Contacts of the helix formed by residues 419 - 438 (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 SER 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A GLN 3.2 5.2 + - - -
418A VAL* 1.3 72.2 - - - +
420A THR* 1.3 68.0 + - - +
421A PRO* 3.2 11.2 - - - +
422A THR* 2.9 36.4 + - - -
423A LEU* 3.1 9.9 + - - +
469A VAL* 5.0 2.4 - - - +
534A LYS* 4.1 2.5 - - - +
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Residues in contact with THR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL 3.5 3.5 + - - -
419A SER* 1.3 68.9 - - - +
421A PRO* 1.3 64.3 - - + +
423A LEU* 3.4 2.7 + - - +
424A VAL* 2.9 36.8 + - + +
500A LYS* 5.6 0.2 + - - -
527A THR* 3.3 36.1 - - + +
530A VAL* 3.6 34.9 - - + +
531A GLU* 2.9 23.2 + - - +
534A LYS* 3.6 11.1 + - - +
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Residues in contact with PRO 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A SER* 3.2 13.5 - - - +
420A THR* 1.3 95.9 - - + +
422A THR* 1.3 64.6 + - - +
424A VAL* 3.2 8.5 + - + +
425A GLU* 3.0 23.9 + - - +
527A THR* 6.2 0.7 - - + -
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Residues in contact with THR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 3.9 8.5 - - + -
419A SER* 2.9 24.8 + - - -
421A PRO* 1.3 77.4 - - - +
423A LEU* 1.3 64.5 + - - +
425A GLU* 3.2 5.6 + - - +
426A VAL* 2.9 28.0 + - + +
460A LEU* 3.9 27.6 - - + -
463A LEU* 4.1 38.1 - - + +
464A HIS* 5.3 2.2 - - - +
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Residues in contact with LEU 423 (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 3.1 - - + -
411A TYR* 4.5 21.1 - - + +
412A THR* 4.1 22.4 - - + +
415A VAL* 4.2 22.4 - - + +
418A VAL* 3.1 50.9 - - + +
419A SER 3.1 4.7 + - - +
420A THR* 3.7 6.3 - - - +
422A THR* 1.3 77.7 - - - +
424A VAL* 1.3 66.2 + - - +
426A VAL* 4.0 5.1 - - + +
427A SER* 2.9 30.3 + - - +
460A LEU* 5.6 4.9 - - + -
530A VAL* 4.3 9.4 - - + -
534A LYS* 4.1 13.9 - - - -
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 4.1 7.9 - - + +
420A THR* 2.9 25.5 + - + +
421A PRO* 3.6 6.7 - - + +
423A LEU* 1.3 75.6 - - - +
425A GLU* 1.3 56.0 + - - +
427A SER* 3.9 1.7 - - - -
428A ARG* 2.7 51.8 + - + +
523A ILE* 4.5 11.7 - - + +
526A GLN* 4.0 16.2 - - + +
527A THR* 3.7 29.2 - - + +
530A VAL* 3.7 23.1 - - + -
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A PRO 3.0 12.2 + - - +
422A THR* 3.5 10.3 - - - +
424A VAL* 1.3 73.6 - - - +
426A VAL* 1.3 69.2 + - + +
428A ARG* 2.9 24.1 + - - +
429A ASN* 3.1 27.9 + - - +
459A GLN* 3.2 31.2 + - - +
463A LEU* 5.1 5.6 - - + -
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TYR* 5.4 3.4 - - + -
422A THR* 2.9 27.2 + - + +
423A LEU* 4.0 5.6 - - + +
425A GLU* 1.3 76.9 - - + +
427A SER* 1.3 59.3 + - - +
429A ASN* 3.6 2.1 + - - +
430A LEU* 2.9 51.2 + - + +
456A VAL* 3.8 7.9 - - + +
457A LEU* 5.1 2.2 - - + -
459A GLN* 4.2 19.7 - - + +
460A LEU* 3.6 52.3 - - + +
463A LEU* 5.3 1.1 - - + -
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 4.3 10.5 - - - +
407A LEU* 3.9 17.2 + - - +
408A LEU* 3.9 31.8 - - - +
411A TYR* 4.3 11.4 - - - +
423A LEU* 2.9 19.7 + - - +
424A VAL 4.0 2.7 - - - -
426A VAL* 1.3 75.3 - - - +
428A ARG* 1.3 66.4 + - - +
430A LEU* 3.4 13.5 + - - +
431A GLY* 3.0 18.0 + - - -
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Residues in contact with ARG 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 2.8 47.2 + - + +
408A LEU* 6.3 0.9 - - + -
424A VAL* 2.7 35.4 + - - +
425A GLU* 2.9 13.7 + - - +
427A SER* 1.3 76.1 - - - +
429A ASN* 1.3 66.8 + - - +
431A GLY 3.0 8.3 + - - -
432A LYS* 3.1 22.1 + - - +
519A LYS* 4.7 9.1 + - - +
522A GLN* 4.1 17.4 + - - +
523A ILE* 4.0 32.5 - - - +
526A GLN* 3.0 27.4 + - - +
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Residues in contact with ASN 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 3.1 25.7 + - - +
426A VAL 3.7 4.7 - - - +
428A ARG* 1.3 75.0 - - - +
430A LEU* 1.3 66.3 + - - +
431A GLY 2.9 1.3 - - - -
432A LYS* 2.7 31.2 + - - +
433A VAL* 3.2 13.5 + - - +
452A TYR* 4.6 3.7 - - + +
