Contacts of the helix formed by residues 416 - 433 (chain A) in PDB entry 1B3U
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 TRP 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A ALA 3.7 3.8 + - - -
415A LYS* 1.3 68.8 - - - +
417A ARG* 1.3 93.5 + - + +
419A ARG* 3.7 27.2 - - - +
420A LEU* 2.9 50.4 + - + +
454A VAL* 4.0 29.8 - - + +
456A ALA* 5.0 9.4 - - + -
457A ILE* 3.8 9.9 - - + +
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Residues in contact with ARG 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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415A LYS* 3.2 43.8 - - + +
416A TRP* 1.3 111.2 - - + +
418A VAL* 1.3 64.6 + - + +
420A LEU* 3.7 4.5 + - - +
421A ALA* 3.2 19.9 + - - +
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Residues in contact with VAL 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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380A ARG* 4.6 21.1 - - - +
410A LEU* 3.9 25.1 - - + +
413A ASP* 3.6 36.1 - - + +
415A LYS* 3.2 27.5 + - + +
416A TRP 3.1 0.4 - - - -
417A ARG* 1.3 77.2 - - + +
419A ARG* 1.3 68.4 + - - +
420A LEU 3.1 1.3 - - - -
421A ALA* 2.9 17.9 + - - +
422A ILE* 3.2 16.1 + - + +
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Residues in contact with ARG 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU 4.2 7.2 - - - -
411A ALA 3.4 25.4 - - - +
412A GLU* 4.1 3.8 - - - +
413A ASP 2.8 49.7 + - - +
414A ALA* 3.3 21.0 + - - +
415A LYS 3.3 6.4 + - - +
416A TRP* 3.7 13.3 - - - +
418A VAL* 1.3 79.1 - - - +
420A LEU* 1.3 63.4 + - - +
422A ILE* 3.3 12.2 + - - +
423A ILE* 3.3 19.0 + - - +
449A TRP* 4.5 9.8 - - - +
452A ASP* 2.9 41.4 + - - -
453A HIS* 3.9 13.0 - - - -
454A VAL* 3.7 7.3 - - - +
457A ILE* 3.3 21.8 - - + +
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Residues in contact with LEU 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 TRP* 2.9 40.3 + - + +
417A ARG* 3.8 5.2 - - - +
419A ARG* 1.3 78.0 - - - +
421A ALA* 1.3 63.3 + - - +
423A ILE* 3.1 20.5 + - + +
424A GLU* 3.2 25.4 + - + +
456A ALA* 4.0 20.4 - - + +
457A ILE* 4.5 6.9 - - + +
460A ALA* 3.8 29.2 - - + -
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Residues in contact with ALA 421 (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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377A PRO* 6.0 2.9 - - + -
380A ARG* 4.1 21.8 - - - +
417A ARG 3.2 11.5 + - - +
418A VAL* 2.9 9.5 + - - +
420A LEU* 1.3 77.9 - - - +
422A ILE* 1.3 63.0 + - + +
424A GLU* 3.0 25.4 + - - +
425A TYR* 3.2 23.7 + - + +
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Residues in contact with ILE 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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380A ARG* 4.6 3.1 - - - -
407A ILE* 4.2 26.7 - - + +
410A LEU* 3.5 47.3 - - + +
411A ALA* 4.4 5.2 - - - +
418A VAL* 3.2 19.4 + - + +
419A ARG 3.6 6.3 - - - +
420A LEU 3.2 0.2 - - - -
421A ALA* 1.3 74.5 - - + +
423A ILE* 1.3 67.1 + - - +
425A TYR* 2.9 48.1 + - + +
426A MET* 3.5 10.1 + - - +
429A LEU* 6.1 0.9 - - + -
449A TRP* 4.2 19.1 - - + -
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Residues in contact with ILE 423 (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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419A ARG 3.3 15.5 + - - +
420A LEU* 3.1 11.4 + - - +
422A ILE* 1.3 76.7 - - - +
424A GLU* 1.3 64.0 + - + +
426A MET* 3.3 19.4 + - - +
427A PRO* 3.8 3.5 - - - +
449A TRP* 3.6 38.3 - - + -
457A ILE* 3.7 41.7 - - + +
460A ALA* 3.7 38.8 - - + +
461A ALA* 4.1 2.9 - - - +
464A ASN* 4.3 12.2 + - + -
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Residues in contact with GLU 424 (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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420A LEU* 3.4 29.9 - - + +
421A ALA* 3.0 15.1 + - - +
423A ILE* 1.3 82.2 - - - +
425A TYR* 1.3 62.8 + - + +
426A MET 3.3 0.2 - - - -
427A PRO* 3.3 20.6 - - - +
428A LEU* 4.6 6.2 + - - +
460A ALA* 5.1 5.1 - - - +
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Residues in contact with TYR 425 (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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377A PRO* 4.4 1.7 + - - +
