Contacts of the helix formed by residues 484 - 500 (chain B) in PDB entry 1JEY
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 ASN 484 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A PRO* 4.5 4.5 - - - +
408A PRO 4.8 0.2 - - - +
409A TYR* 3.8 26.9 + - - -
439A PHE* 3.5 25.1 - - + +
441A ASP* 2.6 18.5 + - + +
442A ASP* 5.3 1.2 + - - +
269B GLN* 5.5 1.0 - - - +
270B GLU 4.8 4.2 + - - -
483B PRO* 1.3 71.4 - - - +
485B PRO* 1.3 75.4 - - - +
486B ARG* 3.1 39.9 + - - +
487B PHE* 3.3 34.8 + - + +
488B GLN* 4.4 1.6 + - - +
515B MET* 5.1 0.2 - - - -
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Residues in contact with PRO 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 3.9 18.7 - - + -
407A PRO* 5.2 0.2 - - + -
408A PRO* 4.3 21.5 - - + +
439A PHE* 3.6 18.4 - - + -
483B PRO 2.9 10.6 - - - +
484B ASN* 1.3 88.1 - - - +
486B ARG* 1.3 63.0 - - - +
487B PHE 3.2 0.4 + - - -
488B GLN* 3.6 4.3 + - + +
489B ARG* 3.1 24.6 + - - +
512B ILE* 4.0 19.2 - - + +
515B MET* 4.3 9.9 - - + -
516B LEU* 4.1 21.1 - - + -
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Residues in contact with ARG 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 5.1 3.7 - - - +
338A LYS* 3.8 27.0 - - + +
340A PHE* 4.3 6.4 - - - -
406A ILE* 5.7 1.2 - - - +
407A PRO* 3.5 39.4 - - + +
409A TYR* 6.3 1.2 - - - -
269B GLN* 5.7 5.3 - - - +
270B GLU 5.8 0.4 - - - -
271B ARG* 6.4 0.4 - - - +
272B VAL* 4.4 16.2 - - + +
484B ASN* 3.1 31.1 + - - +
485B PRO* 1.3 79.6 - - - +
487B PHE* 1.3 81.3 + - + +
489B ARG* 3.7 6.5 - - - +
490B LEU* 2.9 30.1 + - - +
7C A 4.5 6.1 + - - -
8C G 2.9 35.4 + - - -
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Residues in contact with PHE 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ASP* 3.5 19.5 - - - +
44B ARG* 3.7 21.5 - - - +
270B GLU* 3.6 48.7 - - + -
271B ARG* 3.9 3.6 - - - -
272B VAL* 3.7 36.6 - - + -
484B ASN* 3.3 34.3 + - + +
485B PRO 3.2 0.8 - - - -
486B ARG* 1.3 86.8 - - + +
488B GLN* 1.3 64.1 + - + +
489B ARG 3.1 0.9 - - - -
490B LEU* 3.1 7.4 + - + +
491B PHE* 2.9 45.0 + + + -
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Residues in contact with GLN 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.1 47.6 - - + +
43B GLN* 2.7 29.1 + - - -
44B ARG* 4.0 7.1 + - - +
237B PHE* 4.9 1.6 - - - -
483B PRO* 6.1 7.2 - - + -
484B ASN 4.4 1.9 + - - +
485B PRO* 3.6 4.6 + - + +
487B PHE* 1.3 80.1 - - + +
489B ARG* 1.3 56.7 + - - +
491B PHE* 3.3 22.0 - - + -
492B GLN* 3.0 27.9 + - - +
509B GLN* 4.5 6.7 + - - +
511B HIS* 6.2 0.7 - - - +
512B ILE* 4.6 19.7 - - + -
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 4.5 23.4 + - - +
337A LEU* 3.3 30.4 + - - +
339A ARG 5.1 1.4 + - - -
340A PHE* 3.8 15.9 - - + -
485B PRO 3.1 20.3 + - - +
486B ARG 3.7 2.9 - - - +
487B PHE 3.1 0.2 - - - -
488B GLN* 1.3 75.7 - - - +
490B LEU* 1.3 65.3 + - - +
492B GLN* 3.0 27.0 + - - +
493B CYS* 3.2 34.2 + - - -
505B LEU* 5.5 3.0 - - - +
506B PRO 2.8 29.3 + - - -
507B PRO* 3.3 12.7 - - - +
508B ILE* 3.3 32.3 - - + +
509B GLN* 5.6 1.1 - - - +
512B ILE* 5.6 6.4 - - + +
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Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN* 5.0 4.0 - - - +
322A TYR* 5.7 0.4 - - - +
337A LEU* 3.8 36.3 - - + -
272B VAL* 4.1 34.5 - - + -
276B TRP* 4.3 9.9 - - + +
486B ARG 2.9 20.3 + - - +
487B PHE* 3.1 6.9 + - + +
489B ARG* 1.3 78.5 - - - +
491B PHE* 1.3 72.6 + - + +
493B CYS* 3.2 6.8 + - - +
494B LEU* 2.8 55.5 + - + +
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Residues in contact with PHE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 3.5 17.0 - - - +
44B ARG* 3.7 55.9 - - + -
47B PHE* 3.6 48.9 - + + -
48B ALA* 5.2 1.8 - - + -
487B PHE* 2.9 31.6 + + + +
488B GLN* 3.3 26.2 - - - +
