Contacts of the helix formed by residues 443 - 457 (chain B) in PDB entry 5DSG
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 TYR 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B ILE* 3.5 20.4 - - + -
85B SER* 3.6 27.9 + - - -
86B MET* 3.5 27.9 - - + +
89B TYR* 3.8 27.1 - + + -
108B TRP* 3.9 4.0 - - - -
112B ASP* 2.5 24.9 + - - -
116B SER* 5.8 0.2 - - - -
439B TYR* 3.3 16.1 - + - -
440B TRP* 2.9 41.5 + + + +
442B CYS* 1.3 76.3 - - - +
444B VAL* 1.3 62.5 + - - +
445B ASN 3.1 2.5 - - - -
446B SER* 3.0 24.3 + - - -
1201B 0HK 3.6 26.5 - - - -
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Residues in contact with VAL 444 (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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42B LEU* 4.7 18.2 - - + -
86B MET* 4.7 1.1 - - - -
412B THR* 4.4 7.2 - - + -
440B TRP* 3.6 26.5 - - + +
441B LEU* 3.2 30.6 + - + +
443B TYR* 1.3 76.2 - - + +
445B ASN* 1.3 58.0 + - - +
447B THR* 2.8 31.2 + - + +
448B ILE* 2.9 28.9 + - + +
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Residues in contact with ASN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 5.9 0.9 - - - +
78B ASP* 4.7 2.6 - - - +
119B SER* 5.8 4.3 - - - -
123B LEU* 5.2 3.6 - - - +
405B ILE* 4.1 1.4 + - - +
408B ALA* 3.5 6.9 - - - +
409B PHE* 3.2 45.5 - - - +
412B THR* 3.3 23.9 - - - +
413B TRP* 3.8 18.4 + - - +
442B CYS 3.8 2.4 + - - +
443B TYR 3.0 0.4 + - - -
444B VAL* 1.3 77.3 - - - +
446B SER* 1.3 58.0 + - - +
448B ILE* 3.0 4.3 + - - +
449B ASN* 3.0 58.2 + - - -
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Residues in contact with SER 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 3.8 6.7 - - - -
50B ASN* 3.2 14.0 + - - -
78B ASP* 2.9 47.3 + - - +
81B ILE* 3.5 27.7 - - - +
442B CYS 5.2 0.7 + - - -
443B TYR* 3.0 13.9 + - - -
445B ASN* 1.3 80.3 + - - +
447B THR* 1.3 55.9 + - - +
450B PRO* 3.2 19.9 - - - +
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Residues in contact with THR 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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42B LEU* 3.7 20.3 + - + +
45B VAL* 3.7 29.5 - - + +
46B THR* 2.3 35.8 + - - +
86B MET* 3.4 13.9 - - - +
444B VAL* 2.8 19.2 + - + +
446B SER* 1.3 78.0 - - - +
448B ILE* 1.3 64.9 + - + +
450B PRO* 3.3 11.1 - - - +
451B ALA* 4.1 7.4 + - - +
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Residues in contact with ILE 448 (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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408B ALA* 3.7 27.1 - - + -
412B THR* 3.9 27.6 - - + -
444B VAL* 2.9 27.0 + - + +
445B ASN 3.0 6.0 + - - +
447B THR* 1.3 77.0 - - + +
449B ASN* 1.3 65.7 + - - +
451B ALA* 2.9 20.2 + - + +
452B CYS* 3.0 22.8 + - - -
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Residues in contact with ASN 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.9 15.4 - - - +
78B ASP* 2.9 29.3 + - - +
123B LEU* 5.8 0.2 - - - +
405B ILE* 3.5 27.5 - - + +
408B ALA* 4.5 2.1 - - - +
445B ASN* 3.0 45.0 + - - +
448B ILE* 1.3 75.4 - - - +
450B PRO* 1.4 70.0 - - + +
452B CYS* 3.0 11.8 + - - +
453B TYR* 3.0 38.3 + - + +
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Residues in contact with PRO 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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45B VAL 5.7 0.2 - - - +
46B THR* 4.8 1.6 - - - +
49B GLY* 3.9 15.5 - - - -
50B ASN* 3.4 37.2 - - - +
