Contacts of the helix formed by residues 332 - 349 (chain A) in PDB entry 1JEH
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 LEU 332 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE* 6.2 3.8 - - + -
325A ASP* 3.8 0.8 + - - -
330A PRO* 2.8 24.3 + - + +
331A MET* 1.3 82.7 - - - +
333A ALA* 1.3 65.8 + - - +
334A HIS* 3.7 12.6 - - + -
335A LYS* 3.0 11.1 + - + +
336A ALA* 3.0 21.3 + - - +
359A ILE* 3.9 14.4 - - + -
360A PRO 3.2 26.0 - - - +
361A SER* 3.8 21.5 - - - +
362A VAL 5.3 4.5 - - - +
480A FAD 3.1 27.8 + - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO* 3.3 14.3 - - + +
44A CYS* 3.5 16.8 - - - -
49A CYS* 3.8 0.4 - - - -
332A LEU* 1.3 70.3 - - - +
334A HIS* 1.3 55.1 + - - +
336A ALA 3.4 0.7 + - - -
337A GLU* 3.0 31.6 + - - +
480A FAD 2.8 38.5 + - + +
457B HIS* 3.5 27.4 - - + -
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Residues in contact with HIS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.7 20.4 - - + -
333A ALA* 1.3 73.3 - - - +
335A LYS* 1.3 65.7 + - - +
336A ALA 3.3 0.2 - - - -
337A GLU* 3.7 13.1 - - + +
338A GLU* 3.1 28.4 + - - +
359A ILE* 3.7 8.7 - - + +
360A PRO* 2.7 39.4 + - + +
361A SER* 5.2 0.7 - - - -
362A VAL 5.6 1.8 - - - -
480A FAD 3.3 9.9 + + - -
454B CYS* 3.2 29.1 - - - -
455B HIS 3.2 20.2 - - - +
456B ALA* 3.9 9.9 - - + -
457B HIS* 3.2 26.9 + - + +
462B GLU* 4.8 2.0 - - - +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLY 3.4 16.4 + - - -
325A ASP* 4.4 3.0 + - - -
328A PHE 3.7 15.5 - - - +
329A GLY* 3.9 10.1 - - - -
330A PRO* 3.2 40.1 + - + +
331A MET* 4.9 0.2 - - - +
332A LEU* 3.0 21.2 + - + +
334A HIS* 1.3 81.6 - - - +
336A ALA* 1.3 68.4 + - - +
338A GLU* 3.4 5.1 + - - +
339A GLU* 3.1 67.3 + - + +
354A VAL* 4.5 3.1 - - + +
356A TYR* 4.7 7.6 - - + -
359A ILE* 4.1 27.4 - - + -
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.2 38.3 - - + +
324A GLY* 4.0 8.3 - - - -
332A LEU 3.0 11.1 + - - +
333A ALA 3.5 9.4 - - - +
335A LYS* 1.3 82.5 - - - +
337A GLU* 1.3 59.0 + - - +
339A GLU* 3.3 7.3 + - - +
340A GLY 3.0 23.4 + - - -
480A FAD 3.8 18.4 - - - +
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Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO* 3.4 26.4 - - + +
18A TYR* 4.4 7.1 + - - -
19A VAL* 3.4 18.1 - - + +
333A ALA 3.0 21.5 + - - +
334A HIS* 3.7 9.9 - - - +
335A LYS 3.4 0.4 - - - -
336A ALA* 1.3 74.0 - - - +
338A GLU* 1.3 62.3 + - + +
340A GLY 3.3 1.0 + - - -
341A ILE* 3.2 32.8 + - + +
457B HIS* 3.4 33.9 + - - +
462B GLU* 4.4 8.0 - - - +
465B LYS* 6.2 0.5 - - - -
466B GLU* 5.6 0.7 - - - +
476B ILE* 5.5 0.5 - - - +
477B HIS* 3.8 19.6 - - - -
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Residues in contact with GLU 338 (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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334A HIS 3.1 17.6 + - - +
335A LYS* 3.5 9.4 - - - +
336A ALA 3.3 0.2 - - - -
337A GLU* 1.3 78.1 - - + +
339A GLU* 1.3 55.9 + - - +
341A ILE* 3.6 15.7 + - - +
342A ALA* 3.0 28.8 + - - +
353A HIS 4.4 11.4 - - - +
354A VAL* 3.4 22.4 - - + +
355A ASN 5.5 0.3 + - - -
451B ALA 4.7 0.7 - - - +
452B ARG* 3.5 19.2 - - - +
454B CYS* 3.9 25.2 - - + +
465B LYS* 3.2 29.4 + - - -
469B MET* 5.6 0.2 - - - +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 3.6 21.6 - - + -
323A VAL* 3.7 16.6 - - + +
324A GLY* 3.0 25.6 + - - +
327A THR* 4.2 5.3 - - - +
328A PHE 3.6 7.4 - - - +
335A LYS* 3.1 44.4 + - + +
336A ALA* 3.7 6.0 - - - +
337A GLU 3.3 0.2 - - - -
338A GLU* 1.3 74.6 - - - +
340A GLY* 1.3 58.3 + - - +
342A ALA* 4.0 0.2 - - - +
343A ALA* 3.0 34.0 + - - +
354A VAL* 3.8 12.3 - - + -
356A TYR* 2.9 24.6 + - - -
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Residues in contact with GLY 340 (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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16A ALA* 3.6 24.9 - - - -
19A VAL* 4.8 0.2 - - - -
20A ALA* 3.3 16.1 - - - +
323A VAL* 4.6 6.0 - - - +
336A ALA 3.0 11.6 + - - -
337A GLU 3.3 4.2 + - - -
339A GLU* 1.3 75.4 - - - +
341A ILE* 1.3 59.1 + - - +
343A ALA* 4.3 1.8 - - - +
344A VAL* 3.1 30.5 + - - +
