Contacts of the helix formed by residues 432 - 448 (chain A) in PDB entry 1JZ3
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 432 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.8 38.2 - - + +
111A PRO* 4.0 22.0 - - + +
112A PRO* 4.5 4.3 - - + -
193A ASP* 3.8 27.8 - - + -
196A TYR* 3.9 16.4 - + + -
197A LEU* 3.8 36.3 - - + -
426A LEU* 3.5 45.8 - - + +
429A ASP* 3.0 25.1 + - + -
431A ARG* 1.3 83.7 - - + +
433A LEU* 1.3 66.7 + - - +
434A PRO 3.3 1.6 - - - -
435A ALA* 3.5 9.1 + - + +
436A MET* 3.1 26.0 + - - +
467A ASN* 3.6 3.8 - - - +
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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
----------------------------------------------------------
430A PRO* 3.0 11.5 + - + +
432A TRP* 1.3 79.3 - - - +
434A PRO* 1.3 62.4 - - + +
436A MET* 4.5 0.9 - - - -
437A SER* 2.6 37.4 + - - -
467A ASN* 3.3 45.1 - - + +
470A ALA* 4.4 8.7 - - + -
471A LEU* 4.1 24.2 - - + -
433D LEU* 5.6 7.6 - - + -
437D SER* 3.8 27.1 - - - +
441D THR* 5.2 4.9 - - + -
471D LEU* 4.7 10.3 - - + -
474D TRP* 4.7 13.2 - - + +
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Residues in contact with PRO 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO 4.9 7.4 - - - +
20A GLY* 5.7 5.8 - - - +
22A THR* 5.5 1.1 - - + -
430A PRO 3.4 10.1 - - - +
431A ARG* 3.7 10.3 - - - +
432A TRP 3.5 2.2 - - - -
433A LEU* 1.3 99.7 - - + +
435A ALA* 1.3 62.9 + - - +
437A SER* 3.0 20.0 + - - +
438A GLU* 3.2 15.9 + - - +
434D PRO* 3.7 36.8 - - + +
437D SER* 4.6 5.8 - - - +
438D GLU* 4.8 13.2 - - + +
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Residues in contact with ALA 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 4.0 12.9 + - + +
22A THR* 3.9 28.2 - - + +
193A ASP* 5.7 0.9 - - - +
197A LEU* 3.8 20.6 - - + -
431A ARG 5.2 0.4 + - - -
432A TRP* 3.5 17.2 + - + +
434A PRO* 1.3 80.3 - - - +
436A MET* 1.3 64.8 + - - +
438A GLU* 3.5 9.6 + - - +
439A ARG* 3.5 19.1 + - - +
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Residues in contact with MET 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.4 11.9 - - + -
415A ILE* 3.7 37.5 - - + +
426A LEU 4.6 1.6 - - - +
427A THR* 3.6 36.6 - - + -
432A TRP* 3.1 15.0 + - + +
433A LEU* 3.8 3.1 - - - +
435A ALA* 1.3 75.7 - - - +
437A SER* 1.4 66.2 + - - +
439A ARG* 3.0 16.7 + - - +
440A VAL 3.2 8.5 + - - -
467A ASN* 3.6 42.0 - - + -
468A HIS* 4.0 19.3 - - + +
471A LEU* 3.9 13.3 - - + +
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Residues in contact with SER 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU* 2.6 23.7 + - - -
434A PRO* 3.0 19.1 + - - +
436A MET* 1.4 73.4 - - - +
438A GLU* 1.3 53.8 + - - +
440A VAL* 3.1 2.3 + - - +
441A THR* 2.7 42.4 + - - +
471A LEU* 3.6 27.7 - - - +
430D PRO 5.3 0.9 + - - -
433D LEU* 4.0 18.9 - - - +
