Contacts of the helix formed by residues 412 - 424 (chain A) in PDB entry 1JBW
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 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A GLY* 4.2 1.4 - - - -
316A HIS* 3.4 29.2 - - - +
341A GLY 4.5 4.8 + - - -
367A VAL* 3.9 16.8 - - - +
411A GLY* 1.3 80.0 + - - +
413A LEU* 1.3 61.6 + - - +
414A TYR* 3.0 34.7 + - - +
415A LEU* 3.3 14.1 + - - +
416A ALA* 3.5 6.6 + - - +
999A ACQ 3.7 6.5 - - - -
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 3.7 35.2 - - + +
76A ILE* 4.3 7.2 - - + +
299A ALA* 3.7 29.6 - - + +
300A ARG* 2.8 38.1 - - - +
314A GLY* 3.7 21.5 - - - -
412A SER* 1.3 72.9 - - - +
414A TYR* 1.3 55.3 + - - +
415A LEU 3.3 0.2 - - - -
416A ALA* 3.6 4.0 - - + +
417A SER* 2.6 37.4 + - - -
998A MG 4.7 0.7 - - - -
999A ACQ 2.8 36.5 + - + +
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Residues in contact with TYR 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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74A PRO* 3.6 19.3 - - + +
82A ARG* 5.6 0.2 + - - -
367A VAL* 4.2 13.2 - - + -
368A PRO* 4.9 4.1 - - - +
412A SER* 3.0 22.0 - - - +
413A LEU* 1.3 75.5 - - - +
415A LEU* 1.3 60.6 + - - +
417A SER* 3.8 4.9 - - - -
418A ALA* 3.0 27.7 + - - +
996A TMF 3.5 79.1 + + + -
999A ACQ 3.7 18.1 + - - -
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Residues in contact with LEU 415 (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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339A ILE 5.0 0.2 - - - +
340A ALA 4.8 0.2 - - - -
341A GLY* 3.9 20.4 - - - +
365A VAL* 4.4 9.9 - - + -
366A PRO 4.8 3.4 - - - +
367A VAL* 4.4 4.9 - - + +
368A PRO* 3.7 22.4 - - + -
391A TRP* 3.5 37.2 - - + +
409A ILE* 4.2 19.3 - - + -
410A THR 3.6 24.5 - - - +
411A GLY* 4.6 0.9 - - - -
412A SER* 3.3 17.7 + - - +
413A LEU 3.3 0.2 - - - -
414A TYR* 1.3 75.4 - - - +
416A ALA* 1.3 68.6 + - - +
418A ALA* 3.1 1.6 + - - +
419A VAL* 2.9 29.1 + - + +
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Residues in contact with ALA 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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299A ALA* 3.8 22.9 - - + -
312A ILE* 4.1 16.2 - - + +
313A ASP 3.7 26.6 + - - +
409A ILE* 5.4 2.0 - - - -
410A THR* 6.0 0.4 - - - +
411A GLY 5.8 0.2 - - - +
412A SER 3.5 2.8 + - - -
413A LEU* 3.3 13.6 + - - +
415A LEU* 1.3 79.2 - - - +
417A SER* 1.3 57.8 + - - +
419A VAL* 3.2 8.5 + - - +
420A ARG* 2.8 30.6 + - - +
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Residues in contact with SER 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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75A PHE 4.3 1.6 - - - -
76A ILE* 2.6 41.4 + - - -
299A ALA* 5.0 0.4 - - - +
413A LEU 2.6 22.0 + - - -
414A TYR 3.8 1.8 - - - -
416A ALA* 1.3 71.6 - - - +
418A ALA* 1.3 60.4 + - - +
420A ARG* 3.1 1.7 + - - +
421A GLN* 2.8 37.9 + - - +
996A TMF 2.5 32.6 + - - -
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Residues in contact with ALA 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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368A PRO* 4.1 26.9 - - + -
391A TRP* 4.5 7.2 - - + +
414A TYR 3.0 19.1 + - - +
415A LEU 3.1 4.2 + - - +
417A SER* 1.3 75.4 + - - +
419A VAL* 1.3 57.4 + - - +
421A GLN* 3.8 12.0 - - - +
422A THR* 2.6 34.8 + - - +
996A TMF 5.0 0.4 + - - -
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 4.2 1.6 - - + -
312A ILE* 3.9 21.5 - - + -
391A TRP* 3.7 39.5 - - + -
409A ILE* 4.0 30.5 - - + -
415A LEU* 2.9 21.5 + - + +
416A ALA* 3.5 7.6 - - - +
418A ALA* 1.3 73.7 - - - +
420A ARG* 1.3 58.6 + - - +
422A THR* 3.3 1.0 + - - -
423A LEU* 2.9 52.6 + - + +
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Residues in contact with ARG 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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76A ILE* 3.8 21.3 - - - -
77A MET* 3.3 33.4 - - - +
298A PRO* 3.7 13.0 - - - +
299A ALA 4.5 0.4 - - - +
302A GLU* 2.9 42.6 + - - -
304A ILE* 4.6 6.1 - - + -
312A ILE* 3.9 15.2 - - + +
416A ALA 2.8 20.5 + - - +
417A SER* 3.7 6.3 - - - +
419A VAL* 1.3 70.1 - - - +
421A GLN* 1.3 59.4 + - - +
424A LEU* 2.7 65.1 + - + +
425A GLY 3.4 0.7 + - - -
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Residues in contact with GLN 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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75A PHE* 3.6 20.6 - - - -
76A ILE 2.9 15.1 + - - +
77A MET* 3.6 27.3 + - + +
417A SER* 2.8 41.0 + - - +
418A ALA* 3.8 9.6 - - - +
420A ARG* 1.3 73.4 - - - +
422A THR* 1.3 59.8 + - - +
425A GLY* 2.9 35.1 + - - -
996A TMF 3.8 3.2 + - - -
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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
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391A TRP* 3.8 27.2 - - + -
392A GLN* 5.4 4.3 + - + +
418A ALA* 2.6 22.2 + - - +
419A VAL 3.6 3.6 - - - -
420A ARG 3.2 0.2 - - - -
421A GLN* 1.3 81.4 - - - +
423A LEU* 1.3 66.9 + - + +
424A LEU 5.1 0.2 - - - -
425A GLY 5.0 1.4 + - - -
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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
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304A ILE* 4.0 20.6 - - + +
305A SER* 5.9 2.2 - - - -
310A ILE* 4.3 22.7 - - + -
391A TRP* 4.7 10.3 - - + -
395A LEU* 4.9 10.3 - - + -
419A VAL* 2.9 40.4 + - + +
422A THR* 1.3 84.9 - - + +
424A LEU* 1.3 69.8 + - + +
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Residues in contact with LEU 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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77A MET* 4.5 4.9 - - + -
302A GLU* 5.1 0.2 - - - +
304A ILE* 3.7 38.1 - - + +
420A ARG* 2.7 58.8 + - + +
422A THR 5.1 0.2 - - - -
423A LEU* 1.3 92.0 - - + +
425A GLY* 1.3 61.2 + - - +
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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