Contacts of the helix formed by residues 433 - 448 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G GLU* 4.0 2.4 + - - +
432G TRP* 1.3 72.8 - - - +
434G GLY* 1.3 65.6 + - - +
435G ALA* 4.0 7.0 + - - +
436G GLU* 2.8 36.6 + - - +
437G ALA* 2.8 21.5 + - - +
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Residues in contact with GLY 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G ALA* 4.6 9.2 + - - -
270G LYS 4.0 7.4 - - - -
271G SER* 3.6 27.8 - - - -
432G TRP 3.7 1.0 + - - -
433G SER* 1.3 71.6 - - - +
435G ALA* 1.3 58.2 + - - +
437G ALA 3.5 0.2 + - - -
438G SER* 2.7 35.2 + - - -
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Residues in contact with ALA 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ILE* 3.3 41.3 - - + +
266G GLY 6.0 0.2 - - - +
269G ALA* 4.4 11.2 - - + +
433G SER* 3.1 8.0 + - - +
434G GLY* 1.3 75.7 - - - +
436G GLU* 1.3 64.3 + - + +
438G SER* 4.2 0.6 - - - -
439G MET* 3.1 28.8 + - - +
654I ARG* 4.0 18.8 - - - +
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Residues in contact with GLU 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G GLU 3.8 0.5 - - - +
432G TRP* 3.8 17.0 - - + -
433G SER* 2.8 34.2 + - - +
435G ALA* 1.3 76.1 - - + +
437G ALA* 1.3 57.4 + - - +
439G MET* 4.1 3.8 - - - +
440G PHE* 3.0 28.4 + - - +
458G ILE* 4.3 11.1 - - + +
460G THR* 2.7 57.7 + - + +
461G LYS* 2.6 33.0 + - - +
654I ARG* 6.2 1.8 - - - +
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Residues in contact with ALA 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G SER* 3.2 24.9 - - - +
432G TRP* 4.4 15.5 - - + +
433G SER 2.8 17.4 + - - +
434G GLY 3.9 1.8 - - - +
436G GLU* 1.3 70.2 - - - +
438G SER* 1.3 65.9 + - - +
439G MET 3.2 1.1 - - - -
440G PHE* 3.3 6.9 + - - +
441G ARG* 3.0 32.0 + - - +
469G PHE* 4.5 18.3 - - + -
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Residues in contact with SER 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ILE* 4.2 14.9 - - - +
270G LYS 3.1 10.3 + - - -
271G SER* 4.4 0.6 + - - -
272G VAL* 3.1 34.1 + - - +
277G SER* 3.6 20.3 + - - -
434G GLY 2.7 22.1 + - - -
435G ALA* 4.3 0.8 - - - -
437G ALA* 1.3 77.7 - - - +
439G MET* 1.3 51.7 + - - +
441G ARG* 3.4 3.6 + - - +
442G VAL* 2.8 37.9 + - - +
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Residues in contact with MET 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ILE* 4.9 8.0 - - + +
435G ALA 3.1 20.2 + - - +
436G GLU* 4.1 4.5 - - - +
438G SER* 1.3 76.1 - - - +
440G PHE* 1.3 60.4 + - - +
442G VAL* 3.5 14.0 - - + +
443G LEU* 2.9 61.0 + - + +
458G ILE* 5.0 9.4 - - + -
654I ARG* 4.2 20.6 - - + +
657I MET* 3.5 49.8 - - + +
658I LEU* 4.1 19.3 - - + -
661I VAL* 4.5 1.1 - - + -
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Residues in contact with PHE 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G TRP* 4.4 8.3 - + + -
436G GLU 3.0 20.8 + - - +
437G ALA* 3.5 4.9 - - - +
439G MET* 1.3 72.5 - - - +
441G ARG* 1.3 83.6 + - + +
443G LEU* 2.8 16.3 + - - +
444G ILE* 3.0 52.8 + - + +
451G PHE* 5.1 0.7 - + - -
454G ILE* 4.2 5.6 - - + -
458G ILE* 4.4 14.7 - - + +
466G VAL* 3.9 36.8 - - + -
469G PHE* 3.6 30.1 - + + -
470G ARG* 3.7 28.9 - - + -
473G GLU* 4.1 13.7 - - + -
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Residues in contact with ARG 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G SER* 3.4 27.2 + - - -