434D PRO* 4.1 11.8 - - - +
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 2.7 32.0 + - - -
23A GLN* 4.5 11.6 + - - +
26A ARG* 3.1 24.5 + - - -
164A ASP* 4.8 2.4 - - + +
167A LEU* 4.5 0.5 - - - +
434A PRO 3.2 11.4 + - - +
435A ALA* 3.9 7.4 - - - +
436A MET 3.2 0.2 - - - -
437A SER* 1.3 83.3 + - - +
439A ARG* 1.3 61.2 + - + +
441A THR* 3.7 7.6 - - - +
442A ARG* 3.0 46.3 + - + +
430D PRO 6.2 0.4 - - - +
431D ARG* 5.6 3.8 + - - -
434D PRO* 5.3 9.0 - - + +
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Residues in contact with ARG 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 6.2 1.8 - - - +
163A GLN* 4.5 4.0 - - - +
164A ASP* 3.4 45.2 + - + +
167A LEU* 4.1 4.9 - - - +
194A GLY* 3.6 23.8 - - - -
197A LEU* 3.5 29.3 - - - +
198A GLU* 2.9 35.0 + - - +
393A PRO* 5.1 0.3 - - - +
413A ALA* 3.8 10.0 - - - +
414A ASN* 2.9 47.4 + - - +
415A ILE* 3.7 17.5 - - + -
435A ALA* 3.5 16.8 + - - +
436A MET 3.0 8.5 + - - +
438A GLU* 1.3 81.3 - - + +
440A VAL* 1.3 60.4 + - - +
443A MET* 3.6 18.0 + - - +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ALA* 3.8 22.0 - - + -
415A ILE* 4.0 7.0 - - + -
436A MET 3.2 9.8 + - - +
437A SER 3.1 5.7 + - - +
439A ARG* 1.3 78.7 - - - +
441A THR* 1.3 68.2 + - + +
442A ARG 3.3 0.4 - - - -
443A MET* 3.2 8.5 + - + +
444A VAL* 3.1 22.4 + - + +
458A LEU* 4.3 17.0 - - + +
471A LEU* 4.0 24.2 - - + -
474A TRP* 4.2 9.4 - - + -
475A ILE* 3.7 35.2 - - + -
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A SER* 2.7 36.3 + - - +
438A GLU* 3.7 8.1 - - - +
440A VAL* 1.3 77.1 - - + +
442A ARG* 1.3 63.9 + - - +
444A VAL* 3.3 2.4 + - - +
445A GLN* 3.0 31.8 + - - +
471A LEU* 4.9 2.9 - - + -
474A TRP* 3.4 50.8 - - + +
430D PRO* 3.8 23.1 + - + +
433D LEU* 5.1 2.2 - - + -
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Residues in contact with ARG 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 3.4 49.8 - - - +
27A LEU 4.9 5.5 + - - -
29A ALA* 4.0 27.5 - - + +
163A GLN 4.6 0.2 + - - -
164A ASP* 4.4 11.1 + - - +
167A LEU* 3.7 41.6 + - + +
168A PRO* 2.6 28.4 + - - +
169A SER* 4.2 0.2 - - - +
170A GLU 5.3 0.4 - - - +
438A GLU* 3.0 36.7 + - + +
441A THR* 1.3 84.7 + - - +
443A MET* 1.3 64.6 + - - +
445A GLN* 3.6 11.3 + - - +
446A ARG* 3.2 22.7 + - - +
431D ARG* 5.9 3.1 - - - +
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Residues in contact with MET 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.6 15.5 - - - +
393A PRO* 4.0 14.4 - - + -
411A ASP* 3.7 23.1 - - - +
412A GLU 3.4 37.9 - - - +
413A ALA* 3.4 20.9 - - + +
439A ARG 3.6 10.1 - - - +
440A VAL* 3.2 19.6 + - + +
441A THR 3.2 0.2 - - - -
442A ARG* 1.3 76.7 - - - +
444A VAL* 1.3 71.4 + - + +
446A ARG* 3.0 3.1 + - - +
447A ASP* 2.9 25.9 + - - +
456A TRP* 4.0 21.5 - - + -
457A SER 3.9 10.1 - - - +
475A ILE* 5.3 0.9 - - + -