456A VAL* 4.1 16.6 - - + -
459A GLN* 2.6 38.4 + - - +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 4.0 14.8 - - + -
411A TYR* 3.8 37.7 - - + -
426A VAL* 2.9 39.7 + - + +
427A SER* 3.5 15.0 - - - +
428A ARG 3.3 0.2 - - - -
429A ASN* 1.3 75.2 - - - +
431A GLY* 1.3 59.0 + - - +
433A VAL* 3.3 11.0 - - - +
453A LEU* 3.8 25.8 - - + -
456A VAL* 3.4 22.2 - - + -
457A LEU* 4.4 11.0 - - + -
2001A 1FL 3.2 32.4 - - + -
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Residues in contact with GLY 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 4.7 2.6 - - - -
400A GLU* 4.1 8.3 - - - +
403A PHE* 4.0 24.6 - - - -
404A GLN* 4.2 12.6 - - - -
407A LEU* 4.1 3.3 - - - +
427A SER 3.0 9.3 + - - -
428A ARG 3.0 8.7 + - - -
429A ASN 2.9 1.6 - - - -
430A LEU* 1.3 74.9 - - - +
432A LYS* 1.3 65.1 + - - +
433A VAL 3.2 0.7 - - - -
434A GLY* 3.0 15.0 + - - -
435A SER* 3.6 2.9 + - - -
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Residues in contact with LYS 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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187A ASP* 5.6 3.8 + - - -
400A GLU* 4.0 20.8 + - - +
404A GLN* 4.5 7.2 - - - +
428A ARG* 3.1 27.6 + - - +
429A ASN* 2.7 24.9 + - - +
431A GLY* 1.3 69.0 - - - +
433A VAL* 1.3 69.2 + - - +
434A GLY 2.8 2.0 - - - -
435A SER* 2.6 18.4 + - - -
436A LYS* 2.9 13.0 + - + +
452A TYR* 5.0 9.9 - - + +
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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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429A ASN 3.6 5.8 - - - +
430A LEU* 3.3 22.0 - - - +
432A LYS* 1.3 77.2 - - - +
434A GLY* 1.3 55.9 + - - +
436A LYS* 3.6 4.0 - - - +
437A CYS* 2.8 33.5 + - - +
449A ALA* 4.0 33.0 - - + +
452A TYR* 2.9 39.2 - - + -
453A LEU* 4.2 13.7 - - + -
456A VAL* 4.2 4.3 - - + -
2001A 1FL 4.0 16.8 - - + -
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Residues in contact with GLY 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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395A PHE* 3.5 16.6 - - - -
403A PHE* 4.7 2.2 - - - -
430A LEU 4.1 0.2 + - - -
431A GLY 3.0 10.1 + - - -
432A LYS 2.8 2.8 + - - -
433A VAL* 1.3 80.3 - - - +
435A SER* 1.3 55.8 + - - -
438A CYS* 3.1 37.6 + - - +
2001A 1FL 3.3 22.1 - - - -
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Residues in contact with SER 435 (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* 3.4 26.2 - - - -
400A GLU* 2.6 30.7 + - - +
431A GLY 3.6 1.0 + - - -
432A LYS* 2.6 14.4 + - - -
434A GLY* 1.3 73.6 - - - +
436A LYS* 1.3 60.1 + - - +
439A LYS* 4.5 13.7 + - - +
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Residues in contact with LYS 436 (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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432A LYS* 2.9 10.6 + - + +
433A VAL* 3.6 11.9 - - - +
435A SER* 1.3 80.8 - - - +
437A CYS* 1.3 60.2 + - - +
439A LYS* 4.8 1.7 + - - +
440A HIS* 3.4 23.2 + - - -
448A CYS* 3.9 10.9 - - - -
452A TYR* 5.4 15.9 - - + -
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Residues in contact with CYS 437 (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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392A CYS* 4.5 4.5 - - - -
433A VAL* 2.8 26.5 + - - +
436A LYS* 1.3 77.1 - - - +
438A CYS* 1.3 64.6 + - - +
439A LYS 3.1 4.8 + - - -
440A HIS* 3.3 18.7 + - - +
445A ARG* 3.9 11.7 - - - +
448A CYS* 2.0 48.7 - - + -
449A ALA* 3.0 36.8 - - + +
452A TYR* 4.8 3.8 - - - -
2001A 1FL 5.6 0.4 - - - -
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Residues in contact with CYS 438 (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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392A CYS* 2.0 60.6 - - + +
395A PHE* 3.8 19.5 - - + -
396A GLU* 4.6 6.2 - - + +
433A VAL 4.9 0.2 - - - -
434A GLY* 3.1 37.5 + - - +
437A CYS* 1.3 79.1 - - - +
439A LYS* 1.3 61.0 + - - +
440A HIS 3.5 7.2 - - - +
445A ARG* 3.5 18.2 + - - +
2001A 1FL 3.8 6.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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