Contacts of the helix formed by residues 521 - 536 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A THR 5.8 2.0 - - - +
371A PRO 5.8 0.7 - - - -
372A SER* 4.4 15.9 - - - +
375A MET* 3.5 7.6 - - - +
519A ALA 3.5 0.4 - - - -
520A ASN* 1.3 89.7 - - + +
522A PRO* 1.3 76.2 - - - +
523A ALA* 3.4 9.5 + - - +
524A GLU* 3.0 33.6 + - + +
525A LEU* 3.0 22.7 + - - +
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Residues in contact with PRO 522 (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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368A ALA 5.6 1.3 - - - +
370A THR* 5.0 5.8 - - - +
375A MET* 3.5 17.4 - - + -
379A ASN* 4.1 37.7 - - + +
383A VAL* 3.5 29.0 - - + +
521A THR* 1.3 87.7 - - - +
523A ALA* 1.3 56.3 + - - +
525A LEU* 3.4 2.1 + - + +
526A LYS* 3.0 26.2 + - - +
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Residues in contact with ALA 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A THR* 3.2 8.4 + - - +
522A PRO* 1.3 79.4 - - - +
524A GLU* 1.3 61.4 + - + +
526A LYS* 3.5 9.0 + - - +
527A ALA* 3.3 22.3 + - - +
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Residues in contact with GLU 524 (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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372A SER* 5.5 0.3 + - - -
518A VAL 3.8 10.9 - - - +
519A ALA* 3.7 6.4 - - - -
520A ASN* 2.8 39.9 + - - +
521A THR* 3.0 28.1 + - - +
523A ALA* 1.3 74.8 - - + +
525A LEU* 1.3 63.4 + - - +
527A ALA* 3.6 5.4 + - - +
528A ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 525 (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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375A MET* 4.5 6.7 - - + -
380A SER* 3.3 43.3 - - - +
383A VAL* 4.2 11.9 - - + -
384A VAL* 4.9 8.3 - - + -
475A ILE* 4.3 16.2 - - + -
477A MET* 6.2 0.7 - - - -
519A ALA* 3.6 14.9 - - + +
521A THR 3.0 15.7 + - - +
522A PRO 3.6 4.0 - - - +
524A GLU* 1.3 72.9 - - - +
526A LYS* 1.3 61.6 + - - +
528A ALA* 3.7 2.0 - - - +
529A LEU* 2.9 34.4 + - + +
541A ILE* 3.6 31.2 - - + -
543A ALA* 4.2 12.6 - - + -
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Residues in contact with LYS 526 (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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383A VAL* 3.5 24.4 - - + +
386A ASP* 6.6 0.2 - - - -
522A PRO 3.0 17.0 + - - +
523A ALA* 3.6 9.4 - - - +
525A LEU* 1.3 77.9 - - - +
527A ALA* 1.3 62.8 + - - +
529A LEU* 3.8 1.4 - - - +
530A GLU* 3.0 57.4 + - + +
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Residues in contact with ALA 527 (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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523A ALA 3.3 13.5 + - - +
524A GLU* 4.0 5.6 - - - +
526A LYS* 1.3 78.7 - - - +
528A ALA* 1.3 57.1 + - - +
530A GLU* 3.5 8.5 + - - +
531A GLU* 2.9 51.5 + - - +
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Residues in contact with ALA 528 (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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517A TYR* 3.6 38.9 - - + -
518A VAL 5.9 1.1 - - - +
519A ALA* 5.3 1.3 - - + -
524A GLU 3.1 19.1 + - - +
525A LEU* 3.7 4.3 - - - +
527A ALA* 1.3 76.5 - - - +
529A LEU* 1.3 54.5 + - - +
531A GLU* 3.4 1.5 + - - +
532A ALA* 2.8 36.6 + - - +
541A ILE* 3.7 19.1 - - + -
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Residues in contact with LEU 529 (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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383A VAL* 4.8 6.5 - - + +
384A VAL* 4.2 28.9 - - + +
387A PHE* 4.1 34.0 - - + -
447A ILE* 3.8 24.2 - - + -
473A THR* 4.2 12.6 - - + -
475A ILE* 4.1 17.9 - - + -
525A LEU* 2.9 21.0 + - + +
526A LYS* 3.8 2.9 - - - +
528A ALA* 1.3 72.0 - - - +
530A GLU* 1.3 61.0 + - - +
532A ALA* 3.8 0.8 - - - +
533A VAL* 3.0 44.1 + - + +
541A ILE* 3.5 9.1 - - + +
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Residues in contact with GLU 530 (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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387A PHE* 3.8 29.8 - - + -
526A LYS* 3.0 54.6 + - + +
527A ALA* 3.7 8.0 - - - +
529A LEU* 1.3 75.9 - - + +
531A GLU* 1.3 62.8 + - + +
533A VAL* 4.3 1.0 - - - +
534A ALA* 3.2 26.3 + - - +
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Residues in contact with GLU 531 (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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517A TYR* 4.0 24.4 + - - +
527A ALA* 2.9 34.5 + - - +
528A ALA* 3.8 2.9 - - - +
530A GLU* 1.3 75.3 - - + +
532A ALA* 1.3 61.3 + - - +
534A ALA* 3.9 3.6 - - - +
535A SER* 2.9 31.2 + - - -
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Residues in contact with ALA 532 (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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473A THR* 3.5 32.7 + - + -
517A TYR* 4.0 9.8 + - + -
528A ALA 2.8 22.8 + - - +
529A LEU 3.8 1.6 - - - +
531A GLU* 1.3 70.7 - - - +
533A VAL* 1.3 65.6 + - - +
535A SER* 2.6 21.3 + - - -
536A GLY 3.6 2.1 + - - -
537A LYS 4.2 3.1 + - - +
539A CYS* 3.6 26.8 - - + -
541A ILE* 4.5 0.9 - - + -
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Residues in contact with VAL 533 (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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387A PHE* 3.7 33.2 - - + -
391A ASN* 5.2 3.1 - - - +
394A ILE* 4.0 16.6 - - + -
445A PRO* 4.2 24.8 - - + +
446A VAL 5.5 0.9 - - - +
447A ILE* 4.0 12.3 - - + -
471A PRO* 5.7 1.0 - - - +
473A THR* 3.9 14.8 - - - +
529A LEU* 3.0 30.8 + - + +
530A GLU 4.4 0.4 - - - +
532A ALA* 1.3 75.3 - - - +
534A ALA* 1.3 64.2 + - - +
536A GLY* 3.3 13.5 + - - -
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Residues in contact with ALA 534 (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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530A GLU 3.2 18.2 + - - +
531A GLU* 4.1 3.8 - - - +
533A VAL* 1.3 78.3 - - - +
535A SER* 1.3 65.5 + - - +
536A GLY* 3.3 1.4 + - - -
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Residues in contact with SER 535 (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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515A LYS* 4.3 20.2 - - - -
531A GLU 2.9 17.1 + - - -
532A ALA* 2.6 21.0 + - - -
534A ALA* 1.3 77.8 - - - +
536A GLY* 1.3 60.7 + - - +
537A LYS* 3.3 28.0 + - - +
539A CYS* 3.6 10.2 - - - -
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Residues in contact with GLY 536 (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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469A ASN* 4.5 8.3 + - - +
471A PRO* 3.8 28.7 - - - +
532A ALA 3.6 0.6 + - - -
533A VAL 3.3 12.2 + - - -
534A ALA 3.2 4.5 - - - -
535A SER* 1.3 79.0 + - - +
537A LYS* 1.3 61.2 + - - +
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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