Contacts of the helix formed by residues 403 - 424 (chain A) in PDB entry 1B4V
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 ARG 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASP 4.6 2.4 + - - -
103A GLN* 2.7 67.6 + - + +
401A TRP* 4.6 3.4 - - - +
402A THR* 1.3 70.7 - - - +
404A ASP* 1.3 61.5 + - - +
405A GLN 3.0 0.2 - - - -
406A ASN* 3.0 20.1 + - - +
407A ALA 4.2 1.4 + - - -
438A LYS* 4.2 7.0 - - - +
442A ASP* 3.6 38.7 - - - +
443A ASP* 3.1 28.7 + - + +
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Residues in contact with ASP 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 4.7 0.9 + - - +
402A THR* 2.5 33.0 + - - -
403A ARG* 1.3 73.2 - - - +
405A GLN* 1.3 59.1 + - - +
406A ASN 3.0 1.1 - - - -
407A ALA* 3.1 30.6 + - + +
408A PRO* 4.3 1.6 - - - +
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Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ASN* 2.8 19.9 + - - -
384A GLN* 3.0 42.1 + - + +
385A ARG 3.0 30.5 + - - +
400A ASN 4.0 3.6 - - - +
401A TRP* 3.3 30.3 - - + -
402A THR* 2.9 46.3 + - - +
404A ASP* 1.3 80.7 + - - +
406A ASN* 1.3 56.9 + - - +
407A ALA 3.3 1.6 - - - -
408A PRO* 3.7 1.1 - - - +
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Residues in contact with ASN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A MET* 3.9 11.1 - - - +
320A PRO* 4.1 12.6 - - - +
322A GLY* 5.1 1.4 - - - -
323A ASN 4.3 5.1 + - - +
324A ILE* 4.2 9.4 - - + +
382A ASN* 3.4 15.9 - - - +
401A TRP* 3.6 20.8 + - + +
403A ARG 3.0 14.4 + - - +
405A GLN* 1.3 75.7 - - - +
407A ALA* 1.3 64.7 + - - +
408A PRO 3.3 2.9 - - - -
409A ALA* 3.0 16.1 + - - +
410A VAL* 2.9 24.2 + - - +
442A ASP* 2.9 36.5 - - + +
444A PHE 5.2 0.3 - - - +
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Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ARG 4.2 1.2 + - - -
404A ASP* 3.1 21.0 + - + +
406A ASN* 1.3 77.2 - - - +
408A PRO* 1.3 63.8 - - + +
410A VAL* 3.2 6.8 + - - +
411A ASN* 2.9 44.2 + - - +
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Residues in contact with PRO 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASP 5.5 0.2 - - - +
381A LYS 5.2 3.6 - - - +
382A ASN* 3.4 26.7 - - + +
383A PRO* 4.6 8.5 - - + -
384A GLN* 4.5 9.6 - - + +
404A ASP 4.3 1.1 - - - +
405A GLN 3.7 13.5 - - - +
406A ASN 3.5 2.9 - - - -
407A ALA* 1.3 95.0 - - + +
409A ALA* 1.3 59.9 + - - +
411A ASN* 3.4 10.0 + - + +
412A ALA* 3.1 24.8 + - - +
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Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLY* 4.2 3.6 - - - +
324A ILE* 3.6 15.2 - - + +
380A THR* 3.2 31.5 - - - +
382A ASN* 3.8 10.3 - - + +
406A ASN* 3.0 30.4 + - - +
408A PRO* 1.3 78.5 - - - +
410A VAL* 1.3 63.6 + - - +
412A ALA 3.4 1.0 + - - -
413A ALA* 3.0 24.6 + - - +
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Residues in contact with VAL 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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324A ILE* 3.8 13.2 - - + -
406A ASN 2.9 17.0 + - - +
407A ALA* 3.7 9.4 - - - +
409A ALA* 1.3 75.6 - - - +
411A ASN* 1.3 65.5 + - - +
413A ALA* 3.3 3.3 + - - +
414A LYS* 2.8 34.8 + - + +
440A PHE* 4.0 32.7 - - + -
442A ASP* 3.7 32.3 - - + +
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Residues in contact with ASN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA* 2.9 32.8 + - - +
408A PRO* 3.6 9.2 - - + +
410A VAL* 1.3 83.3 - - - +
412A ALA* 1.3 56.8 + - - +
414A LYS* 3.8 7.7 - - - +
415A ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASP 3.9 21.3 - - - +
356A SER* 4.4 7.9 - - - +
357A SER 4.3 1.8 - - - +
358A VAL* 3.5 23.3 - - + +
380A THR* 4.1 11.9 - - + -
381A LYS 5.4 1.6 - - - +
408A PRO 3.1 16.5 + - - +
409A ALA 3.8 3.4 - - - +
411A ASN* 1.3 72.7 - - - +
413A ALA* 1.3 66.3 + - - +
415A ALA* 3.4 6.7 + - - +
416A LEU 3.2 17.3 + - - -
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 4.0 24.0 - - + -
326A THR* 5.5 0.9 - - + -
358A VAL* 4.1 9.4 - - - +
378A ALA* 4.1 19.7 - - + -
380A THR* 4.1 1.5 - - + +
409A ALA 3.0 16.4 + - - +
410A VAL 3.8 3.4 - - - +
412A ALA* 1.3 75.3 - - - +
414A LYS* 1.3 63.1 + - - +
416A LEU* 3.4 2.6 + - - +
417A PHE* 3.1 33.7 + - + -
440A PHE* 4.1 8.3 - - + -
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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 VAL* 2.8 27.5 + - + +
411A ASN* 3.8 8.3 - - - +
413A ALA* 1.3 70.4 - - - +
415A ALA* 1.3 60.3 + - - +
418A ASP* 2.8 71.1 + - - +
428A TYR* 3.1 6.1 + - - -
