Contacts of the helix formed by residues 404 - 421 (chain B) in PDB entry 2A79
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 LEU 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334B PHE* 4.8 20.4 - - + -
400B LEU 3.1 24.9 - - - +
401B THR* 3.6 14.8 - - - +
402B ILE 2.7 9.9 + - - -
403B ALA* 1.3 81.2 - - - +
405B PRO* 1.3 66.9 - - + +
406B VAL 3.0 4.0 - - - +
407B PRO* 2.8 21.6 - - - +
408B VAL* 4.4 5.7 - - - +
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Residues in contact with PRO 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLU* 4.2 19.3 - - + +
328B LEU 5.1 0.2 - - - +
330B LEU* 5.1 4.7 - - + -
331B LEU* 3.7 38.8 - - + +
401B THR 3.6 7.4 - - - +
402B ILE 3.4 11.2 - - - +
404B LEU* 1.3 95.8 - - + +
406B VAL* 1.3 62.5 + - - +
407B PRO 3.5 0.2 - - - -
408B VAL* 3.1 13.0 + - + +
409B ILE* 3.0 37.8 + - + +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ILE* 3.1 29.6 - - + +
403B ALA* 4.0 10.1 - - - -
405B PRO* 1.3 76.4 - - + +
407B PRO* 1.3 72.6 - - + +
408B VAL 3.0 0.5 + - - -
409B ILE* 3.1 8.8 + - - +
410B VAL* 2.8 42.3 + - + +
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Residues in contact with PRO 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ALA 4.7 5.8 - - - +
404B LEU* 2.8 29.8 - - - +
406B VAL* 1.3 87.8 - - + +
408B VAL* 1.3 57.7 + - + +
410B VAL* 3.9 6.3 - - + +
411B SER* 2.9 30.5 + - - -
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLU* 3.2 41.1 - - + +
404B LEU 4.4 9.4 - - - +
405B PRO* 3.4 13.0 - - + +
406B VAL 3.0 0.6 - - - -
407B PRO* 1.3 76.7 - - + +
409B ILE* 1.3 62.7 + - - +
411B SER* 3.1 6.6 + - - -
412B ASN* 2.7 47.5 + - - +
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 6.3 2.7 - - + -
320B THR* 4.9 10.3 - - - +
321B LEU* 5.5 11.9 - - + -
324B SER* 4.2 17.3 - - - +
327B GLU* 4.7 9.0 - - + -
328B LEU* 4.8 23.1 - - + -
331B LEU* 5.9 2.2 - - + -
405B PRO* 3.0 25.9 + - + +
406B VAL* 3.8 7.0 - - - +
408B VAL* 1.3 74.9 - - - +
410B VAL* 1.3 55.9 + - + +
412B ASN* 3.3 9.5 + - - +
413B PHE* 2.7 36.2 + - + +
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 2.8 39.6 + - + +
407B PRO* 3.9 6.3 - - + +
409B ILE* 1.3 74.3 - - + +
411B SER* 1.3 57.1 + - - +
412B ASN 3.0 1.8 - - - -
413B PHE* 4.3 7.4 - - + -
414B ASN* 2.6 46.9 + - + +
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B PRO 2.9 19.9 + - - -
408B VAL* 3.6 6.1 - - - -
410B VAL* 1.3 77.5 - - - +
412B ASN* 1.3 59.7 + - - +
414B ASN* 4.4 6.3 + - - +
415B TYR* 3.2 25.3 + - - +
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Residues in contact with ASN 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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320B THR* 3.8 9.6 - - + -
323B ALA* 5.9 2.1 - - - +
324B SER* 3.4 24.0 - - - -
327B GLU* 4.6 0.2 - - - +
408B VAL* 2.7 45.2 + - - +
409B ILE* 3.5 6.0 - - - +
411B SER* 1.3 78.5 - - - +
413B PHE* 1.3 60.1 + - - +
415B TYR* 3.3 4.3 + - - +
416B PHE* 2.8 51.0 + - + -
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Residues in contact with PHE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLY* 4.6 5.8 - - - -
316B ILE* 3.4 34.9 - - + +
317B LEU* 4.0 23.1 - - + -
320B THR* 3.3 17.2 - - + +
409B ILE* 2.7 24.3 + - + +
410B VAL* 3.7 8.1 - - + +
412B ASN* 1.3 73.0 - - - +
414B ASN* 1.3 57.5 + - + +
415B TYR 3.1 0.2 + - - -
416B PHE* 3.1 2.1 + - - +
417B TYR* 2.6 54.1 + + + +
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Residues in contact with ASN 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B VAL* 2.6 30.2 + - + +
411B SER* 4.4 5.5 + - - +
413B PHE* 1.3 78.1 - - + +
415B TYR* 1.3 55.5 + - - +
417B TYR* 3.8 13.8 - - - +
418B HIS* 2.9 33.3 + - - +
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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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130B GLU 5.2 1.0 + - - -
131B GLY* 4.4 17.2 - - - -
411B SER 3.2 20.1 + - - +
412B ASN* 3.3 6.2 + - - +
413B PHE 3.0 0.8 - - - -
414B ASN* 1.3 76.3 - - - +
416B PHE* 1.3 72.3 + + - +
417B TYR 3.1 1.6 - - - -
418B HIS* 4.1 2.8 - - + +
419B ARG* 2.7 51.0 + - + +
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Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE* 3.7 19.8 - - + +
319B GLN* 3.7 51.4 - - + +
320B THR* 3.5 18.4 - - + -
323B ALA* 4.3 16.6 - - + -
412B ASN* 2.8 38.2 + - + +
413B PHE 3.7 2.7 - - - +
415B TYR* 1.3 86.0 - + - +
417B TYR* 1.3 57.2 + - - +
419B ARG* 4.3 4.4 - - + +
420B GLU* 3.1 29.8 + - - +
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Residues in contact with TYR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE* 3.6 30.9 - - + +
413B PHE* 2.6 38.7 + + + +
414B ASN* 3.8 15.0 - - - +
416B PHE* 1.3 72.3 - - - +
418B HIS* 1.3 65.5 + - + +
420B GLU* 3.4 1.2 + - - +
421B THR* 3.0 42.9 + - - -
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Residues in contact with HIS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ASN* 2.9 25.7 + - - +
415B TYR* 4.1 4.0 - - + +
417B TYR* 1.3 84.2 - - + +
419B ARG* 1.3 62.3 + - - +
421B THR* 3.7 17.4 + - - -
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Residues in contact with ARG 419 (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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415B TYR* 2.7 42.6 + - + +
416B PHE* 4.3 5.4 - - + +
418B HIS* 1.3 72.2 - - - +
420B GLU* 1.3 64.2 + - - +
421B THR 4.5 2.8 - - - -
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ILE* 4.6 15.7 - - + -
319B GLN* 5.9 2.7 - - - +
416B PHE 3.1 21.6 + - - +
417B TYR 3.8 2.7 - - - +
419B ARG* 1.3 76.4 - - - +
421B THR* 1.3 67.0 + - - +
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Residues in contact with THR 421 (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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417B TYR* 3.0 35.0 + - - -
418B HIS* 3.9 15.0 - - - -
419B ARG 3.4 3.0 - - - +
420B GLU* 1.3 83.1 - - - +
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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