +
419A LEU* 1.3 60.9 + - - +
420A VAL* 4.1 0.7 - - + -
434A GLY 2.9 18.4 + - - +
435A LEU* 3.4 15.0 - - + +
436A LEU* 2.8 36.7 + - - +
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Residues in contact with LEU 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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378A VAL* 4.7 1.1 - - + -
379A SER 2.9 9.1 + - - +
380A ILE* 3.2 24.1 - - + +
381A TYR 2.8 24.3 + - - -
397A THR* 3.2 37.7 - - + +
417A LEU* 3.8 29.2 - - + +
418A ASP* 1.3 80.9 - - - +
420A VAL* 1.3 61.2 + - - +
436A LEU* 3.3 15.0 - - + -
438A PHE* 3.9 29.2 - - + -
443A LEU* 4.4 13.5 - - + -
462A ILE* 4.5 7.6 - - + -
466A LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 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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289A PHE* 5.0 1.3 - - + -
328A LEU* 3.8 15.3 - - + -
362A ILE* 4.0 11.9 - - + -
366A MET* 4.0 23.8 - - - -
381A TYR* 3.7 14.8 - - + -
419A LEU* 1.3 78.8 - - - +
421A ALA* 1.3 67.5 + - - +
422A ILE* 3.3 19.6 + - + +
435A LEU* 3.6 29.8 - - + -
436A LEU 2.9 11.9 + - - +
437A THR* 3.6 3.2 - - + -
438A PHE* 2.9 29.3 + - - -
443A LEU* 4.1 3.8 - - - -
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Residues in contact with ALA 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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289A PHE* 5.2 1.6 - - - -
366A MET* 5.8 0.9 - - - +
381A TYR 2.9 17.5 + - - +
382A ALA* 4.3 13.8 - - + -
383A VAL* 4.7 2.9 + - - +
420A VAL* 1.3 73.4 - - - +
422A ILE* 1.3 63.6 + - - +
423A PRO* 3.6 7.1 - - - +
438A PHE* 3.8 5.6 - - - -
440A GLU* 4.1 20.5 - - + +
443A LEU* 3.9 12.4 - - + +
444A LEU* 4.0 28.5 - - + -
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Residues in contact with ILE 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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275A TYR* 4.0 5.8 - - - +
277A PHE* 4.3 4.9 - - + -
289A PHE* 4.2 14.8 - - + -
291A ALA* 3.8 22.9 - - + -
292A THR 5.7 0.2 - - - +
362A ILE* 4.1 3.8 - - + -
420A VAL* 3.9 19.1 - - + +
421A ALA* 1.3 75.6 - - - +
423A PRO* 1.3 71.9 - - + +
424A ASP 3.1 25.6 + - - +
425A PHE* 4.0 15.0 - - + +
437A THR* 3.5 33.9 - - + -
438A PHE 2.9 13.1 + - - +
439A ARG* 4.0 3.1 - - - -
440A GLU* 3.5 18.5 + - - -
922A GLN* 5.4 0.3 - - - +
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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