Contacts of the helix formed by residues 521 - 536 (chain B) in PDB entry 2JI8
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 THR 521 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370B THR 5.8 2.5 - - - +
371B PRO 5.6 0.2 - - - -
372B SER* 3.9 24.2 - - - +
375B MET* 3.5 8.3 - - - +
519B ALA 3.5 0.4 - - - -
520B ASN* 1.3 85.0 + - + +
522B PRO* 1.3 69.6 - - + +
523B ALA* 3.6 8.4 + - - +
524B GLU* 3.1 29.6 + - - +
525B LEU* 2.9 27.4 + - - +
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Residues in contact with PRO 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA 5.6 0.9 - - - +
370B THR* 5.2 3.6 - - - +
375B MET* 3.6 15.7 - - + -
379B ASN* 4.0 36.8 - - + +
383B VAL* 3.6 25.2 - - + +
521B THR* 1.3 87.0 - - + +
523B ALA* 1.3 56.8 + - - +
525B LEU* 3.4 1.5 + - + -
526B LYS* 2.9 30.9 + - - +
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Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B THR* 3.3 8.1 + - - +
522B PRO* 1.3 80.0 - - - +
524B GLU* 1.3 63.2 + - + +
526B LYS* 3.4 7.3 + - - +
527B ALA* 3.1 25.3 + - - +
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B SER* 5.4 0.9 + - - -
518B VAL 3.7 11.5 - - - +
519B ALA* 4.0 8.9 - - - +
520B ASN* 2.8 35.8 + - - +
521B THR* 3.1 25.8 + - - +
523B ALA* 1.3 74.4 - - + +
525B LEU* 1.3 66.4 + - - +
527B ALA* 4.1 3.5 - - - +
528B ALA* 3.1 26.0 + - - +
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Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B MET* 4.6 7.4 - - + -
380B SER* 3.1 42.4 - - - +
383B VAL* 4.0 13.0 - - + -
384B VAL* 4.6 7.9 - - + -
475B ILE* 4.1 24.0 - - + -
477B MET* 5.2 1.3 - - + -
519B ALA* 3.6 13.5 - - + +
521B THR 2.9 16.0 + - - +
522B PRO* 3.4 6.3 + - + +
524B GLU* 1.3 77.5 - - - +
526B LYS* 1.3 56.8 + - - +
528B ALA* 3.7 1.4 - - - +
529B LEU* 2.9 33.1 + - + +
541B ILE* 3.6 28.7 - - + -
543B ALA* 4.4 5.8 - - + -
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Residues in contact with LYS 526 (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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383B VAL* 3.5 24.2 - - + +
386B ASP* 6.4 2.2 - - - -
522B PRO 2.9 17.5 + - - +
523B ALA* 3.8 7.2 - - - +
524B GLU 3.3 0.2 - - - -
525B LEU* 1.3 78.4 - - - +
527B ALA* 1.3 57.4 + - - +
529B LEU* 3.4 2.7 + - - +
530B GLU* 3.0 59.1 + - + +
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Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ALA 3.1 14.4 + - - +
524B GLU* 4.2 4.5 - - - +
526B LYS* 1.3 80.6 - - - +
528B ALA* 1.3 57.0 + - - +
530B GLU* 4.0 8.7 - - - +
531B GLU* 3.1 30.3 + - - +
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Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B TYR* 3.6 39.4 - - + -
518B VAL 6.0 0.2 - - - +
519B ALA* 5.3 0.9 - - + -
524B GLU 3.1 19.4 + - - +
525B LEU 3.7 3.1 - - - +
527B ALA* 1.3 75.1 - - - +
529B LEU* 1.3 54.7 + - - +
531B GLU* 3.4 2.0 + - - +
532B ALA* 2.8 36.4 + - - +
541B ILE* 3.7 19.3 - - + -
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Residues in contact with LEU 529 (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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383B VAL* 4.7 8.1 - - + -
384B VAL* 4.3 26.5 - - + -
387B PHE* 3.9 34.5 - - + -
447B ILE* 3.9 15.3 - - + -
473B THR* 3.8 23.3 - - + -
475B ILE* 4.1 13.7 - - + -
525B LEU* 2.9 19.9 + - + +
526B LYS* 3.9 4.0 - - - +
528B ALA* 1.3 74.9 - - - +
530B GLU* 1.3 58.4 + - - +
532B ALA* 4.4 0.7 - - - -
533B VAL* 3.0 47.8 + - + +
541B ILE* 3.5 8.5 - - + +
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PHE* 3.8 30.5 - - + -
526B LYS* 3.0 53.0 + - + +
527B ALA* 4.0 7.4 - - - +
529B LEU* 1.3 76.6 - - - +
531B GLU* 1.3 60.7 + - - +
533B VAL* 4.3 0.7 - - - +
534B ALA* 3.2 27.0 + - - +
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Residues in contact with GLU 531 (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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515B LYS* 4.6 8.0 + - - -
517B TYR* 2.8 31.9 + - - +
527B ALA 3.1 19.9 + - - +
528B ALA* 3.8 4.0 - - - +
530B GLU* 1.3 74.3 - - - +
532B ALA* 1.3 64.2 + - - +
534B ALA* 3.9 4.1 - - - +
535B SER* 3.1 25.1 + - - -
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B THR* 3.4 31.0 + - + +
517B TYR* 4.0 8.0 + - + -
528B ALA 2.8 22.4 + - - +
529B LEU 3.8 1.3 - - - +
531B GLU* 1.3 74.5 - - - +
533B VAL* 1.3 61.5 + - - +
535B SER* 2.8 20.6 + - - -
536B GLY* 3.6 2.9 + - - -
537B LYS 4.3 3.1 - - - +
539B CYS* 3.5 31.0 - - + -
541B ILE* 4.7 0.4 - - + -
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PHE* 3.6 36.8 - - + -
391B ASN* 5.8 0.9 - - + -
394B ILE* 4.1 13.9 - - + -
445B PRO* 4.4 24.3 - - + +
446B VAL 5.5 0.7 - - - +
447B ILE* 4.1 11.4 - - + -
471B PRO* 5.9 0.3 - - - +
473B THR* 4.0 10.8 - - - +
529B LEU* 3.0 34.7 + - + +
530B GLU 4.3 0.4 - - - +
532B ALA* 1.3 74.2 - - - +
534B ALA* 1.3 64.7 + - - +
535B SER 3.3 0.7 + - - -
536B GLY* 3.4 11.4 + - - -
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Residues in contact with ALA 534 (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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530B GLU 3.2 18.5 + - - +
531B GLU* 3.9 5.6 - - - +
533B VAL* 1.3 80.6 - - - +
535B SER* 1.3 61.0 + - - +
536B GLY* 3.5 0.5 + - - -
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Residues in contact with SER 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B TYR* 5.8 1.6 - - - -
531B GLU* 3.1 17.5 + - - -
532B ALA 2.8 18.2 + - - -
533B VAL 3.2 0.2 - - - -
534B ALA* 1.3 77.6 - - - +
536B GLY* 1.3 61.6 + - - +
537B LYS* 3.2 36.8 + - - +
539B CYS* 3.9 8.1 - - - -
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Residues in contact with GLY 536 (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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445B PRO* 6.3 0.7 - - - -
469B ASN* 4.3 8.5 + - - +
471B PRO* 3.8 30.7 - - - +
532B ALA 3.6 1.6 + - - -
533B VAL 3.4 10.0 + - - -
534B ALA 3.3 3.8 - - - -
535B SER* 1.3 78.0 + - - +
537B LYS* 1.3 66.2 + - - +
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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