272G VAL* 3.2 36.6 - - - +
273G GLN* 3.9 22.0 + - - +
274G ARG* 3.4 23.2 - - + +
437G ALA* 3.0 18.4 + - - +
438G SER 3.4 7.9 - - - +
440G PHE* 1.3 85.6 - - + +
442G VAL* 1.3 63.4 + - - +
444G ILE* 3.3 24.9 - - + +
445G GLY 3.6 0.2 + - - -
469G PHE* 4.9 5.7 - - - -
473G GLU* 3.4 38.2 + - - +
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Residues in contact with VAL 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ILE* 5.6 0.4 - - + -
274G ARG* 2.7 39.6 + - + +
277G SER* 3.7 26.0 - - - -
278G LEU* 4.2 9.9 - - + -
438G SER 2.8 27.9 + - - +
439G MET* 3.5 12.6 - - + +
440G PHE 3.1 0.2 - - - -
441G ARG* 1.3 76.8 - - - +
443G LEU* 1.3 63.7 + - - +
445G GLY 3.1 3.3 + - - -
446G THR* 3.6 4.0 + - - +
658I LEU* 4.1 17.9 - - + -
661I VAL* 4.0 34.8 - - + -
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Residues in contact with LEU 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G MET* 2.9 38.7 + - + +
440G PHE 2.8 10.0 + - - +
442G VAL* 1.3 71.8 - - - +
444G ILE* 1.3 49.9 + - - +
446G THR* 3.1 8.2 + - + +
447G TYR* 2.6 61.2 + - + +
454G ILE* 3.8 27.8 - - + +
457G LEU* 4.0 26.7 - - + -
458G ILE* 3.7 31.9 - - + +
657I MET* 5.6 0.9 - - + -
661I VAL* 4.7 9.0 - - + -
674I ILE* 5.4 0.9 - - + -
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Residues in contact with ILE 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440G PHE* 3.0 57.3 + - + +
441G ARG* 3.3 22.4 - - + +
443G LEU* 1.3 73.0 - - - +
445G GLY* 1.3 65.3 + - - +
446G THR 3.3 0.2 - - - -
448G TYR* 3.5 29.5 + - - +
449G ASP* 5.3 6.5 - - - +
451G PHE* 5.3 6.7 - - + -
454G ILE* 4.4 14.8 - - + -
470G ARG* 5.5 12.6 - - - +
473G GLU* 6.3 0.7 - - + -
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Residues in contact with GLY 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ARG* 3.5 28.3 - - - -
441G ARG 3.6 1.2 + - - -
442G VAL 3.1 4.9 + - - -
444G ILE* 1.3 84.2 - - - +
446G THR* 1.3 56.3 + - - +
448G TYR* 3.3 29.4 + - - -
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Residues in contact with THR 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G ARG* 4.0 14.8 - - - +
442G VAL 3.6 3.1 + - - +
443G LEU* 3.1 17.4 + - + +
445G GLY* 1.3 78.5 - - - +
447G TYR* 1.3 87.1 + - + +
448G TYR* 3.4 16.3 - - - -
661I VAL* 4.4 15.2 - - + +
664I HIS* 2.8 40.3 + - + +
665I ASP* 4.0 4.7 + - - -
671I ILE* 3.8 12.4 - - + +
674I ILE* 5.7 2.5 - - + -
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Residues in contact with TYR 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443G LEU* 2.6 31.1 + - + +
446G THR* 1.3 100.0 - - + +
448G TYR* 1.3 68.4 + - - +
449G ASP 3.8 0.9 - - - -
450G ASN* 3.6 23.1 - - + +
453G ALA* 3.5 31.9 - - + -
454G ILE* 3.7 19.7 - - + -
457G LEU* 3.2 34.1 - - + +
671I ILE* 3.4 43.6 + - + -
674I ILE* 3.7 11.5 - - + +
675I ASP* 4.0 10.0 + - + +
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Residues in contact with TYR 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308G ARG 5.3 2.8 + - - -
309G LYS 4.8 4.1 + - - -
310G ASN* 2.7 56.0 + - + +
339G THR* 5.7 10.3 - - + -
444G ILE* 3.5 20.8 + - - +
445G GLY* 3.3 23.2 + - - -
446G THR* 3.4 22.0 - - - -
447G TYR* 1.3 78.5 - - - +
449G ASP* 1.3 73.2 + - - +
450G ASN* 3.4 1.0 + - - +
454G ILE* 4.9 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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