53B VAL* 3.9 14.8 - - + -
446B SER 3.2 16.2 - - - +
447B THR* 3.3 11.9 - - - +
449B ASN* 1.4 92.9 - - + +
451B ALA* 1.3 55.7 + - - +
453B TYR* 3.1 17.1 + - + +
454B ALA* 2.9 28.6 + - - +
464B PHE* 4.7 3.8 - - + -
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Residues in contact with ALA 451 (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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447B THR 4.1 5.5 + - - +
448B ILE* 2.9 17.5 + - + +
450B PRO* 1.3 76.9 - - - +
452B CYS* 1.3 61.7 + - - +
454B ALA* 3.3 6.7 + - - +
455B LEU* 2.9 32.7 + - - +
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Residues in contact with CYS 452 (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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401B THR* 4.6 2.7 - - + +
404B ALA* 3.9 38.8 - - + -
405B ILE* 4.4 13.5 - - + -
408B ALA* 4.9 0.2 - - - -
448B ILE* 3.0 35.6 + - - -
449B ASN* 3.0 12.5 + - - +
451B ALA* 1.3 77.9 - - - +
453B TYR* 1.3 57.4 + - + +
455B LEU* 4.6 2.0 - - - -
456B CYS* 2.9 40.8 + - - +
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Residues in contact with TYR 453 (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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50B ASN* 5.4 1.1 - - - -
53B VAL* 3.6 42.4 - - + -
71B LEU* 3.2 52.9 + - + +
74B LEU* 3.5 23.0 - - - +
75B ALA* 4.9 5.4 - - + -
78B ASP* 5.7 0.4 - - - -
401B THR* 4.4 10.1 - - + -
405B ILE* 3.5 23.8 - - + -
449B ASN* 3.0 27.0 + - + +
450B PRO* 3.1 10.3 + - + +
452B CYS* 1.3 78.8 - - - +
454B ALA* 1.3 59.2 + - - +
456B CYS* 5.4 0.2 - - - -
457B ASN* 3.4 30.4 + - - +
460B PHE* 3.8 21.2 - + + +
464B PHE* 5.2 0.7 - - + -
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Residues in contact with ALA 454 (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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450B PRO 2.9 15.7 + - - +
451B ALA* 3.3 7.4 + - - +
453B TYR* 1.3 76.3 - - - +
455B LEU* 1.3 59.9 + - - +
457B ASN 3.5 12.5 - - - +
460B PHE* 4.8 2.2 - - - -
461B LYS* 4.4 17.5 - - + +
464B PHE* 3.6 28.7 - - + -
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Residues in contact with LEU 455 (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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400B ARG* 6.0 3.8 - - - +
451B ALA 2.9 17.6 + - - +
452B CYS* 4.1 4.0 - - - +
454B ALA* 1.3 80.9 - - - +
456B CYS* 1.3 71.7 + - - +
457B ASN 3.3 3.4 + - - +
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Residues in contact with CYS 456 (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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397B LYS* 4.1 22.3 - - - +
400B ARG* 4.7 20.0 + - - +
401B THR* 3.2 39.6 + - + +
404B ALA* 4.3 15.3 - - - -
452B CYS* 2.9 25.2 + - - +
453B TYR* 5.4 0.2 - - - -
455B LEU* 1.3 85.5 - - - +
457B ASN* 1.3 60.0 + - - +
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Residues in contact with ASN 457 (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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63B LEU* 4.8 5.3 - - - +
398B VAL* 6.3 1.0 - - - +
401B THR* 5.6 2.5 - - + +
453B TYR* 3.4 18.4 + - - +
454B ALA 3.5 17.5 - - - +
455B LEU 3.3 2.1 - - - -
456B CYS* 1.3 81.6 - - - +
458B ALA* 1.3 76.3 + - - +
459B THR* 2.8 22.7 + - - -
460B PHE* 3.6 30.3 - - + -
461B LYS* 3.9 8.7 + - - +
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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