Contacts of the helix formed by residues 417 - 434 (chain A) in PDB entry 2BAP
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 ALA 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A TYR* 3.2 29.5 - - + +
416A GLU* 1.3 77.0 - - + +
418A ARG* 1.3 51.1 + - - +
419A PRO* 3.2 3.8 - - - -
420A GLN* 2.8 29.5 + - + +
421A TYR* 2.6 33.3 + - - +
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Residues in contact with ARG 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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411A VAL* 3.5 21.2 + - + -
412A ARG 3.1 22.9 - - - -
413A ASN* 2.5 52.9 + - - +
415A TYR* 2.9 27.2 + - + +
417A ALA* 1.3 73.5 - - - +
419A PRO* 1.4 73.2 - - + +
421A TYR* 3.4 2.9 - - - +
422A TYR* 2.9 49.7 + - + -
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Residues in contact with PRO 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 TYR 4.3 0.4 - - - +
416A GLU 3.5 11.9 - - - +
417A ALA 3.3 0.4 - - - -
418A ARG* 1.4 94.7 - - + +
420A GLN* 1.3 82.2 + - - +
422A TYR* 3.4 5.1 + - + +
423A LYS* 2.9 30.2 + - - +
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Residues in contact with GLN 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 GLU 3.9 2.4 - - - +
417A ALA* 2.8 40.2 + - + +
419A PRO* 1.3 96.9 - - - +
421A TYR* 1.3 61.9 + - - +
423A LYS* 3.0 32.2 + - - +
424A LEU* 2.9 27.9 + - + +
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Residues in contact with TYR 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A VAL* 3.6 44.5 - - + +
415A TYR* 3.8 16.8 - + + -
417A ALA 2.6 15.7 + - - +
418A ARG* 3.4 14.8 - - - +
420A GLN* 1.3 73.0 - - - +
422A TYR* 1.3 60.8 + + + +
424A LEU* 2.9 33.2 + - + +
425A ILE* 2.9 38.3 + - + +
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Residues in contact with TYR 422 (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 LEU* 2.6 45.5 + - + -
409A LEU* 3.7 18.1 - - + +
411A VAL* 4.0 20.9 + - + +
418A ARG* 2.9 57.5 + - + +
419A PRO* 4.0 4.0 - - + +
421A TYR* 1.3 71.5 - + - +
423A LYS* 1.3 57.3 + - - +
425A ILE* 3.4 15.1 + - + +
426A GLU* 2.8 34.5 + - - +
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Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PRO 2.9 12.3 + - - +
420A GLN* 3.0 48.3 + - - +
422A TYR* 1.3 76.4 - - - +
424A LEU* 1.3 66.9 + - + +
426A GLU* 2.8 29.4 - - + +
427A GLU* 3.3 16.0 + - - +
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLN* 2.9 19.8 + - + +
421A TYR* 2.9 15.8 + - + +
423A LYS* 1.3 86.4 - - + +
425A ILE* 1.3 62.6 + - + +
427A GLU* 3.2 15.3 + - - +
428A CYS* 3.1 26.9 + - - -
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 4.4 27.1 - - + +
411A VAL* 5.3 1.8 - - + -
421A TYR* 2.9 48.4 + - + +
422A TYR* 3.4 15.0 + - + +
424A LEU* 1.3 72.5 - - + +
426A GLU* 1.3 66.8 + - - +
428A CYS* 3.0 15.3 + - + -
429A VAL* 2.9 36.6 + - + +
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Residues in contact with GLU 426 (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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375A ARG* 5.0 9.6 + - - -
422A TYR 2.8 14.5 + - - +
423A LYS* 2.8 25.0 - - + +
425A ILE* 1.3 74.1 - - - +
427A GLU* 1.3 63.0 + - - +
429A VAL* 3.3 8.5 - - - +
430A SER* 2.8 46.9 + - - -
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Residues in contact with GLU 427 (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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423A LYS* 4.3 14.4 - - - +
424A LEU* 3.2 15.2 + - - +
426A GLU* 1.3 83.9 - - - +
428A CYS* 1.3 56.3 + - - +
430A SER* 2.6 24.2 + - - +
431A GLN* 2.7 36.5 + - + +
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Residues in contact with CYS 428 (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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424A LEU* 3.1 29.2 + - - -
425A ILE* 3.0 22.9 + - + +
427A GLU* 1.3 77.5 - - - +
429A VAL* 1.3 63.7 + - - +
431A GLN* 3.1 12.4 + - - +
432A ILE* 3.0 32.4 + - + +
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Residues in contact with VAL 429 (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 LEU* 6.0 3.4 - - + -
425A ILE* 2.9 29.3 + - + +
426A GLU* 3.3 14.1 - - - +
428A CYS* 1.3 72.7 - - - +
430A SER* 1.3 50.2 + - - +
432A ILE* 3.0 16.1 + - + +
433A VAL* 2.8 55.1 + - + +
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Residues in contact with SER 430 (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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426A GLU* 2.9 25.2 + - - -
427A GLU* 2.6 39.8 + - - +
429A VAL* 1.3 74.9 - - - +
431A GLN* 1.3 58.2 + - - +
433A VAL* 4.6 3.8 - - - +
434A LEU* 2.9 40.3 + - - +
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Residues in contact with GLN 431 (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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335A HIS* 5.2 8.0 + - - -
427A GLU* 2.7 33.6 + - + +
428A CYS* 3.3 10.6 - - - +
430A SER* 1.3 73.9 + - - +
432A ILE* 1.3 60.3 + - + +
435A HIS* 2.9 53.8 + - + +
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Residues in contact with ILE 432 (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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323A VAL* 5.1 0.7 - - - +
327A SER* 2.6 39.6 + - - +
331A ARG* 6.5 0.7 - - + -
428A CYS* 3.0 27.2 + - + +
429A VAL* 3.3 19.3 - - + +
431A GLN* 1.3 79.5 - - + +
433A VAL* 1.3 64.0 + - + +
434A LEU 5.0 0.5 - - - -
435A HIS 5.3 1.4 - - - -
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Residues in contact with VAL 433 (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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323A VAL* 3.4 28.4 - - + +
367A LEU* 3.7 15.4 - - + +
429A VAL* 2.8 43.3 + - + +
430A SER* 4.5 2.7 - - - +
432A ILE* 1.3 77.3 - - + +
434A LEU* 1.3 62.9 + - + +
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Residues in contact with LEU 434 (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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323A VAL* 5.6 1.4 - - - +
326A ARG* 5.8 2.9 - - - -
360A GLY 5.5 1.0 - - - +
364A PHE* 3.7 51.4 - - + +
367A LEU* 3.7 28.3 - - + +
368A LYS* 3.8 33.0 - - + +
371A LEU* 4.5 12.8 - - + -
430A SER* 2.9 19.4 + - - +
433A VAL* 1.3 83.1 - - + +
435A HIS* 1.3 67.4 + - - +
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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