Contacts of the helix formed by residues 396 - 412 (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 ILE 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A ASN* 3.3 26.6 + - - +
395A GLY* 1.3 72.4 - - - -
397A ARG* 1.3 65.4 + - + +
399A LEU* 4.4 3.8 - - + -
400A SER* 2.9 29.9 + - - -
433A LEU* 4.1 31.0 - - + +
436A GLU* 4.0 31.4 - - + +
437A PHE* 4.2 24.0 - - + -
160B ALA* 5.7 4.3 - - + -
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Residues in contact with ARG 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY* 4.8 4.5 - - - -
396A ILE* 1.3 86.9 - - + +
398A GLN* 1.3 93.7 + - + +
400A SER* 3.9 4.4 - - - -
401A GLN* 2.9 52.1 + - - +
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Residues in contact with GLN 398 (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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357A LYS* 4.7 10.8 - - - +
361A ILE* 4.2 27.9 - - + +
365A LEU* 5.2 3.7 - - + +
394A ILE* 4.1 13.1 - - + +
395A GLY 3.4 19.8 + - - +
396A ILE 3.4 0.2 - - - -
397A ARG* 1.3 120.2 - - + +
399A LEU* 1.3 63.4 + - - +
401A GLN* 3.5 15.8 + - - +
402A SER* 3.4 21.0 + - - -
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 5.1 4.7 - - + -
368A PHE* 4.3 27.6 - - + -
387A LEU* 4.4 10.5 - - + +
390A VAL* 4.4 10.8 - - + -
391A ASN* 4.0 36.6 - - + +
394A ILE* 3.7 19.2 - - + +
395A GLY 3.0 17.7 + - - +
396A ILE* 3.9 5.4 - - + +
398A GLN* 1.3 75.9 - - - +
400A SER* 1.3 54.4 + - - +
402A SER* 3.1 4.5 + - - -
403A LEU* 2.7 46.6 + - + +
433A LEU* 4.1 20.0 - - + -
437A PHE* 6.2 0.2 - - + -
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 2.9 21.6 + - - +
397A ARG* 3.9 4.7 - - - -
399A LEU* 1.3 76.8 - - - +
401A GLN* 1.3 61.9 + - - +
403A LEU* 4.3 1.8 - - - +
404A LEU* 2.8 49.2 + - - +
437A PHE* 3.9 32.9 + - - -
439A ASP* 4.7 6.1 + - - -
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Residues in contact with GLN 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ARG* 2.9 37.2 + - - +
398A GLN* 3.7 24.8 + - - +
399A LEU 3.3 0.2 - - - -
400A SER* 1.3 77.2 - - - +
402A SER* 1.3 56.5 + - - +
404A LEU* 5.3 0.7 - - - -
405A PRO* 3.5 19.5 - - - +
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 3.7 30.5 - - - +
368A PHE* 4.5 2.4 - - - -
369A LEU* 3.5 37.1 - - - +
398A GLN 3.4 9.5 + - - -
399A LEU* 3.1 9.3 + - - -
400A SER 3.0 0.4 - - - -
401A GLN* 1.3 80.8 - - - +
403A LEU* 1.3 62.2 + - - +
404A LEU 3.7 0.2 - - - -
405A PRO* 3.5 9.2 - - - +
406A ALA 4.4 2.4 + - - -
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Residues in contact with LEU 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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368A PHE* 4.0 14.6 - - + -
369A LEU* 4.8 1.3 - - - -
372A LEU* 3.3 31.9 - - + -
384A ILE* 4.8 7.4 - - + -
387A LEU* 4.0 28.0 - - + -
399A LEU* 2.7 35.0 + - + +
400A SER* 4.3 0.9 - - - +
402A SER* 1.3 73.6 - - - +
404A LEU* 1.3 65.1 + - - +
406A ALA* 3.1 13.5 + - - +
407A ILE* 3.1 35.7 + - + +
429A LEU* 4.3 1.1 - - + -
433A LEU* 4.3 5.4 - - + -
437A PHE* 4.1 17.3 - - + -
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A SER* 2.8 34.7 + - - +
401A GLN* 5.3 0.4 - - - -
403A LEU* 1.3 74.1 - - - +
405A PRO* 1.3 61.0 - - + +
407A ILE* 3.0 12.8 + - + +
408A VAL* 2.8 36.7 + - + +
437A PHE* 5.0 8.3 - - + -
439A ASP* 3.8 19.1 - - - +
441A LYS* 3.7 39.7 - - + -
442A LEU* 4.1 30.5 - - + -
445A LEU* 5.2 0.9 - - + -
