Contacts of the helix formed by residues 480 - 495 (chain A) in PDB entry 1JEQ
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 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS* 6.3 0.2 - - - +
280A ALA 4.5 6.5 + - - -
479A GLU* 1.3 69.4 - - - +
481A PRO* 1.3 68.1 - - - +
482A VAL* 3.0 22.5 + - - +
483A LEU* 3.1 34.0 + - + +
484A GLN* 3.0 25.2 + - - +
426B PHE* 3.3 37.1 - - + -
428B GLU* 3.1 18.3 + - - +
429B ASP* 5.5 1.8 + - - -
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Residues in contact with PRO 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLU 3.2 8.8 - - - +
480A ASN* 1.3 87.3 - - - +
482A VAL* 1.3 56.0 + - - +
484A GLN* 3.6 6.1 - - + +
485A GLN* 3.1 27.0 + - - +
503A ALA* 5.3 2.6 - - - +
505A ASP* 3.3 39.7 - - - +
507A THR* 3.4 13.9 - - + +
333B TYR* 3.7 20.1 - - + -
403B PRO* 4.1 13.9 - - + -
426B PHE* 3.5 18.2 - - + -
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Residues in contact with VAL 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LYS* 4.4 30.7 - - + +
480A ASN* 3.0 9.5 + - - +
481A PRO* 1.3 73.7 - - - +
483A LEU* 1.3 68.7 - - + +
485A GLN* 3.1 3.3 + - - +
486A HIS* 2.9 21.5 + - + +
332B LYS* 6.0 4.0 - - + -
333B TYR* 3.6 39.5 - - + +
402B ASN* 3.2 32.5 - - + +
403B PRO* 4.2 10.1 - - + -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 4.8 6.7 - - + -
280A ALA* 3.6 36.8 - - + +
281A LEU 3.7 4.7 - - - +
282A LYS* 3.6 40.8 - - + +
480A ASN* 3.1 34.4 + - + +
482A VAL* 1.3 80.1 - - + +
484A GLN* 1.3 64.7 + - - +
486A HIS* 3.2 3.9 + - + +
487A PHE* 3.0 48.0 + - + -
428B GLU* 4.3 16.6 - - + +
429B ASP* 5.5 0.2 - - - +
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Residues in contact with GLN 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 5.8 7.4 - - - +
479A GLU* 3.6 37.1 + - + +
480A ASN 3.0 19.5 + - - +
481A PRO* 3.6 7.0 - - + +
483A LEU* 1.3 77.4 - - - +
485A GLN* 1.3 54.9 + - - +
487A PHE* 3.3 1.3 + - - -
488A ARG* 2.7 61.9 + - - +
503A ALA* 4.2 19.1 - - + -
427B MET* 5.9 0.4 - - - -
428B GLU* 2.6 31.3 + - - +
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Residues in contact with GLN 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A PRO 3.1 11.3 + - - +
482A VAL* 3.4 11.4 - - - +
484A GLN* 1.3 79.2 - - - +
486A HIS* 1.3 64.8 + - - +
488A ARG* 3.6 4.3 - - - +
489A ASN* 2.6 56.1 + - - +
500A PRO* 5.6 0.4 - - - +
501A GLU 5.5 1.7 + - - -
502A GLN* 3.2 27.2 + - - +
503A ALA* 3.9 23.3 + - + +
331B MET* 3.7 15.4 + - - +
332B LYS 4.4 0.8 + - - -
333B TYR* 3.9 29.4 - - + +
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Residues in contact with HIS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LYS* 3.2 47.3 + - + +
283A PRO* 4.3 6.0 + - + +
482A VAL* 2.9 15.5 + - + +
483A LEU* 3.4 9.9 - - - +
485A GLN* 1.3 75.3 - - - +
487A PHE* 1.3 80.9 + + - +
489A ASN* 3.1 6.9 + - - +
490A LEU* 2.8 46.5 + - + +
314B PHE* 3.9 42.2 - + - -
323B PHE* 4.7 11.7 - + - -
331B MET 5.6 0.9 - - - -
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Residues in contact with PHE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 4.1 14.8 - - + -
76A ILE* 3.2 57.2 - - + -
283A PRO* 3.4 42.2 - - + -
483A LEU* 3.0 37.5 + - + +
484A GLN* 4.2 1.6 - - - +
486A HIS* 1.3 87.0 - + - +
488A ARG* 1.3 69.4 + - - +