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Residues in contact with ILE 341 (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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19A VAL* 3.8 15.5 - - + -
23A LYS* 4.0 32.7 - - + +
337A GLU* 3.2 18.8 + - + +
338A GLU* 3.8 22.4 - - - +
340A GLY* 1.3 75.4 - - - +
342A ALA* 1.3 59.8 + - - +
344A VAL* 3.2 4.7 + - - +
345A GLU* 2.9 51.0 + - - +
452B ARG* 6.2 0.7 - - - +
465B LYS* 5.6 2.2 - - - -
469B MET* 4.7 19.1 - - + -
476B ILE* 4.8 12.3 - - + -
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 3.6 23.8 - - + -
338A GLU 3.0 19.2 + - - +
341A ILE* 1.3 76.2 - - - +
343A ALA* 1.3 60.6 - - - +
345A GLU* 3.5 14.2 + - - +
346A MET* 3.2 28.2 + - - +
352A GLY* 4.0 2.1 - - - -
353A HIS 4.0 19.1 - - - +
354A VAL* 3.8 9.2 - - + -
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Residues in contact with ALA 343 (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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150A ILE* 4.2 16.2 - - + -
313A PHE* 4.1 8.7 - - + -
321A LYS* 3.7 23.5 - - + +
323A VAL* 3.9 18.4 - - + -
339A GLU 3.0 18.7 + - - +
340A GLY 4.3 2.9 - - - +
342A ALA* 1.3 74.8 - - - +
344A VAL* 1.3 62.1 + - - +
346A MET* 3.2 16.6 - - - +
347A LEU* 3.4 14.5 - - - +
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Residues in contact with VAL 344 (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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8A VAL* 6.0 0.2 - - + -
10A ILE* 5.1 0.2 - - + -
20A ALA* 3.2 20.6 - - + +
23A LYS* 3.7 7.4 - - + -
24A ALA* 3.4 38.1 - - + +
27A LEU* 3.6 18.5 - - + +
29A PHE* 4.2 4.3 - - + -
150A ILE* 3.8 20.2 - - + -
340A GLY 3.1 20.8 + - - +
341A ILE 3.2 3.9 + - - +
343A ALA* 1.3 73.3 - - - +
345A GLU* 1.3 62.6 + - - +
346A MET 3.2 0.2 - - - -
347A LEU* 3.1 21.0 + - + +
348A LYS* 3.4 8.3 + - - +
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Residues in contact with GLU 345 (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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23A LYS* 4.7 13.0 - - - -
27A LEU* 4.1 11.4 - - + -
341A ILE* 2.9 34.3 + - + +
342A ALA* 3.5 19.3 - - - +
343A ALA 3.4 0.2 - - - -
344A VAL* 1.3 75.3 - - - +
346A MET* 1.3 56.4 + - - +
348A LYS* 5.0 0.2 - - - -
349A THR* 2.8 37.7 + - - +
351A HIS 3.1 15.8 - - - +
352A GLY* 3.8 10.5 - - - -
353A HIS 4.5 1.7 + - - -
452B ARG* 3.0 36.8 + - - -
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Residues in contact with MET 346 (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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311A ASP 4.0 13.5 - - - +
312A GLN* 3.1 47.3 - - + +
313A PHE* 3.6 27.1 - - + -
321A LYS* 4.1 11.7 - - - +
342A ALA 3.2 14.6 + - - +
343A ALA 3.2 12.1 - - - +
344A VAL 3.2 0.2 - - - -
345A GLU* 1.3 77.2 - - - +
347A LEU* 1.3 58.3 + - - +
350A GLY* 3.1 29.2 + - - +
351A HIS* 3.8 15.9 - - - +
352A GLY 3.4 24.5 - - - +
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Residues in contact with LEU 347 (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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8A VAL* 3.7 29.6 - - + -
29A PHE* 3.6 23.2 - - + -
148A ASN* 3.7 30.0 + - + +
150A ILE* 4.0 19.1 - - + -
318A PRO 5.5 4.5 - - - +
319A HIS 5.5 0.7 - - - +
321A LYS* 3.9 22.9 - - + +
343A ALA 3.4 13.9 - - - +
344A VAL* 3.1 13.3 + - + +
346A MET* 1.3 80.8 - - - +
348A LYS* 1.3 57.5 + - - +
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Residues in contact with LYS 348 (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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27A LEU* 3.2 56.4 + - + +
28A GLY* 4.6 7.9 - - - -
29A PHE* 3.7 21.2 - - + -
344A VAL 3.4 1.4 + - - +
345A GLU 3.4 2.5 + - - +
347A LEU* 1.3 77.7 - - - +
349A THR* 1.3 66.8 + - - +
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Residues in contact with THR 349 (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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27A LEU* 5.8 0.3 - - - +
345A GLU* 2.8 16.6 + - - +
348A LYS* 1.3 86.8 + - - +
350A GLY* 1.3 57.6 + - - +
351A HIS* 4.1 19.0 - - + +
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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