Contacts of the helix formed by residues 407 - 420 (chain A) in PDB entry 3AR2
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 PHE 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A ILE* 4.2 9.0 - - + -
380A ASN* 3.6 27.1 - - - -
382A PHE* 4.0 23.6 - + - -
397A LYS* 4.6 8.7 - - + -
402A ILE* 3.5 34.3 - - + -
403A ARG 4.6 1.6 - - - -
404A SER 2.9 10.1 + - - +
406A GLN* 1.3 102.1 - - + +
408A ASP* 1.3 57.0 + - - +
409A GLY 3.2 0.7 - - - +
410A LEU* 2.7 41.2 + - + +
411A VAL* 3.2 12.9 + - - +
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A GLY 5.2 1.8 + - - +
406A GLN 3.9 4.9 + - - +
407A PHE* 1.3 69.4 - - - +
409A GLY* 1.3 64.2 + - - +
411A VAL* 2.9 27.9 + - - +
412A GLU* 3.2 11.8 + - - +
531A GLY* 3.6 26.9 - - - +
532A THR* 3.6 26.1 + - + +
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Residues in contact with GLY 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE* 3.5 27.0 - - - +
407A PHE 3.1 1.8 + - - -
408A ASP* 1.3 78.2 - - - +
410A LEU* 1.3 57.2 + - - +
412A GLU* 3.7 3.3 + - - -
413A LEU* 3.1 26.0 + - - +
529A ARG* 5.5 2.9 - - - -
531A GLY* 3.9 20.2 - - - -
594A VAL* 3.7 11.2 - - - +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A MET* 4.1 26.0 - - + -
368A ILE* 3.6 25.2 - - + +
382A PHE* 3.6 44.6 - - + -
395A VAL* 4.8 0.4 - - + -
404A SER* 3.8 28.5 - - - +
407A PHE* 2.7 27.1 + - + +
409A GLY* 1.3 71.0 - - - -
411A VAL* 1.3 59.0 + - - +
413A LEU* 3.7 3.8 - - + -
414A ALA* 2.8 26.3 + - - +
452A MET* 3.4 24.7 - - + +
454A VAL* 4.6 1.1 - - - -
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A GLY* 4.2 23.6 - - - +
407A PHE 3.2 15.2 + - - +
408A ASP* 2.9 23.1 + - - +
410A LEU* 1.3 77.2 - - - +
412A GLU* 1.3 62.5 + - - +
414A ALA* 3.3 2.4 + - - +
415A THR* 2.9 27.3 + - - +
454A VAL* 4.4 13.6 - - + +
455A PHE* 3.8 34.8 - - + -
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ASP 3.2 7.0 + - - +
409A GLY* 4.0 4.0 - - - +
411A VAL* 1.3 77.7 - - - +
413A LEU* 1.3 57.9 + - - +
415A THR* 2.6 32.5 + - - -
416A ILE* 2.8 16.3 + - + +
513A PHE* 5.0 4.7 - - + -
529A ARG* 2.4 54.9 + - - +
531A GLY 4.6 1.4 - - - +
566A THR* 3.0 31.0 + - + +
594A VAL* 3.4 21.6 - - + +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A MET* 4.1 22.2 - - + -
367A PHE 4.8 0.4 - - - +
368A ILE* 4.2 5.4 - - + -
409A GLY 3.1 17.8 + - - +
410A LEU* 3.4 20.6 - - + +
412A GLU* 1.3 77.5 - - - +
414A ALA* 1.3 61.8 + - - +
416A ILE* 3.6 6.9 + - - +
417A CYS* 3.2 36.3 + - - -
448A LEU* 4.6 0.9 - - + -
452A MET* 4.2 9.0 - - - -
564A LEU* 3.9 26.4 - - + +
594A VAL* 3.6 7.4 - - + +
595A GLY* 3.9 26.0 - - - +
596A VAL 4.3 3.4 - - - +
597A VAL* 4.3 9.0 - - + -
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A LEU 2.8 20.8 + - - +
