Contacts of the helix formed by residues 399 - 415 (chain A) in PDB entry 2BXE
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 GLY 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A PHE* 3.0 21.4 + - - +
396A GLU 4.8 0.8 + - - -
397A GLN 3.4 2.0 - - - -
398A LEU* 1.3 80.3 - - - +
400A GLU* 1.3 65.0 + - - -
401A TYR 3.6 1.6 - - - -
403A PHE* 3.0 21.8 + - - +
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Residues in contact with GLU 400 (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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395A PHE* 4.0 14.3 - - + -
399A GLY* 1.3 71.6 - - - -
401A TYR* 1.3 59.2 + - - +
403A PHE* 3.3 4.4 + - - +
404A GLN* 2.9 55.9 + - + +
431A GLY 4.1 2.6 - - - +
432A LYS* 4.0 24.2 - - - +
435A SER* 2.6 32.6 + - - +
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Residues in contact with TYR 401 (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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399A GLY 3.6 0.4 - - - -
400A GLU* 1.3 74.3 - - - +
402A LYS* 1.3 76.9 + - + +
404A GLN* 2.9 23.6 + - - +
405A ASN* 3.0 32.3 + - - -
522A GLN* 3.1 47.3 - - + +
525A LYS* 3.3 40.5 + - - +
526A GLN* 3.7 25.4 - - + +
548A MET* 4.8 9.5 - - + +
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Residues in contact with LYS 402 (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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398A LEU* 3.7 40.0 + - + +
399A GLY 4.0 1.4 + - - -
401A TYR* 1.3 88.4 - - + +
403A PHE* 1.3 56.9 + - - +
405A ASN* 3.1 15.0 + - - +
406A ALA* 2.8 29.6 + - - +
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Residues in contact with PHE 403 (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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391A ASN* 3.6 34.8 - - + -
394A LEU* 3.8 30.1 - - + -
395A PHE* 4.1 22.9 - + + -
398A LEU* 4.2 8.7 - - + +
399A GLY 3.0 22.5 + - - +
400A GLU* 3.4 5.6 - - - +
401A TYR 3.1 0.2 - - - -
402A LYS* 1.3 77.2 - - - +
404A GLN* 1.3 61.9 + - - +
406A ALA* 3.6 4.7 + - + +
407A LEU* 3.2 50.0 + - + +
410A ARG* 5.7 1.1 - - - -
431A GLY* 4.0 20.0 - - - -
434A GLY* 4.7 2.0 - - - -
2001A 1FL 3.8 29.6 - + - -
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Residues in contact with GLN 404 (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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400A GLU* 2.9 41.5 + - + +
401A TYR* 2.9 21.6 + - - +
403A PHE* 1.3 74.7 - - - +
405A ASN* 1.3 56.5 + - - +
407A LEU* 3.1 8.7 + - - +
408A LEU* 2.8 36.1 + - + +
427A SER* 4.3 14.8 - - - +
428A ARG* 2.8 57.6 + - + +
431A GLY* 4.2 11.9 - - - -
432A LYS* 4.5 9.9 - - - +
522A GLN* 4.6 1.6 - - - +
526A GLN* 3.7 18.6 + - - +
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Residues in contact with ASN 405 (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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401A TYR* 3.0 43.4 + - - -
402A LYS* 3.1 15.5 + - + +
404A GLN* 1.3 73.1 - - - +
406A ALA* 1.3 67.9 + - - +
408A LEU* 2.8 21.9 + - - +
409A VAL* 2.9 18.8 + - - +
526A GLN* 2.9 33.5 + - - +
529A LEU* 4.2 17.1 - - + +
548A MET* 4.8 11.2 - - - +
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Residues in contact with ALA 406 (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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394A LEU* 5.2 5.8 - - + -
398A LEU* 4.6 11.9 - - + -
402A LYS 2.8 13.9 + - - +
403A PHE* 3.7 13.0 - - + +
405A ASN* 1.3 76.9 - - - +
407A LEU* 1.3 65.3 + - + +
409A VAL* 3.1 8.7 + - - +
410A ARG* 3.0 38.5 + - - +
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Residues in contact with LEU 407 (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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403A PHE* 3.2 45.2 + - + +
404A GLN* 3.1 9.5 + - - +
406A ALA* 1.3 78.8 - - + +
408A LEU* 1.3 57.1 - - - +
410A ARG* 3.6 31.9 - - - +
411A TYR* 2.9 43.1 + - + +
427A SER* 3.9 10.2 + - - +
430A LEU* 4.0 29.4 - - + +
431A GLY* 4.1 2.5 - - - +
2001A 1FL 4.0 26.5 - - + -
