Contacts of the helix formed by residues 433 - 447 (chain J) in PDB entry 5LS6
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 SER 433 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431J GLU 3.8 2.2 + - - -
432J TRP* 1.3 75.3 - - - +
434J GLY* 1.3 63.7 + - - +
435J ALA* 3.3 9.5 + - - +
436J GLU* 2.6 43.1 + - - +
437J ALA* 3.3 21.5 + - - +
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Residues in contact with GLY 434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J ALA* 3.6 22.8 + - - +
270J LYS 3.7 2.1 - - - +
271J SER* 3.5 23.0 - - - -
433J SER* 1.3 72.8 - - - +
435J ALA* 1.3 60.8 + - - +
437J ALA* 4.8 0.2 - - - -
438J SER* 3.2 24.9 + - - -
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Residues in contact with ALA 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264J ILE* 3.5 39.7 - - + +
269J ALA* 4.0 12.8 - - + +
433J SER* 3.2 10.0 + - - +
434J GLY* 1.3 75.8 - - - +
436J GLU* 1.3 66.0 + - + +
437J ALA 3.2 0.7 + - - -
438J SER* 3.3 3.0 + - - -
439J MET* 3.0 24.5 + - - +
654L ARG* 4.3 15.5 - - - +
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Residues in contact with GLU 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431J GLU 4.3 1.0 - - - +
432J TRP* 3.6 19.9 - - + -
433J SER* 2.6 43.1 + - - +
435J ALA* 1.3 81.1 - - + +
437J ALA* 1.3 52.4 + - - +
439J MET* 3.4 6.6 + - - +
440J PHE* 2.7 35.0 + - - +
458J ILE* 4.2 9.8 - - + +
460J THR* 3.1 37.0 + - + +
461J LYS* 2.7 34.0 + - - +
654L ARG* 5.9 4.5 - - - +
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Residues in contact with ALA 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271J SER* 3.1 25.6 - - - +
432J TRP* 4.4 2.4 - - + -
433J SER 3.3 14.5 + - - +
434J GLY* 4.0 1.3 - - - +
435J ALA 3.2 0.6 - - - -
436J GLU* 1.3 75.8 - - - +
438J SER* 1.3 58.8 + - - +
440J PHE* 3.3 7.0 + - - +
441J ARG* 2.8 40.5 + - - +
469J PHE* 4.1 27.8 - - + -
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Residues in contact with SER 438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J ILE* 4.2 13.7 - - - -
270J LYS 3.5 5.2 + - - -
271J SER* 3.3 1.4 + - - -
272J VAL* 2.6 46.3 + - - +
273J GLN 5.0 0.2 - - - +
277J SER* 3.6 13.9 + - - -
434J GLY 3.2 12.0 + - - -
435J ALA 3.3 6.4 + - - -
437J ALA* 1.3 75.7 - - - +
439J MET* 1.3 58.6 + - - +
441J ARG* 3.4 2.0 + - - +
442J VAL* 2.9 35.9 + - - +
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Residues in contact with MET 439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J ILE* 4.7 7.7 - - + +
435J ALA 3.0 18.4 + - - +
436J GLU* 3.5 9.2 - - - +
438J SER* 1.3 73.8 - - - +
440J PHE* 1.3 59.2 + - - +
442J VAL* 3.6 11.3 - - + +
443J LEU* 2.9 64.8 + - + +
458J ILE* 4.6 11.4 - - + -
654L ARG* 4.3 26.9 - - + +
657L MET* 3.4 53.4 - - + +
658L LEU* 4.5 12.6 - - + -
661L VAL* 5.0 1.3 - - + -
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Residues in contact with PHE 440 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432J TRP* 4.5 9.0 - + + -
436J GLU 2.7 21.2 + - - +
437J ALA* 3.5 9.6 - - - +
439J MET* 1.3 71.0 - - - +
441J ARG* 1.3 63.8 + - + +
443J LEU* 2.8 6.2 + - - +
444J ILE* 2.8 78.2 + - + +
451J PHE* 5.0 0.4 - + - -
454J ILE* 4.1 14.1 - - + -