411A VAL 3.7 3.1 - - - +
413A LEU* 1.3 74.6 - - - +
415A THR* 1.3 66.7 + - - +
417A CYS* 3.2 8.4 + - - +
418A ALA* 2.9 25.6 + - - +
449A VAL* 4.2 10.6 - - + +
452A MET* 3.9 14.1 - - + -
454A VAL* 3.7 21.3 - - + -
475A ILE* 3.8 12.0 - - + +
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Residues in contact with THR 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A VAL* 2.9 25.8 + - - +
412A GLU* 2.6 20.1 + - + -
414A ALA* 1.3 71.6 - - - +
416A ILE* 1.3 57.5 + - - +
418A ALA* 3.3 1.2 + - - +
419A LEU* 2.9 56.0 + - + +
455A PHE* 5.0 4.7 - - - -
475A ILE* 3.9 22.5 - - + +
478A LEU* 5.5 6.3 - - + +
479A MET* 5.0 5.2 - - + -
513A PHE* 4.0 20.2 - - + -
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A GLU* 2.8 17.9 + - + +
413A LEU* 3.8 5.6 - - - +
415A THR* 1.3 75.5 - - - +
417A CYS* 1.3 66.0 + - - +
418A ALA 3.0 0.7 + - - -
420A CYS* 2.8 34.0 + - + +
513A PHE* 3.7 26.9 - - + -
514A VAL 3.6 20.2 - - - +
515A LYS* 4.6 1.8 - - + -
564A LEU* 3.8 17.5 - - + -
565A ALA 3.5 13.0 - - - +
566A THR* 3.2 35.7 - - + -
594A VAL* 3.9 22.2 - - + -
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Residues in contact with CYS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU* 3.2 31.2 + - - +
414A ALA* 3.5 8.7 - - - +
416A ILE* 1.3 78.3 - - - +
418A ALA* 1.3 56.5 + - - +
420A CYS 4.5 1.4 - - - +
421A ASN* 3.3 27.0 - - - +
445A LEU* 3.8 36.6 - - + +
448A LEU* 4.6 9.9 - - - -
449A VAL* 3.7 18.4 - - + +
515A LYS* 5.6 0.9 - - - -
564A LEU* 3.5 22.0 - - - -
597A VAL* 4.7 2.5 - - - -
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A ALA 2.9 15.7 + - - +
415A THR 3.7 3.1 - - - +
417A CYS* 1.3 77.9 - - - +
419A LEU* 1.3 65.0 + - + +
421A ASN* 3.7 15.5 - - - +
449A VAL* 4.1 3.3 - - + +
472A ASN* 3.2 32.5 - - + +
475A ILE* 4.0 27.1 - - + -
476A ARG* 5.2 9.3 + - + +
481A LYS* 5.9 0.2 - - - -
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A THR* 2.9 30.1 + - + +
416A ILE 4.1 0.4 - - - +
418A ALA* 1.3 79.1 - - - +
420A CYS* 1.3 58.0 + - - +
421A ASN 3.1 7.2 + - - -
475A ILE* 4.0 10.1 - - + +
476A ARG* 4.1 31.6 - - + -
479A MET* 3.8 24.9 - - + +
481A LYS* 3.3 34.7 + - + +
496A VAL* 3.4 10.5 - - + +
498A CYS* 4.2 6.5 - - - -
513A PHE* 3.2 42.4 - - + -
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Residues in contact with CYS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A ILE* 2.8 26.2 + - + +
417A CYS 4.5 0.3 - - - +
419A LEU* 1.3 70.1 - - - +
421A ASN* 1.3 60.9 + - - +
494A MET* 3.4 46.9 - - - -
495A SER* 4.3 1.8 - - - -
496A VAL* 4.0 10.1 - - + -
513A PHE* 3.4 22.2 - - + +
515A LYS* 2.9 37.3 + - + +
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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