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Residues in contact with PRO 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 GLN 3.5 24.0 - - - +
402A SER 3.5 7.0 - - - +
403A LEU 3.4 4.5 - - - -
404A LEU* 1.3 96.7 - - + +
406A ALA* 1.3 60.1 + - - +
408A VAL* 3.5 10.2 - - + +
409A GLU* 3.1 22.5 + - - +
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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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369A LEU* 4.3 15.9 - - + -
372A LEU* 3.9 23.6 - - + -
373A LYS* 4.5 24.7 - - + +
402A SER 4.4 0.6 + - - +
403A LEU 3.1 9.2 + - - +
405A PRO* 1.3 76.2 - - - +
407A ILE* 1.3 67.5 + - - +
409A GLU* 3.4 7.7 + - - +
410A LEU* 3.0 29.4 + - + +
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Residues in contact with ILE 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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372A LEU* 5.2 3.4 - - + -
384A ILE* 5.2 7.2 - - + -
403A LEU* 3.1 47.1 + - + +
404A LEU* 3.0 11.1 + - + +
406A ALA* 1.3 73.4 - - - +
408A VAL* 1.3 67.2 + - - +
410A LEU* 3.0 11.5 + - + +
411A ALA* 2.7 21.7 + - - +
422A ILE* 4.2 20.1 - - + +
425A TYR* 6.1 1.8 - - + -
426A MET* 5.9 2.0 - - - -
429A LEU* 4.2 25.4 - - + -
437A PHE* 4.2 10.5 - - + -
442A LEU* 4.7 9.9 - - + -
445A LEU* 3.9 18.4 - - + -
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 2.8 25.2 + - + +
405A PRO* 3.5 11.2 - - + +
407A ILE* 1.3 78.1 - - - +
409A GLU* 1.3 66.0 + - - +
411A ALA* 2.9 11.4 + - - +
412A GLU* 3.2 29.7 + - - +
441A LYS* 3.5 42.4 - - + +
445A LEU* 3.8 23.2 - - + +
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Residues in contact with GLU 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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373A LYS* 3.3 36.5 + - - +
405A PRO 3.1 10.9 + - - +
406A ALA* 3.6 9.1 - - - +
408A VAL* 1.3 84.2 - - - +
410A LEU* 1.3 62.9 + - + +
412A GLU* 3.4 19.8 + - - +
413A ASP* 3.6 10.0 + - - +
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Residues in contact with LEU 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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372A LEU* 3.8 34.1 - - + +
373A LYS* 5.1 13.7 - - + +
374A ASP 5.8 0.4 - - - +
380A ARG* 4.2 18.4 - - - +
406A ALA* 3.0 17.8 + - + +
407A ILE* 3.0 11.8 + - + +
409A GLU* 1.3 74.6 - - + +
411A ALA* 1.3 63.7 + - - +
412A GLU 3.0 6.5 + - - -
413A ASP* 3.1 25.0 + - - +
418A VAL* 3.9 19.8 - - + +
419A ARG* 4.2 2.6 - - - -
422A ILE* 3.5 33.6 - - + +
425A TYR* 5.1 1.3 - - + -
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Residues in contact with ALA 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 ILE 2.7 20.4 + - - +
408A VAL 2.9 6.0 + - - +
410A LEU* 1.3 73.2 - - - +
412A GLU* 1.3 58.1 + - + +
413A ASP 3.5 0.4 - - - -
419A ARG* 3.4 13.0 - - - +
422A ILE* 4.1 10.0 - - + +
445A LEU* 3.7 23.1 - - + -
449A TRP* 3.1 47.5 + - + +
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Residues in contact with GLU 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 VAL* 3.2 25.5 + - - +
409A GLU* 3.6 17.2 - - - +
410A LEU 3.0 0.8 - - - -
411A ALA* 1.3 80.9 - - + +
413A ASP* 1.3 65.3 + - - +
414A ALA* 3.7 0.7 + - - -
419A ARG* 4.1 4.0 - - - +
445A LEU* 5.7 2.1 - - - +
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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
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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