440A PHE* 3.5 36.7 - - + -
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A SER* 6.0 5.8 - - - -
411A ASN 3.0 18.6 + - - +
412A ALA* 3.7 7.0 - - - +
414A LYS* 1.3 77.5 - - - +
416A LEU* 1.3 63.1 + - - +
418A ASP* 3.6 8.4 + - - +
419A ARG* 3.3 25.2 + - - +
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Residues in contact with LEU 416 (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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186A LEU* 3.9 23.8 - - + -
348A ILE* 4.4 17.0 - - + -
350A ALA* 3.5 29.4 - - + -
356A SER 5.7 1.8 - - - +
358A VAL* 3.9 25.1 - - + +
360A ALA* 4.9 1.1 - - + -
412A ALA 3.2 9.5 + - - +
413A ALA 3.7 7.0 - - - +
414A LYS 3.2 0.6 - - - -
415A ALA* 1.3 79.6 - - - +
417A PHE* 1.3 87.9 + - + +
419A ARG* 3.0 37.4 + - - +
420A ILE* 3.4 9.1 + - + +
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Residues in contact with PHE 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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326A THR* 3.7 23.3 - - + -
328A ARG* 4.1 6.9 - - + -
348A ILE* 4.2 3.4 - - + -
358A VAL* 4.8 0.7 - - + -
360A ALA* 3.7 21.5 - - + -
376A TYR* 3.4 56.3 - + + -
378A ALA* 4.4 12.3 - - + -
413A ALA 3.1 24.9 + - - +
416A LEU* 1.3 90.6 - - + +
418A ASP* 1.3 58.0 - - - +
419A ARG 3.2 0.2 - - - -
420A ILE* 3.2 25.6 + - + +
421A ASN* 2.8 31.7 + - - -
428A TYR* 3.2 26.7 - - + +
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Residues in contact with ASP 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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414A LYS* 2.8 51.2 + - - +
415A ALA* 3.7 9.7 - - - +
416A LEU 3.2 0.2 - - - -
417A PHE* 1.3 76.5 - - - +
419A ARG* 1.3 56.9 + - + +
421A ASN* 3.3 6.6 + - - +
422A LYS* 2.8 31.9 + - - +
428A TYR* 2.8 29.2 + - - -
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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
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184A ALA* 3.6 25.9 + - + +
185A GLY 4.9 2.4 + - - -
186A LEU* 3.5 33.0 - - + +
350A ALA* 5.5 1.6 - - - +
415A ALA* 3.3 17.5 + - - +
416A LEU* 3.0 21.7 + - - +
418A ASP* 1.3 80.3 - - + +
420A ILE* 1.3 55.5 + - - +
422A LYS* 3.7 7.7 - - - +
423A ALA* 3.1 29.1 + - - +
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Residues in contact with ILE 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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180A GLN* 3.9 10.8 - - + +
181A ALA* 4.1 8.3 - - + -
184A ALA* 3.9 9.4 - - + -
186A LEU* 3.6 30.1 - - + -
328A ARG* 3.5 32.3 - - - +
348A ILE* 4.0 22.0 - - + -
376A TYR* 5.5 2.0 - - - +
416A LEU* 3.4 8.0 + - + +
417A PHE* 3.2 29.9 + - + +
419A ARG* 1.3 73.9 - - - +
421A ASN* 1.3 65.3 + - - +
423A ALA 3.4 0.5 + - - -
424A ASN* 2.9 41.0 + - - +
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Residues in contact with ASN 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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328A ARG* 2.8 19.9 + - - +
417A PHE 2.8 13.3 + - - +
418A ASP* 3.7 6.6 + - - +
420A ILE* 1.3 77.0 - - - +
422A LYS* 1.3 52.1 + - - +
425A GLY* 2.7 33.3 + - - -
426A THR* 2.8 47.6 + - - +
427A ILE* 4.0 1.7 + - - +
428A TYR* 3.4 53.3 - - - +
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Residues in contact with LYS 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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418A ASP 2.8 17.9 + - - +
419A ARG* 3.7 7.6 - - - +
421A ASN* 1.3 78.9 - - - +
423A ALA* 1.3 61.6 + - - +
424A ASN 3.4 0.7 + - - -
425A GLY* 3.7 6.2 + - - -
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Residues in contact with ALA 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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183A LYS* 3.5 41.1 - - + +
184A ALA* 3.7 7.4 - - + +
419A ARG 3.1 17.5 + - - +
420A ILE 3.9 2.9 - - - +
422A LYS* 1.3 76.7 - - - +
424A ASN* 1.3 63.5 + - - +
425A GLY 3.7 0.2 - - - -
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Residues in contact with ASN 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLN* 2.8 66.6 + - - +
183A LYS* 3.4 26.7 + - - +
328A ARG* 4.1 0.7 - - - +
331A HIS* 2.7 32.3 + - - +
420A ILE* 2.9 28.4 + - - +
423A ALA* 1.3 83.5 - - - +
425A GLY* 1.3 56.9 + - - +
426A THR* 4.0 8.5 - - + +
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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
------------------------------------------------------------
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