458J ILE* 4.2 14.8 - - + +
466J VAL* 4.0 26.7 - - + -
469J PHE* 4.3 13.7 - + + -
470J ARG* 3.8 26.5 - - + -
473J GLU* 4.3 22.9 - - + -
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Residues in contact with ARG 441 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271J SER* 3.0 32.1 + - - -
272J VAL* 3.3 33.1 + - - +
273J GLN* 4.1 20.3 - - - +
274J ARG* 3.3 30.7 - - + +
437J ALA* 2.8 27.8 + - - +
438J SER 3.4 4.9 + - - +
440J PHE* 1.3 83.6 - - + +
442J VAL* 1.3 62.6 + - - +
444J ILE* 3.6 11.2 - - + +
445J GLY 3.6 7.1 + - - -
469J PHE* 4.9 2.2 - - - -
473J GLU* 3.3 34.0 + - - +
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Residues in contact with VAL 442 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J ARG* 2.7 39.8 + - - +
277J SER* 4.0 17.9 - - - -
278J LEU* 4.0 7.9 - - + -
438J SER 2.9 21.6 + - - +
439J MET* 3.6 10.8 - - + +
441J ARG* 1.3 74.8 - - - +
443J LEU* 1.3 66.1 + - - +
445J GLY 3.0 4.9 + - - -
446J THR* 3.3 4.2 + - - +
658L LEU* 3.9 25.8 - - + -
661L VAL* 3.7 39.3 - - + -
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Residues in contact with LEU 443 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439J MET* 2.9 47.5 + - + +
440J PHE* 2.8 10.8 + - - +
442J VAL* 1.3 72.8 - - + +
444J ILE* 1.3 49.6 + - - +
446J THR* 3.1 9.9 + - + +
447J TYR* 2.5 70.4 + - + +
454J ILE* 3.9 20.0 - - + +
457J LEU* 3.9 15.3 - - + -
458J ILE* 3.6 39.3 - - + +
657L MET* 5.7 1.3 - - + -
661L VAL* 5.0 6.1 - - + -
674L ILE* 5.5 1.3 - - + -
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Residues in contact with ILE 444 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440J PHE* 2.8 70.4 + - + +
441J ARG* 3.6 14.4 - - + +
443J LEU* 1.3 69.2 - - - +
445J GLY* 1.3 62.9 + - - +
448J TYR* 3.5 30.2 + - - +
449J ASP* 4.7 12.7 - - - +
451J PHE* 4.9 6.1 - - + -
454J ILE* 4.1 17.5 - - + -
470J ARG* 5.1 15.7 - - - +
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Residues in contact with GLY 445 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J ARG* 3.5 28.3 - - - -
441J ARG 3.6 2.4 + - - -
442J VAL 3.0 5.3 + - - -
444J ILE* 1.3 81.6 - - - +
446J THR* 1.3 58.2 + - - +
447J TYR 3.8 0.2 - - - -
448J TYR* 3.6 27.8 + - - -
665L ASP* 5.5 0.9 - - - +
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Residues in contact with THR 446 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J ARG* 3.7 15.9 + - - -
442J VAL 3.3 3.1 + - - +
443J LEU* 3.1 23.0 + - + +
445J GLY* 1.3 77.8 - - - +
447J TYR* 1.3 77.3 + - + +
448J TYR* 3.9 5.0 - - - -
661L VAL* 4.4 16.4 - - + +
664L HIS* 2.8 38.0 + - + +
665L ASP* 4.6 3.4 + - - -
671L ILE* 3.1 21.5 - - + +
674L ILE* 6.2 2.7 - - + -
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Residues in contact with TYR 447 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443J LEU* 2.5 32.4 + - + +
446J THR* 1.3 93.7 - - + +
448J TYR* 1.3 72.6 + - - +
449J ASP 3.6 0.4 - - - -
450J ASN* 3.4 28.8 + - + +
453J ALA* 3.4 30.7 - - + -
454J ILE* 3.6 22.2 - - + -
457J LEU* 3.1 37.6 - - + +
671L ILE* 4.1 29.6 + - + -
674L ILE* 4.2 7.3 - - + +
675L ASP* 3.9 21.8 + - - +
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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