Contacts of the helix formed by residues 445 - 464 (chain L) in PDB entry 3J8B
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 445 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420L PHE* 5.2 14.1 - - + -
442L GLN* 4.4 12.8 + - - +
443L GLN 3.7 3.0 + - - -
444L LEU* 1.3 78.7 - - - +
446L VAL* 1.3 67.7 + - - +
447L PHE 3.1 2.9 + - - -
448L SER* 3.5 17.6 + - - -
449L ASP* 3.6 11.2 + - + +
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Residues in contact with VAL 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442L GLN* 6.2 0.6 - - - +
444L LEU* 3.2 13.1 - - + +
445L LYS* 1.3 77.1 - - - +
447L PHE* 1.3 64.1 + - - +
449L ASP* 3.3 6.0 + - - +
450L GLU* 3.1 22.4 + - - +
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Residues in contact with PHE 447 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445L LYS 3.4 0.8 - - - -
446L VAL* 1.3 79.2 - - - +
448L SER* 1.3 62.7 + - - +
450L GLU* 3.2 7.6 + - - +
451L VAL* 2.9 24.2 + - - +
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Residues in contact with SER 448 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413L PHE* 6.3 3.4 - - - -
420L PHE* 5.3 11.4 - - - -
445L LYS* 3.5 14.4 + - - -
446L VAL 3.4 0.8 - - - -
447L PHE* 1.3 78.1 - - - +
449L ASP* 1.3 58.5 + - - +
451L VAL* 3.2 7.8 + - - +
452L GLN* 2.9 29.7 + - - +
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Residues in contact with ASP 449 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444L LEU 5.7 1.1 - - - +
445L LYS* 3.6 10.5 + - + +
446L VAL* 3.3 9.1 + - - +
447L PHE 3.3 0.6 - - - -
448L SER* 1.3 74.6 - - - +
450L GLU* 1.3 68.1 - - - +
452L GLN* 3.2 7.5 + - - +
453L GLN* 3.0 23.0 + - - +
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Residues in contact with GLU 450 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446L VAL 3.1 14.0 + - - +
447L PHE* 3.2 10.3 + - - +
449L ASP* 1.3 76.6 - - - +
451L VAL* 1.3 63.9 + - - +
453L GLN* 3.2 8.7 + - - +
454L GLN* 3.1 20.6 + - - +
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Residues in contact with VAL 451 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373L ILE* 6.4 2.7 - - + -
447L PHE 2.9 13.2 + - - +
448L SER* 3.5 10.5 - - - +
450L GLU* 1.3 77.3 - - - +
452L GLN* 1.3 62.5 + - - +
454L GLN* 3.2 9.2 + - - +
455L ALA* 3.0 21.6 + - - +
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Residues in contact with GLN 452 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409L TYR* 6.0 6.3 - - + -
448L SER 2.9 16.1 + - - +
449L ASP* 3.2 7.8 + - - +
451L VAL* 1.3 77.8 - - - +
453L GLN* 1.3 63.1 + - - +
455L ALA* 3.0 9.8 + - - +
456L GLN* 2.9 24.8 + - - +
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Residues in contact with GLN 453 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449L ASP 3.0 12.6 + - - +
450L GLU* 3.6 9.2 - - - +
452L GLN* 1.3 78.4 - - - +
454L GLN* 1.3 64.6 + - - +
456L GLN* 3.3 13.1 + - - +
457L LEU* 3.5 10.4 + - - +
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Residues in contact with GLN 454 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450L GLU 3.1 12.3 + - - +
451L VAL* 3.2 11.2 + - - +
453L GLN* 1.3 76.1 - - - +
455L ALA* 1.3 63.2 + - - +
457L LEU* 3.1 18.1 + - - +
458L SER* 3.5 9.9 + - - -
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Residues in contact with ALA 455 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401L MET* 6.0 5.4 - - + -