380A ARG* 2.7 46.4 + - + +
381A LEU* 4.0 27.8 + - + +
384A ILE* 3.7 41.1 - - + -
407A ILE* 6.1 2.5 - - + -
410A LEU* 5.1 2.9 - - + -
421A ALA* 3.3 20.8 - - + +
422A ILE* 2.9 41.7 + - + +
424A GLU* 1.3 79.8 - - + +
426A MET* 1.3 66.2 + - - +
427A PRO 3.3 0.2 - - - -
428A LEU* 2.8 22.1 + - + +
429A LEU* 2.8 23.7 + - + +
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Residues in contact with MET 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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407A ILE* 5.9 1.6 - - - -
422A ILE* 3.5 13.5 + - - +
423A ILE 3.3 8.6 + - - +
425A TYR* 1.3 76.9 - - - +
427A PRO* 1.3 59.9 - - + +
429A LEU* 3.0 29.4 + - + +
430A ALA* 2.8 31.3 + - - +
438A PHE* 3.5 33.0 - - + -
442A LEU* 3.5 30.3 - - + -
446A CYS* 4.2 14.1 - - - -
449A TRP* 4.5 13.0 - - + -
464A ASN* 3.1 40.4 - - - +
468A LEU* 5.2 0.9 - - + -
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Residues in contact with PRO 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 ILE 3.8 5.6 - - - +
424A GLU* 3.3 21.5 - - - +
426A MET* 1.3 94.8 - - + +
428A LEU* 1.3 59.2 + - + +
430A ALA* 4.1 5.7 - - + +
431A GLY* 3.0 25.1 + - - -
464A ASN* 4.2 7.8 - - - +
467A LYS* 6.3 3.8 - - + -
468A LEU* 5.9 1.3 - - + -
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Residues in contact with LEU 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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381A LEU* 4.2 15.9 - - + -
384A ILE* 4.3 14.4 - - + -
385A SER* 3.7 25.1 - - - +
424A GLU 4.7 6.7 - - - +
425A TYR* 2.8 18.4 + - + +
427A PRO* 1.3 78.0 - - + +
429A LEU* 1.3 57.3 + - - +
431A GLY* 3.9 0.6 - - - -
432A GLN* 3.0 48.3 + - + +
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Residues in contact with LEU 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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384A ILE* 4.5 9.9 - - + -
387A LEU* 3.5 28.7 - - + -
403A LEU* 4.3 8.1 - - + -
407A ILE* 4.2 20.2 - - + -
422A ILE* 6.1 1.3 - - + -
425A TYR* 2.8 29.6 + - + +
426A MET* 3.4 39.3 - - + +
428A LEU* 1.3 75.8 - - - +
430A ALA* 1.3 60.1 + - - +
432A GLN* 4.8 2.2 - - - -
433A LEU* 2.8 38.8 + - + +
434A GLY 3.8 0.2 + - - -
437A PHE* 3.9 23.6 - - + -
438A PHE* 4.3 2.7 - - - -
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Residues in contact with ALA 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 MET 2.8 15.0 + - - +
427A PRO* 4.1 6.1 - - + +
429A LEU* 1.3 72.8 - - - +
431A GLY* 1.3 59.9 + - - +
434A GLY* 2.9 27.7 + - - +
438A PHE* 3.4 30.9 - - + -
468A LEU* 4.2 12.3 - - + -
471A LYS* 4.0 17.9 - - + -
472A PHE* 4.0 13.9 - - + -
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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
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427A PRO 3.0 18.3 + - - -
428A LEU 3.9 1.1 - - - -
430A ALA* 1.3 79.4 - - - +
432A GLN* 1.3 59.8 + - - +
434A GLY 4.9 0.3 + - - -
471A LYS* 4.4 14.1 - - - +
157B VAL 4.8 9.2 - - - +
158B SER* 5.1 0.9 - - - -
159B SER 5.1 1.0 + - - -
162B LYS* 5.0 8.0 + - - -
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Residues in contact with GLN 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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384A ILE 2.9 19.7 - - - +
385A SER* 3.3 16.9 + - - -
387A LEU* 2.9 35.0 - - + +
388A ASP* 3.1 35.9 + - - +
428A LEU* 3.0 29.8 + - + +
429A LEU* 4.2 1.1 - - - +
431A GLY* 1.3 78.9 - - - +
433A LEU* 1.3 71.1 + - + +
434A GLY 3.5 0.4 - - - -
159B SER* 2.8 37.5 + - - -
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Residues in contact with LEU 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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387A LEU* 3.7 38.1 - - + +
391A ASN* 3.7 38.4 - - + +
396A ILE* 4.1 7.1 - - + +
399A LEU* 4.1 9.4 - - + -
403A LEU* 4.3 5.2 - - + -
429A LEU* 2.8 20.8 + - + +
432A GLN* 1.3 81.4 - - + +
434A GLY* 1.3 64.8 + - - +
436A GLU* 3.4 21.3 - - - +
437A PHE* 3.7 42.2 - - + +
158B SER* 3.8 5.8 - - - -
159B SER* 4.4 0.7 - - - +
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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