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Residues in contact with LEU 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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404A GLN* 2.8 10.8 + - + +
405A ASN* 2.8 21.9 + - - +
407A LEU* 1.3 75.5 - - - +
409A VAL* 1.3 61.0 + - - +
411A TYR* 3.4 1.2 + - - +
412A THR* 2.6 34.7 + - - +
423A LEU* 4.3 3.8 - - + +
424A VAL* 4.1 21.3 - - + +
427A SER* 3.9 17.5 + - - +
428A ARG* 6.3 0.7 - - + -
526A GLN* 3.4 52.0 - - + +
529A LEU* 4.7 9.4 - - + -
530A VAL* 3.3 29.6 - - + -
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Residues in contact with VAL 409 (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 ASN 2.9 17.9 + - - +
406A ALA* 3.5 8.7 - - - +
408A LEU* 1.3 77.4 - - - +
410A ARG* 1.3 66.4 + - - +
412A THR* 3.5 2.4 - - - -
413A LYS* 3.0 50.3 + - + +
529A LEU* 4.2 19.7 - - + -
533A VAL* 4.3 11.4 - - + +
541A LYS* 5.7 7.0 - - + -
544A LEU* 3.8 34.5 - - + -
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Residues in contact with ARG 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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391A ASN* 3.4 18.8 + - - -
394A LEU* 4.2 18.2 - - - +
403A PHE* 5.7 1.2 - - - -
406A ALA* 3.0 23.6 + - - +
407A LEU* 3.6 25.0 - - - +
409A VAL* 1.3 83.3 - - - +
411A TYR* 1.3 66.1 + - + +
413A LYS* 3.5 8.0 + - - +
414A LYS* 3.2 36.0 + - - +
492A GLU* 4.6 1.0 - - - +
2001A 1FL 2.9 39.1 + - - -
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Residues in contact with TYR 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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407A LEU* 2.9 31.3 + - + +
408A LEU 4.3 0.7 - - - +
410A ARG* 1.3 80.3 - - + +
412A THR* 1.3 59.1 + - - +
414A LYS* 3.0 21.0 + - + +
415A VAL* 3.0 44.8 + - + +
423A LEU* 4.5 12.1 - - + -
426A VAL* 5.4 2.9 - - + -
427A SER* 4.3 10.3 - - - +
430A LEU* 3.8 25.4 - - + -
457A LEU* 3.9 19.5 - - + +
460A LEU* 4.6 12.3 - - + -
488A PHE* 3.8 27.1 - + + +
2001A 1FL 2.5 47.6 + + - -
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Residues in contact with THR 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 LEU* 2.6 25.3 + - - +
409A VAL 3.5 3.8 - - - -
411A TYR* 1.3 77.0 - - - +
413A LYS* 1.3 58.4 + - - +
415A VAL 4.6 0.2 - - - -
416A PRO* 3.0 37.7 - - + +
423A LEU* 4.1 22.5 - - + +
530A VAL* 4.0 20.6 - - + +
533A VAL* 3.9 23.8 - - + -
534A LYS* 3.8 31.2 - - + +
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Residues in contact with LYS 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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409A VAL* 3.0 40.2 + - + +
410A ARG* 3.7 8.5 - - - +
412A THR* 1.3 78.4 - - - +
414A LYS* 1.3 57.8 + - - +
416A PRO* 3.7 8.3 - - - +
492A GLU 3.9 10.3 - - - +
493A VAL* 3.2 20.4 - - + +
494A ASP 3.0 24.1 + - - -
533A VAL* 3.9 15.3 - - + -
536A LYS 5.3 0.2 - - - -
537A PRO* 3.2 29.2 - - + +
539A ALA* 3.2 20.6 + - - -
540A THR* 4.6 5.9 - - - +
541A LYS* 4.8 4.4 - - - +
544A LEU* 5.1 2.2 - - - -
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Residues in contact with LYS 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 ARG* 3.2 30.3 - - - +
411A TYR* 3.0 26.0 + - + +
413A LYS* 1.3 79.1 - - - +
415A VAL* 1.3 67.5 + - + +
416A PRO* 3.5 4.4 - - - +
472A ARG* 2.2 34.6 + - - +
488A PHE* 2.7 34.4 + - + +
489A SER* 3.6 5.3 + - - +
491A LEU* 3.3 25.5 + - + +
492A GLU* 3.3 17.9 - - - +
494A ASP* 3.9 0.5 - - - +
2001A 1FL 3.3 31.0 + - - -
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Residues in contact with VAL 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 TYR* 3.0 26.8 + - + +
412A THR 3.4 3.3 - - - +
414A LYS* 1.3 89.3 - - + +
416A PRO* 1.4 64.3 - - - +
417A GLN* 3.2 6.7 - - - -
418A VAL* 3.2 34.3 + - + +
423A LEU* 4.2 12.8 - - + +
460A LEU* 5.5 2.7 - - + -
470A SER* 3.9 11.2 - - - +
472A ARG* 4.3 11.4 - - + +
473A VAL* 3.5 24.9 - - + +
488A PHE* 5.0 5.4 - - + -
491A LEU* 4.5 9.6 - - + -
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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