451L VAL 3.0 13.2 + - - +
452L GLN* 3.0 13.3 + - - +
454L GLN* 1.3 77.5 - - - +
456L GLN* 1.3 63.6 + - - +
457L LEU 3.4 0.2 + - - -
458L SER* 3.4 16.8 + - - -
459L THR* 4.6 1.9 + - - -
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Residues in contact with GLN 456 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404L GLY 5.6 1.6 - - - +
406L PRO* 5.6 9.9 - - + -
452L GLN 2.9 11.6 + - - +
453L GLN* 3.7 11.0 - - - +
454L GLN 3.2 0.2 - - - -
455L ALA* 1.3 77.7 - - - +
457L LEU* 1.3 62.8 + - - +
458L SER 3.3 0.9 + - - -
459L THR* 3.9 11.4 + - - -
460L ILE* 4.8 1.9 + - - +
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Residues in contact with LEU 457 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453L GLN 3.5 7.6 + - - +
454L GLN* 3.1 13.6 + - - +
456L GLN* 1.3 79.2 - - - +
458L SER* 1.3 64.3 + - - +
459L THR 3.1 1.4 + - - -
460L ILE* 3.3 17.3 + - - +
461L ARG* 3.7 8.5 + - - +
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Residues in contact with SER 458 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454L GLN 3.5 6.6 + - - -
455L ALA* 3.4 11.6 + - - -
456L GLN 3.3 2.0 + - - -
457L LEU* 1.3 78.0 - - - +
459L THR* 1.3 62.9 + - - +
461L ARG* 3.2 10.8 + - - +
462L SER* 3.1 20.3 + - - -
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Residues in contact with THR 459 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404L GLY* 4.8 21.8 - - - -
455L ALA 4.6 1.0 + - - -
456L GLN 3.9 8.8 + - - -
457L LEU 3.1 1.0 + - - -
458L SER* 1.3 79.1 - - - +
460L ILE* 1.3 63.7 + - - +
462L SER* 3.0 24.3 + - - -
463L PHE* 3.6 3.8 + - - +
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Residues in contact with ILE 460 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456L GLN 4.8 1.9 + - - +
457L LEU* 3.3 11.2 + - - +
459L THR* 1.3 75.1 - - - +
461L ARG* 1.3 65.6 + - - +
462L SER 3.2 0.5 + - - -
463L PHE* 3.4 18.9 + - - +
464L LEU 3.7 1.7 + - - -
501L VAL* 5.1 3.3 - - - +
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Residues in contact with ARG 461 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457L LEU 3.7 6.3 + - - +
458L SER* 3.2 11.8 + - - +
460L ILE* 1.3 77.3 - - - +
462L SER* 1.3 50.4 + - - +
464L LEU* 2.4 42.3 + - - +
500L LEU* 4.0 33.4 - - + +
501L VAL* 4.2 12.8 - - + -
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Residues in contact with SER 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458L SER 3.1 11.8 + - - -
459L THR* 3.0 20.3 + - - -
461L ARG* 1.3 73.0 - - - +
463L PHE* 1.3 64.8 + - - +
464L LEU* 3.3 6.0 + - - +
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Residues in contact with PHE 463 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459L THR 3.6 3.9 + - - +
460L ILE* 3.4 12.6 + - - +
461L ARG 3.2 0.4 - - - -
462L SER* 1.3 77.8 - - - +
464L LEU* 1.3 69.2 + - - +
465L LYS 3.2 13.5 + - - +
466L LEU* 4.7 2.1 - - - +
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Residues in contact with LEU 464 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460L ILE 3.7 1.8 + - - -
461L ARG* 2.4 33.0 + - - +
462L SER* 3.6 7.4 - - - +
463L PHE* 1.3 74.2 - - - +
465L LYS* 1.3 70.2 + - - +
466L LEU* 3.2 5.9 + - + +
500L LEU 5.8 2.5 - - - +
501L VAL* 4.8 10.5 - - - +
502L TRP 5.7 0.2 - - - -
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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