Contacts of the helix formed by residues 416 - 433 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B ALA 3.6 5.2 + - - -
415B LYS* 1.3 72.4 - - - +
417B ARG* 1.3 81.7 + - + +
419B ARG* 3.5 28.8 - - - +
420B LEU* 2.9 54.6 + - + +
454B VAL* 3.9 28.0 - - + -
456B ALA* 5.1 10.5 - - + -
457B ILE* 3.7 11.9 - - + +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B LYS* 3.0 40.5 + - + +
416B TRP* 1.3 110.3 - - + +
418B VAL* 1.3 64.2 + - + +
420B LEU* 3.5 6.4 - - + +
421B ALA* 3.4 17.7 + - - +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ARG* 4.8 19.7 - - - +
410B LEU* 4.1 21.5 - - + +
413B ASP* 3.5 36.3 - - + +
415B LYS* 2.8 27.8 + - + +
417B ARG* 1.3 78.5 - - + +
419B ARG* 1.3 58.2 + - - +
420B LEU 3.0 1.3 - - - -
421B ALA* 2.7 33.1 + - - +
422B ILE* 3.2 6.3 + - + +
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU 4.1 7.4 - - - +
411B ALA 3.5 25.4 - - - +
412B GLU* 4.4 2.7 - - - +
413B ASP 2.6 51.6 + - - +
414B ALA* 3.4 20.4 + - - +
415B LYS 3.1 1.7 + - - +
416B TRP* 3.5 17.9 - - - +
418B VAL* 1.3 77.9 - - - +
420B LEU* 1.3 61.7 + - - +
421B ALA 3.3 0.7 + - - -
422B ILE* 3.3 13.7 + - - +
423B ILE* 3.4 19.7 + - - +
449B TRP* 4.6 9.4 + - - +
452B ASP* 3.0 40.3 + - - -
453B HIS* 3.3 24.6 + - - -
454B VAL* 3.7 0.8 - - - +
457B ILE* 3.1 22.0 - - + +
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TRP* 2.9 41.3 + - + +
417B ARG* 3.5 8.7 - - + +
418B VAL 3.0 0.2 - - - -
419B ARG* 1.3 79.0 - - - +
421B ALA* 1.3 60.8 + - - +
423B ILE* 3.7 5.4 + - - +
424B GLU* 3.1 42.7 + - + +
456B ALA* 4.8 14.1 - - + +
457B ILE* 4.5 9.3 - - + +
460B ALA* 4.2 24.5 - - + -
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PRO* 6.3 3.1 - - + -
380B ARG* 4.0 23.8 - - - +
417B ARG 3.4 9.4 + - - +
418B VAL* 2.7 22.5 + - - +
420B LEU* 1.3 72.5 - - - +
422B ILE* 1.3 64.8 + - - +
424B GLU* 2.9 26.6 + - - +
425B TYR* 3.5 16.8 + - + +
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ARG* 4.9 2.2 - - - +
407B ILE* 4.3 25.8 - - + +
410B LEU* 3.3 60.6 - - + +
411B ALA* 4.3 1.8 - - - -
418B VAL* 3.2 8.8 + - + +
419B ARG 3.3 6.7 + - - +
421B ALA* 1.3 76.2 - - - +
423B ILE* 1.3 55.7 + - - +
425B TYR* 2.7 52.0 + - + +
426B MET* 3.4 8.5 + - - +
429B LEU* 6.2 0.4 - - + -
449B TRP* 3.7 26.9 - - + -
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ARG 3.4 14.3 + - - +
420B LEU* 3.9 9.0 - - - +
421B ALA 3.3 0.2 - - - -
422B ILE* 1.3 77.0 - - - +
424B GLU* 1.3 64.6 + - + +
426B MET* 3.2 18.9 + - - +
427B PRO* 3.3 5.4 - - - +
449B TRP* 3.6 47.3 - - + -
457B ILE* 3.8 31.4 - - + +
460B ALA* 4.0 32.3 - - + +
461B ALA* 4.1 4.0 - - - +
464B ASN* 4.1 17.1 - - + +
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU* 3.1 37.5 - - + +
421B ALA* 2.9 16.2 + - - +
423B ILE* 1.3 80.2 - - - +
425B TYR* 1.3 62.5 + - + +
427B PRO* 3.0 23.5 - - - +
428B LEU* 4.2 7.4 - - - +
460B ALA* 5.6 2.2 - - - +
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Residues in contact with TYR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PRO* 4.6 2.1 + - - +
380B ARG* 2.7 42.6 + - + +
381B LEU* 3.4 40.6 + - + +
384B ILE* 3.6 37.5 - - + -
407B ILE* 6.3 2.0 - - + -
410B LEU* 5.3 0.7 - - + -
421B ALA* 3.6 16.7 - - + +
422B ILE* 2.7 52.9 + - + +