489B ARG 3.3 0.2 - - - -
490B LEU* 1.3 91.6 - - + +
492B GLN* 1.3 66.1 + - - +
494B LEU* 4.4 2.0 - - + -
495B LEU* 2.9 26.9 + - - +
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Residues in contact with GLN 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 3.7 14.5 - - - +
488B GLN 3.0 17.6 + - - +
489B ARG* 3.0 37.4 + - - +
491B PHE* 1.3 76.1 - - - +
493B CYS* 1.3 55.6 + - - +
495B LEU* 3.6 1.9 + - - +
496B HIS* 2.8 29.1 + - + +
506B PRO* 3.6 20.9 - - + +
507B PRO 3.2 21.1 + - - +
509B GLN* 3.3 42.2 + - - +
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Residues in contact with CYS 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 5.5 2.0 - - + -
337A LEU* 4.0 28.9 - - + -
489B ARG* 3.2 42.6 + - - +
490B LEU 3.2 8.9 + - - +
491B PHE 3.1 0.4 - - - -
492B GLN* 1.3 78.6 - - - +
494B LEU* 1.3 67.0 + - - +
496B HIS* 2.9 7.4 + - - +
497B ARG* 2.8 26.7 + - - +
505B LEU* 4.1 23.3 - - + +
506B PRO* 4.5 9.6 - - - -
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN* 3.5 17.7 - - - +
322A TYR* 3.2 25.8 - - + +
327A ILE* 3.2 38.0 - - + +
329A LEU* 5.2 3.4 - - + -
47B PHE* 3.6 35.9 - - + -
276B TRP* 3.6 24.7 - - + -
490B LEU* 2.8 40.1 + - + +
491B PHE* 3.8 2.9 - - + +
493B CYS* 1.3 72.0 - - - +
495B LEU* 1.3 61.7 + - - +
497B ARG* 3.5 1.0 + - - -
498B ALA* 3.2 16.3 + - - +
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR* 4.5 7.2 - - + -
43B GLN* 3.3 25.8 - - + +
47B PHE* 3.7 8.2 - - + -
88B PHE* 4.1 13.9 - - + -
91B LEU* 3.9 36.6 - - + +
95B GLU* 3.7 21.5 - - - +
491B PHE 2.9 17.3 + - - +
492B GLN 3.8 3.1 - - - +
494B LEU* 1.3 73.1 - - - +
496B HIS* 1.3 68.7 + - - +
498B ALA* 2.9 14.7 + - + +
499B LEU* 3.0 38.5 + - + +
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Residues in contact with HIS 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLU* 5.7 2.5 - - - -
492B GLN* 2.8 20.7 + - + +
493B CYS 2.9 4.2 + - - +
495B LEU* 1.3 77.8 - - - +
497B ARG* 1.3 57.7 + - - +
499B LEU* 5.3 0.2 - - - -
500B HIS* 2.9 56.6 + + + +
503B GLU* 3.8 24.8 + - + +
504B PRO 3.5 22.0 + - - -
505B LEU* 4.7 2.0 - - + +
506B PRO* 3.5 40.8 - - + +
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Residues in contact with ARG 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ILE* 3.7 20.0 - - + -
328A ILE 3.3 30.0 + - - +
329A LEU* 3.4 12.6 - - + +
333A GLU* 2.6 43.0 + - - -
493B CYS 2.8 18.9 + - - +
494B LEU 3.9 0.2 - - - +
496B HIS* 1.3 73.3 + - - +
498B ALA* 1.3 63.0 + - - +
500B HIS 4.2 4.4 + - - -
501B PRO* 3.4 42.1 + - - +
503B GLU 2.3 32.7 + - - -
504B PRO* 4.1 2.2 - - - +
505B LEU* 3.4 23.3 - - + +
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Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ARG* 2.6 43.2 + - - +
326A GLN 6.0 0.9 - - - -
327A ILE* 4.3 14.3 - - + +
88B PHE* 4.3 20.4 - - + -
494B LEU 3.2 13.4 + - - +
495B LEU 2.9 10.3 + - - +
497B ARG* 1.3 79.5 - - - +
499B LEU* 1.3 60.7 + - + +
500B HIS 3.5 0.2 + - - -
501B PRO* 4.0 7.1 - - - +
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Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 4.5 13.5 - - - +
88B PHE* 4.3 9.2 - - + +
92B GLU* 3.9 53.5 - - + +
95B GLU* 3.7 22.2 - - + +
495B LEU* 3.0 38.5 + - + +
496B HIS* 5.3 0.2 - - - -
498B ALA* 1.3 81.9 - - + +
500B HIS* 1.3 83.0 + - + +
501B PRO* 3.8 4.3 - - - +
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Residues in contact with HIS 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLU* 3.5 20.2 - - - -
496B HIS* 2.9 39.5 + + + +
497B ARG* 3.7 3.5 + - - +
499B LEU* 1.3 104.8 + - + +
501B PRO* 1.3 66.8 - - - +
502B ARG 3.4 2.5 - - - -
503B GLU* 3.4 39.8 + - + +
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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