490A LEU* 3.7 11.7 - - + -
491A GLU* 2.9 29.1 + - - +
315B ARG 4.6 5.8 - - - -
316B TYR* 3.7 25.9 - + + -
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Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.3 23.6 - - - +
76A ILE* 6.1 0.6 - - - +
484A GLN* 2.7 54.7 + - - +
485A GLN* 3.6 5.8 - - - +
487A PHE* 1.3 83.3 + - - +
489A ASN* 1.3 64.2 + - - +
491A GLU* 2.9 31.4 + - - +
492A ALA* 3.1 21.1 + - - +
500A PRO* 4.5 1.3 - - - +
501A GLU* 2.9 64.5 + - + +
503A ALA* 5.0 6.1 - - + +
316B TYR* 3.8 9.9 + - - -
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Residues in contact with ASN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN* 2.6 50.3 + - - +
486A HIS* 3.4 7.0 - - - +
488A ARG* 1.3 75.0 - - - +
490A LEU* 1.3 66.9 + - - +
492A ALA* 3.0 4.5 + - - +
493A LEU* 2.9 27.9 + - - +
500A PRO* 2.8 41.2 - - - +
323B PHE* 5.0 7.2 - - + -
331B MET* 3.1 42.4 + - + +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO* 5.9 0.2 - - + -
486A HIS* 2.8 35.0 + - + +
487A PHE* 3.7 15.7 - - + +
489A ASN* 1.3 76.7 - - - +
491A GLU* 1.3 60.5 + - - +
493A LEU* 3.5 5.4 + - + +
494A ALA* 3.0 24.3 + - - +
314B PHE* 3.5 22.0 - - + -
315B ARG 3.4 24.0 - - - +
316B TYR* 4.1 8.9 - - + -
321B VAL* 4.1 26.6 - - + +
323B PHE* 3.7 32.5 - - + -
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Residues in contact with GLU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.6 4.2 - - - +
113A ALA* 4.6 1.8 - - + -
116A ILE* 4.4 18.9 - - - +
117A LEU* 5.4 1.2 + - - -
487A PHE 2.9 16.3 + - - +
488A ARG* 2.9 34.5 + - - +
490A LEU* 1.3 74.1 - - - +
492A ALA* 1.3 68.2 + - - +
494A ALA* 2.9 4.7 + - - +
495A LEU* 2.9 48.3 + - + +
497A LEU* 6.0 1.0 - - - +
316B TYR* 3.1 35.9 + - + +
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ARG 3.1 5.8 + - - +
489A ASN 3.0 8.6 + - - +
491A GLU* 1.3 79.6 - - - +
493A LEU* 1.3 62.4 + - + +
495A LEU 3.3 0.7 + - - -
496A ASP 3.2 1.6 + - - -
497A LEU* 2.7 50.5 + - + +
499A GLU 3.6 11.2 - - - +
500A PRO* 3.4 35.7 - - + -
501A GLU 4.9 0.4 - - - +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ASN 2.9 18.3 + - - +
490A LEU* 3.8 3.8 - - + +
492A ALA* 1.3 77.2 - - + +
494A ALA* 1.3 57.6 - - - +
495A LEU 2.9 4.9 - - - -
496A ASP* 2.9 22.7 + - - +
497A LEU 5.5 5.2 - - - +
500A PRO* 6.4 1.6 - - + -
321B VAL* 3.6 24.9 - - + +
322B PRO 5.2 1.3 - - - +
323B PHE* 4.0 21.3 - - + -
328B GLU* 4.1 14.4 - - - +
331B MET* 3.8 31.9 - - + -
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Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA* 3.9 7.1 - - + +
114A LYS* 5.2 8.3 - - - +
490A LEU 3.0 16.9 + - - +
491A GLU 2.9 5.6 + - - +
493A LEU* 1.3 75.6 - - - +
495A LEU* 1.3 63.4 + - - +
496A ASP* 3.4 1.1 + - - +
316B TYR* 4.5 4.0 - - + -
319B ASP* 3.8 28.1 - - + +
321B VAL* 3.9 22.4 - - + +
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA* 3.4 42.8 - - + +
114A LYS* 3.7 18.8 - - + +
117A LEU* 4.4 27.6 - - + -
491A GLU* 2.9 38.6 + - + +
492A ALA 3.8 3.4 - - - +
494A ALA* 1.3 80.1 - - - +
496A ASP* 1.3 68.1 + - - +
497A LEU* 2.6 29.0 + - + +
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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
------------------------------------------------------------
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