424B GLU* 1.3 77.3 - - + +
426B MET* 1.3 51.2 + - - +
427B PRO 3.2 1.1 - - - -
428B LEU* 2.6 13.6 + - + +
429B LEU* 2.6 45.1 + - + -
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Residues in contact with MET 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ILE* 5.1 2.9 - - + -
422B ILE* 3.4 13.0 + - - +
423B ILE 3.2 10.0 + - - +
425B TYR* 1.3 76.6 - - - +
427B PRO* 1.3 65.2 - - + +
429B LEU* 3.3 31.4 + - + +
430B ALA* 2.7 32.4 + - - +
438B PHE* 4.0 26.0 - - + -
442B LEU* 3.9 30.7 - - + -
446B CYS* 4.3 11.9 - - - -
449B TRP* 4.3 24.2 - - + -
464B ASN* 3.2 28.9 - - - +
468B LEU* 5.1 1.3 - - + -
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Residues in contact with PRO 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ILE 3.3 7.2 - - - +
424B GLU* 3.0 22.2 - - - +
425B TYR 3.3 0.2 - - - -
426B MET* 1.3 96.8 - - + +
428B LEU* 1.3 58.8 + - + +
430B ALA* 3.4 6.5 + - + +
431B GLY* 2.8 25.5 + - - -
464B ASN* 4.2 10.3 - - - +
467B LYS* 6.1 5.2 - - + -
468B LEU* 5.7 2.2 - - + -
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 3.9 28.3 - - + -
384B ILE* 4.3 10.1 - - + -
385B SER* 4.1 13.5 - - - +
424B GLU 4.2 8.3 - - - +
425B TYR* 2.6 24.3 + - + +
427B PRO* 1.3 71.7 - - + +
429B LEU* 1.3 60.3 + - - +
430B ALA 3.0 1.3 - - - -
431B GLY* 3.1 2.0 + - - -
432B GLN* 2.8 48.0 + - + +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ILE* 4.0 17.5 - - + +
387B LEU* 3.5 29.8 - - + -
403B LEU* 4.3 12.6 - - + -
407B ILE* 3.4 25.4 - - + -
422B ILE* 6.2 0.7 - - + -
425B TYR* 2.6 32.3 + - + +
426B MET* 3.4 32.3 - - + +
428B LEU* 1.3 72.5 - - - +
430B ALA* 1.3 54.2 + - - +
432B GLN* 4.6 2.2 - - - -
433B LEU* 2.7 42.3 + - + +
437B PHE* 3.8 16.9 - - + -
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B MET 2.7 18.9 + - - +
427B PRO* 3.5 8.5 - - + +
429B LEU* 1.3 74.7 - - - +
431B GLY* 1.3 63.1 + - - +
434B GLY* 2.9 27.9 + - - +
438B PHE* 3.8 26.9 - - + -
468B LEU* 5.4 7.4 - - + -
471B LYS* 4.2 15.1 - - + -
472B PHE* 4.2 13.1 - - + -
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Residues in contact with GLY 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B PRO 2.8 18.9 + - - -
428B LEU 3.6 2.0 - - - -
430B ALA* 1.3 74.3 - - - +
432B GLN* 1.3 62.3 + - - +
434B GLY* 5.0 0.3 + - - -
471B LYS* 4.2 16.9 - - - +
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Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ILE 2.8 22.6 - - - +
385B SER* 2.9 27.8 + - - +
387B LEU* 3.0 28.2 - - + +
388B ASP* 3.2 38.9 + - - +
391B ASN* 4.8 6.8 - - - +
428B LEU* 2.8 27.6 + - + +
429B LEU* 4.1 1.6 - - - +
431B GLY* 1.3 82.2 - - - +
433B LEU* 1.3 73.9 + - + +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B LEU* 4.5 10.8 - - + -
391B ASN* 3.0 37.4 + - + +
396B ILE* 4.2 12.9 - - + +
399B LEU* 3.9 15.7 - - + -
403B LEU* 4.0 16.2 - - + -
429B LEU* 2.7 28.3 + - + +
432B GLN* 1.3 83.2 - - + +
434B GLY* 1.3 59.3 + - - +
436B GLU* 3.6 10.7 - - - +
437B PHE* 3.7 52.4 - - + +
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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
------------------------------------------------------------
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