Contacts of the helix formed by residues 443 - 456 (chain B) in PDB entry 6A5T
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 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B HIS* 3.5 26.6 + - - -
158B ILE* 3.3 42.7 - - - +
159B GLY* 4.0 0.6 - - - -
417B LEU* 5.5 0.2 - - - -
441B VAL* 2.5 13.5 + - - -
442B LYS* 1.3 69.3 - - - +
444B THR* 1.3 62.5 + - - +
445B THR* 3.1 2.0 - - - +
447B THR* 3.5 20.8 + - - -
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Residues in contact with THR 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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442B LYS* 2.7 19.0 + - + +
443B SER* 1.3 77.8 - - - +
445B THR* 1.3 69.4 + - - +
447B THR* 4.0 4.9 - - - -
448B SER* 3.0 29.8 + - - +
46T A 5.4 6.6 + - - -
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Residues in contact with THR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 4.3 13.6 - - + +
416B LYS* 4.7 15.9 - - + -
417B LEU* 3.2 43.9 - - + +
420B GLU* 4.5 10.3 + - - +
442B LYS* 2.7 27.7 + - - +
443B SER* 3.1 0.8 - - - -
444B THR* 1.3 84.3 + - - +
446B ILE* 1.3 61.0 + - + +
448B SER* 4.5 0.2 - - - -
449B GLY* 2.9 22.7 + - - -
46T A 5.7 0.3 + - - -
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Residues in contact with ILE 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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158B ILE* 3.8 44.1 + - + +
159B GLY* 4.4 7.4 - - - -
160B LYS 4.9 4.9 - - - +
161B VAL* 5.9 0.4 - - + -
410B PHE* 3.9 32.3 - - + -
413B LEU* 4.6 21.0 - - + +
414B PHE* 5.0 9.0 - - + -
417B LEU* 4.6 13.7 - - + -
443B SER 4.4 1.6 + - - -
445B THR* 1.3 91.0 - - + +
447B THR* 1.3 58.0 + - - +
449B GLY* 4.5 1.8 - - - +
450B LEU* 2.9 43.3 + - + +
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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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157B HIS* 5.9 0.7 - - - -
159B GLY* 3.7 1.6 - - - -
160B LYS* 3.4 42.7 + - + +
443B SER 3.5 19.6 + - - -
444B THR* 3.6 3.6 + - - -
445B THR 3.2 0.8 - - - -
446B ILE* 1.3 76.1 - - - +
448B SER* 1.3 71.5 + - - +
449B GLY 3.1 0.2 + - - -
450B LEU* 4.2 1.9 - - - +
451B LYS* 2.9 44.7 + - + +
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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
----------------------------------------------------------
444B THR* 3.0 26.2 + - - -
445B THR 4.5 0.2 - - - -
447B THR* 1.3 77.0 - - - +
449B GLY* 1.3 62.5 + - - +
451B LYS* 4.5 5.8 - - - -
452B TYR* 3.0 26.7 + - - +
462B GLN* 5.6 5.0 - - - +
45T C 5.1 11.1 + - - -
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Residues in contact with GLY 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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413B LEU* 3.5 24.9 - - - -
445B THR 2.9 15.1 + - - -
447B THR 3.0 0.2 - - - -
448B SER* 1.3 78.9 - - - +
450B LEU* 1.3 57.7 + - - +
452B TYR* 3.9 1.4 - - - +
453B SER* 2.9 34.2 + - - -
461B GLU* 6.5 0.4 - - - -
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Residues in contact with LEU 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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160B LYS 4.6 13.7 - - - +
161B VAL* 4.9 6.5 - - + -
162B PRO* 4.7 21.1 - - + -
406B LEU* 4.5 20.2 - - + -
409B LEU* 3.7 31.2 - - + +
