Contacts of the helix formed by residues 439 - 451 (chain B) in PDB entry 5J1T
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 ASP 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B THR* 3.8 11.4 - - - -
429B SER 5.6 0.4 - - - -
430B ASP 5.3 0.2 - - - +
431B THR 3.6 22.9 - - - +
432B PRO* 3.5 10.4 - - + +
433B THR* 2.9 25.8 + - + +
437B HIS 3.9 0.8 + - - -
438B MET* 1.4 73.9 - - - +
440B SER* 1.3 60.0 + - - +
441B ASP* 3.2 11.9 + - - +
442B LYS* 2.8 52.0 + - - +
443B LEU* 2.8 29.6 + - - +
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 4.2 7.7 + - - -
404A BTB 3.3 17.2 - - - -
423B TRP* 2.9 31.3 + - - +
427B THR* 3.8 8.7 - - - +
429B SER 4.6 4.9 + - - -
430B ASP* 4.0 31.2 + - - -
439B ASP* 1.3 73.3 - - - +
441B ASP* 1.3 61.5 + - - +
443B LEU* 3.2 2.4 + - - +
444B SER* 2.9 29.1 + - - -
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Residues in contact with ASP 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 5.2 1.0 - - - -
173A ASP* 5.4 1.1 - - - +
208A ASN* 3.4 35.5 - - + +
209A ALA* 4.3 2.9 - - - -
210A GLY* 3.3 21.1 + - - -
211A ALA* 3.5 8.0 + - - +
212A GLU* 3.0 34.2 + - - +
430B ASP 5.2 5.9 + - - +
432B PRO* 5.2 10.8 - - - +
439B ASP* 3.2 8.6 + - - +
440B SER* 1.3 78.5 - - - +
442B LYS* 1.3 59.8 + - + +
444B SER* 2.5 26.9 + - - -
445B GLY 3.7 1.4 + - - -
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Residues in contact with LYS 442 (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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173A ASP* 3.3 41.7 - - - +
174A LYS* 4.1 22.0 - - + +
376B LEU* 4.3 9.6 - - + -
379B TYR* 2.7 28.8 + - - -
433B THR* 3.1 10.1 + - - -
434B SER 2.9 19.6 + - - -
435B PHE 3.7 6.3 - - - -
437B HIS 2.8 29.2 + - - +
438B MET* 3.9 10.7 - - - +
439B ASP* 2.8 44.6 + - - +
441B ASP* 1.3 70.2 - - + +
443B LEU* 1.3 67.1 + - - +
445B GLY 3.3 0.2 + - - -
446B LEU* 3.3 5.0 + - - +
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Residues in contact with LEU 443 (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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422B LEU* 3.8 15.7 - - + +
423B TRP* 3.4 57.9 - - + +
426B PHE* 4.0 18.4 - - + -
427B THR* 4.0 10.1 - - + -
438B MET* 3.6 11.9 - - + -
439B ASP 2.8 16.8 + - - +
440B SER* 3.2 5.8 + - - +
442B LYS* 1.3 77.9 - - - +
444B SER* 1.3 62.0 + - - +
446B LEU* 3.1 26.5 + - + -
447B TRP* 2.9 26.6 + - + +
450B ILE* 6.5 0.2 - - + -
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 5.1 15.7 - - - -
104A THR* 3.6 25.9 + - - +
208A ASN* 4.3 5.2 + - - +
211A ALA* 5.4 3.1 - - - +
315A ASP 5.3 1.3 - - - -
316A LYS* 5.1 0.5 - - - +
404A BTB 5.7 0.4 - - - -
423B TRP* 3.7 17.4 - - - -
440B SER 2.9 13.1 + - - -
441B ASP* 2.5 24.7 + - - -
443B LEU* 1.3 76.7 - - - +
445B GLY* 1.3 57.3 + - - +
447B TRP* 3.4 2.8 + - - +
448B SER* 3.0 28.8 + - - -
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Residues in contact with GLY 445 (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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104A THR* 3.7 7.9 - - - -
208A ASN* 4.4 4.5 + - - -
401A ATP 4.3 1.3 - - - -
379B TYR* 3.2 19.2 + - - -
441B ASP 3.7 1.0 + - - -
442B LYS 3.3 4.6 + - - -
444B SER* 1.3 80.6 + - - +
446B LEU* 1.3 64.3 + - - +
448B SER* 3.2 13.2 + - - -
449B ARG* 2.9 33.7 + - - -
