Contacts of the helix formed by residues 406 - 415 (chain B) in PDB entry 2AX1
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 ASN 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398B GLU* 3.8 5.0 - - - +
403B THR 4.5 6.7 + - - +
404B PRO 3.7 12.4 + - - -
405B VAL* 1.3 78.9 - - - +
407B SER* 1.3 63.0 + - - +
408B TRP* 3.1 24.6 + - + +
409B LEU* 3.1 19.1 + - + +
410B GLY* 3.5 7.6 + - - -
443B LEU* 3.8 25.8 - - + +
444B ASP 2.9 41.1 + - - +
445B CYS* 4.8 4.5 - - - +
446B GLN 5.4 1.1 + - - -
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Residues in contact with SER 407 (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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391B PRO 5.1 0.2 + - - -
394B ARG* 3.5 32.4 - - - +
395B ALA 4.8 0.3 + - - -
398B GLU* 2.8 26.6 + - - -
405B VAL* 3.6 9.0 - - - +
406B ASN* 1.3 75.2 - - - +
408B TRP* 1.3 59.0 + - - +
410B GLY* 3.2 4.3 + - - +
411B ASN* 2.9 41.8 + - - -
1002B 5EE 4.9 2.2 - - - +
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Residues in contact with TRP 408 (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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391B PRO 5.7 0.9 - - - -
395B ALA* 4.6 7.2 - - + -
398B GLU* 3.1 29.1 + - + +
406B ASN* 3.1 21.7 + - - -
407B SER* 1.3 82.3 + - - +
409B LEU* 1.3 93.1 + - + +
411B ASN* 3.3 9.3 + - - +
412B ILE* 2.9 45.5 + - + +
425B LEU* 4.4 4.4 - - + +
429B PHE* 3.3 74.2 - + + -
430B PHE* 6.0 1.3 - + - -
433B LEU* 4.2 24.5 - - + -
443B LEU* 3.4 33.2 - - + -
456B PRO* 5.1 1.1 - - + -
459B LEU* 5.4 2.9 - - + -
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Residues in contact with LEU 409 (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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406B ASN* 3.1 13.8 + - + +
408B TRP* 1.3 110.1 - - + +
410B GLY* 1.3 64.4 + - - +
412B ILE* 3.3 3.6 + - + +
413B ILE* 3.0 35.8 + - + +
443B LEU* 3.9 30.1 - - + -
444B ASP 4.9 0.4 - - - +
445B CYS* 4.0 20.4 - - + -
454B ILE* 4.1 20.2 - - + +
456B PRO* 4.8 7.0 - - + -
459B LEU* 4.2 30.7 - - + -
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Residues in contact with GLY 410 (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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406B ASN 3.5 5.6 + - - -
407B SER* 3.2 8.1 + - - -
409B LEU* 1.3 77.7 - - - +
411B ASN* 1.3 55.3 + - - +
413B ILE* 3.4 3.6 + - - +
414B MET* 2.9 35.5 + - - +
445B CYS* 3.6 21.2 - - - -
446B GLN 4.6 3.1 - - - -
447B ILE* 5.4 0.9 - - - -
1002B 5EE 3.4 16.8 - - - -
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Residues in contact with ASN 411 (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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386B ARG* 5.3 0.3 - - - -
391B PRO* 3.6 36.9 + - - +
394B ARG* 5.7 1.2 - - - +
407B SER* 2.9 34.3 + - - +
408B TRP* 3.6 6.4 - - - +
410B GLY* 1.3 73.1 - - - +
412B ILE* 1.3 59.8 + - - +
415B TYR* 2.8 47.6 + - + +
420B TRP* 4.7 3.4 - - + -
421B ALA* 4.5 0.7 - - - +
425B LEU* 3.8 18.4 - - + +
1002B 5EE 3.2 22.0 - - - +
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Residues in contact with ILE 412 (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 TRP* 2.9 46.6 + - + +
409B LEU* 3.7 5.2 - - - +
411B ASN* 1.3 74.6 - - - +
413B ILE* 1.3 57.7 + - - +
416B ALA* 2.9 32.1 + - - +
421B ALA* 4.5 7.9 - - - +
425B LEU* 3.8 22.9 - - + +
426B MET* 3.9 52.0 - - + +
429B PHE* 4.9 0.9 - - + -
430B PHE* 5.4 2.2 - - + -
459B LEU* 4.2 28.7 - - + -
463B ILE* 4.4 3.1 - - + -
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Residues in contact with ILE 413 (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* 3.0 24.9 + - + +
410B GLY* 3.7 4.3 - - - +
412B ILE* 1.3 80.6 - - - +
414B MET* 1.3 67.6 + - - +
416B ALA* 4.2 1.5 - - - +
445B CYS* 4.3 7.6 - - - -
447B ILE* 4.7 4.9 - - + -
454B ILE* 3.5 36.3 - - + -
459B LEU* 3.8 24.2 - - + -
462B ILE* 4.2 10.8 - - + -
463B ILE* 5.3 4.1 - - - +
466B LEU* 3.7 25.2 - - + +
467B HIS* 2.8 27.4 + - - -
550B TRP* 4.2 10.1 - - + -
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Residues in contact with MET 414 (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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197B PRO* 3.6 34.7 - - + +
384B LEU* 5.0 2.3 - - - +
410B GLY* 2.9 23.1 + - - +
413B ILE* 1.3 82.4 - - + +
415B TYR* 1.3 66.3 + - + +
416B ALA 3.6 0.2 - - - -
417B PRO* 4.5 0.5 - - - +
447B ILE* 4.4 10.1 - - + -
448B TYR* 3.8 15.3 - - + -
466B LEU* 5.3 0.2 - - - -
467B HIS* 3.5 15.9 - - - -
551B PHE* 3.8 28.5 - - + -
1002B 5EE 3.7 68.5 - - + +
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Residues in contact with TYR 415 (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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366B CYS 4.5 0.5 + - - -
367B SER 4.3 0.3 + - - -
368B SER* 2.6 25.2 + - - -
384B LEU* 3.4 21.8 - - + -
385B THR* 3.8 26.5 - - - -
386B ARG* 3.5 30.1 + - + -
411B ASN* 2.8 36.5 + - - +
412B ILE 3.8 1.8 - - - -
414B MET* 1.3 78.2 - - + +
416B ALA* 1.3 62.2 + - - +
417B PRO* 3.2 6.5 - - - -
418B THR* 2.7 33.4 + - + +
420B TRP* 3.6 27.6 - + + -
421B ALA* 3.2 4.7 - - + +
1002B 5EE 3.3 38.5 + - + +
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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