410B PHE* 4.4 17.5 - - + -
413B LEU* 4.3 4.7 - - + +
446B ILE* 2.9 39.2 + - + +
447B THR 4.2 1.3 - - - +
449B GLY* 1.3 70.4 - - - -
451B LYS* 1.3 63.6 + - - +
453B SER* 3.1 5.0 + - - -
454B LEU* 3.0 33.9 + - + +
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Residues in contact with LYS 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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110B THR* 3.9 30.4 + - + +
196B ILE* 4.3 17.2 - - + +
197B ASN* 3.9 34.3 + - - +
447B THR* 2.9 35.8 + - + +
448B SER* 4.3 4.7 - - - +
450B LEU* 1.3 77.8 - - - +
452B TYR* 1.3 58.8 + - - +
454B LEU* 3.4 4.2 + - - +
455B ALA* 2.9 29.8 + - + +
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Residues in contact with TYR 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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448B SER* 3.0 20.2 + - - +
449B GLY* 4.0 1.8 - - - +
451B LYS* 1.3 72.8 - - - +
453B SER* 1.3 69.8 + - - +
454B LEU 3.0 2.7 + - - -
455B ALA* 3.2 11.7 + - + +
456B THR* 3.4 31.6 + - + +
457B GLY 4.0 1.9 + - - -
458B ASN* 3.8 25.4 + - + -
460B GLY 4.8 3.8 - - - -
461B GLU 5.2 0.4 - - - -
462B GLN* 3.9 51.3 + - + +
465B ALA* 5.7 4.3 - - + +
42T C 4.2 3.8 - - - -
43T A 3.2 50.3 + - - +
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Residues in contact with SER 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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409B LEU* 3.1 35.6 - - - +
413B LEU* 5.1 1.7 - - - +
449B GLY 2.9 20.8 + - - -
450B LEU* 3.1 7.2 + - - -
452B TYR* 1.3 79.3 - - - +
454B LEU* 1.3 62.4 + - - +
457B GLY* 3.0 23.7 - - - -
458B ASN 4.7 4.3 - - - -
459B TRP* 4.2 11.6 - - - -
460B GLY 3.4 22.8 + - - -
461B GLU* 5.3 0.5 - - - -
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Residues in contact with LEU 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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162B PRO* 5.0 10.1 - - + -
194B PHE* 3.6 24.9 - - + -
196B ILE* 3.4 34.8 - - + -
201B LYS* 4.0 12.6 - - + +
203B LEU* 4.6 9.6 - - + -
406B LEU* 5.4 6.3 - - + -
450B LEU* 3.0 24.7 + - + +
451B LYS 4.2 2.0 - - - +
453B SER* 1.3 78.6 - - - +
455B ALA* 1.3 65.2 + - - +
456B THR 3.3 2.8 + - - -
457B GLY* 3.7 4.6 + - - +
459B TRP* 4.0 26.7 - - + -
473B SER* 3.8 32.0 + - - +
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Residues in contact with ALA 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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196B ILE* 4.6 9.2 - - + +
197B ASN* 4.6 12.8 - - - +
201B LYS* 3.9 14.3 + - - +
451B LYS* 2.9 18.5 + - + +
452B TYR* 3.2 8.9 + - + +
454B LEU* 1.3 80.2 - - - +
456B THR* 1.3 61.4 + - - +
41T A 4.6 0.7 + - - +
42T C 3.2 45.1 - - - +
43T A 4.4 3.6 - - - +
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Residues in contact with THR 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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452B TYR* 3.4 32.8 + - + +
454B LEU 4.3 0.7 - - - -
455B ALA* 1.3 75.1 - - - +
457B GLY* 1.3 65.5 + - - +
458B ASN* 3.1 15.7 + - - +
471B GLY* 4.8 3.1 + - - -
473B SER 4.7 7.0 - - - +
4P U 6.0 1.1 - - - +
5P C 4.3 16.1 + - - +
41T A 5.1 7.9 - - + +
42T C 3.3 42.8 - - - +
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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