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Residues in contact with LEU 446 (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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367B PHE* 4.3 12.3 - - + -
375B THR* 3.3 37.9 - - - +
376B LEU* 5.4 0.2 - - - -
378B PHE* 3.7 30.3 - - + -
379B TYR* 3.3 25.4 + - + +
422B LEU* 6.3 0.2 - - + -
426B PHE* 4.8 0.9 - - + -
438B MET* 4.1 5.6 - - + -
442B LYS 3.3 8.5 + - - +
443B LEU* 3.1 26.7 + - + +
445B GLY* 1.3 72.9 - - - +
447B TRP* 1.3 68.2 + - - +
449B ARG* 3.0 15.4 + - + +
450B ILE* 3.1 29.7 + - + +
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Residues in contact with TRP 447 (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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315A ASP* 4.9 7.8 + - + +
316A LYS* 3.8 30.6 - - + +
297B ILE* 3.9 9.0 - - + -
415B GLU* 3.7 18.6 + - + +
418B VAL* 3.6 35.0 - - + -
419B ARG* 3.6 36.0 - - + +
422B LEU* 3.8 22.0 - - + -
423B TRP* 3.7 27.4 - + + -
443B LEU* 2.9 21.1 + - + +
444B SER 3.6 4.3 - - - +
446B LEU* 1.3 78.2 - - - +
448B SER* 1.3 60.9 + - - +
449B ARG 3.1 1.2 + - - -
450B ILE* 4.0 8.5 - - + -
451B SER* 2.7 60.8 + - - -
454B VAL* 4.3 6.5 - - + -
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Residues in contact with SER 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 2.7 29.5 + - - -
316A LYS* 3.6 31.6 - - - +
319A LYS* 3.7 23.9 - - - +
320A THR* 3.3 20.0 - - - +
444B SER 3.0 9.5 + - - -
445B GLY* 3.2 12.5 + - - -
447B TRP* 1.3 76.6 - - - +
449B ARG* 1.3 58.8 + - - +
452B HIS* 4.4 2.8 + - - -
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Residues in contact with ARG 449 (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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170A ASP* 5.5 0.6 + - - -
171A GLN* 3.2 16.7 - - - +
208A ASN* 5.7 0.2 + - - -
319A LYS* 3.1 16.8 - - + +
401A ATP 2.9 41.8 + - - -
402A MG 3.9 2.6 - - - -
295B THR* 4.4 3.1 - - - -
378B PHE 5.2 0.7 - - - +
379B TYR* 3.6 31.6 - - - +
382B CYS* 3.5 36.5 - - + +
383B ASP* 2.8 39.1 + - - +
384B HIS* 4.9 3.1 - - + +
445B GLY* 2.9 34.9 + - - +
446B LEU* 3.0 9.2 + - + +
448B SER* 1.3 84.1 + - - +
450B ILE* 1.3 60.1 + - + +
451B SER 3.7 0.7 - - - -
452B HIS* 3.5 21.1 + - - -
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Residues in contact with ILE 450 (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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295B THR* 3.8 15.7 - - - +
297B ILE* 3.4 26.8 + - + +
367B PHE* 3.7 30.5 - - + -
378B PHE* 4.4 3.8 - - + -
382B CYS* 4.0 24.2 - - + -
396B LEU* 3.9 21.3 - - + -
422B LEU* 4.4 6.1 - - + -
443B LEU* 6.5 0.2 - - + -
446B LEU* 3.1 36.3 + - + +
447B TRP* 3.9 24.0 - - + +
449B ARG* 1.3 81.5 - - - +
451B SER* 1.3 60.8 + - - +
452B HIS* 3.5 5.2 + - - -
453B LEU 5.1 0.2 + - - -
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Residues in contact with SER 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LYS* 2.9 41.3 + - - +
320A THR* 3.9 4.9 - - - +
297B ILE* 4.2 0.2 - - - -
415B GLU* 4.4 4.4 - - - +
447B TRP* 2.7 57.3 + - - -
449B ARG 3.7 0.6 - - - -
450B ILE* 1.3 76.8 - - - +
452B HIS* 1.3 64.8 + - - +
453B LEU 3.3 3.1 + - - -
454B VAL* 4.0 16.5 - - - +
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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