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Residues in contact with VAL 444 (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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440A VAL 3.1 14.6 + - - +
441A THR 3.9 2.9 - - - +
443A MET* 1.3 86.9 - - + +
445A GLN* 1.3 64.9 + - + +
446A ARG 3.1 0.5 + - - -
448A ARG* 3.2 36.6 + - + +
456A TRP* 3.8 45.3 - - + +
474A TRP* 3.9 23.6 - - + -
475A ILE* 4.3 14.1 - - + -
478A VAL* 4.2 14.6 - - + -
479A ASP* 4.8 6.1 - - + -
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Residues in contact with GLN 445 (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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28A ALA* 6.2 1.4 - - - +
29A ALA* 3.5 41.9 + - + +
30A HIS* 3.4 15.8 - - - -
31A PRO* 3.4 12.1 - - - +
224A ASP* 4.8 11.5 + - - +
226A HIS* 6.3 1.3 - - - +
441A THR* 3.0 18.5 + - - +
442A ARG* 3.9 7.3 - - - +
443A MET 3.2 0.4 - - - -
444A VAL* 1.3 77.8 - - + +
446A ARG* 1.3 61.0 + - - +
448A ARG* 4.4 12.8 - - - +
474A TRP* 4.9 8.2 - - + -
430D PRO* 3.4 34.2 - - - +
431D ARG* 5.9 2.5 - - - +
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 5.4 1.8 - - + -
30A HIS 3.5 18.6 - - - +
31A PRO* 3.5 4.6 - - - +
32A PRO* 3.5 30.2 - - + +
144A ASP* 5.5 1.2 + - - -
167A LEU* 3.7 14.8 - - - +
168A PRO* 3.8 39.5 - - + +
210A ARG* 4.2 8.9 - - - +
393A PRO* 3.5 8.5 - - - +
394A ASN 2.8 29.7 + - - -
396A PRO* 4.3 21.3 - - + +
399A TYR* 3.2 17.8 + - - -
442A ARG 3.2 16.2 + - - +
443A MET 3.0 3.6 + - - +
445A GLN* 1.3 81.6 - - - +
447A ASP* 1.4 89.6 + - - +
448A ARG 3.6 0.7 - - - -
449A ASN 5.2 0.5 + - - -
450A HIS* 4.7 1.9 - - - -
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Residues in contact with ASP 447 (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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32A PRO* 6.0 0.2 - - - +
399A TYR* 3.4 14.4 + - - -
411A ASP* 2.4 34.1 - - - +
443A MET* 2.9 16.8 + - - +
446A ARG* 1.4 125.2 + - - +
448A ARG* 1.3 64.1 + - - +
449A ASN 3.1 5.7 + - - -
450A HIS* 3.1 30.5 + - + +
453A VAL* 4.3 6.0 - - + +
456A TRP* 3.9 8.1 - - + -
482A ARG* 4.3 2.9 + - - -
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 5.2 1.8 - - + -
226A HIS* 3.4 58.3 + - + +
227A VAL 4.8 2.3 - - - +
444A VAL* 3.2 25.5 + - + +
445A GLN* 4.4 14.9 - - - +
446A ARG 3.6 0.6 - - - -
447A ASP* 1.3 76.3 - - - +
449A ASN* 1.3 70.8 + - - +
450A HIS 3.4 0.7 - - - -
456A TRP* 3.8 10.3 - - + -
478A VAL* 3.2 39.4 + - - +
479A ASP* 4.3 16.4 + - - +
480A PRO* 5.6 0.8 - - - +
482A ARG* 2.8 37.4 + - - +
8401A DMS 3.9 4.2 - - - +
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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
------------------------------------------------------------
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