Contacts of the helix formed by residues 483 - 493 (chain B) in PDB entry 2JIH
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 ASP 483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A HIS* 3.5 13.1 + - + -
474A PRO* 5.9 0.3 - - - +
1557A CD 2.3 30.4 - - - -
479B GLY 3.9 5.0 + - - -
480B THR 5.4 0.2 + - - -
481B SER 4.2 1.2 + - - -
482B TYR* 1.3 75.8 - - - +
484B ALA* 1.3 64.8 + - - +
485B ASN* 3.0 11.5 + - - +
486B ARG* 3.0 26.7 + - - +
487B GLN* 3.0 23.4 + - - +
532B THR* 4.4 6.1 - - + -
533B SER* 5.5 10.8 - - - +
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Residues in contact with ALA 484 (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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483B ASP* 1.3 76.9 - - - +
485B ASN* 1.3 57.5 + - - +
487B GLN* 3.4 11.8 + - - +
488B CYS* 2.9 32.6 + - - -
498B HIS* 3.7 33.4 - - + +
509B LEU* 4.0 9.3 - - + +
528B TRP* 4.4 8.7 - - + -
532B THR* 3.9 16.0 - - + +
533B SER 5.4 0.9 - - - +
1563B NI 4.5 6.3 - - + -
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Residues in contact with ASN 485 (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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472A GLN* 4.2 16.2 + - - +
1557A CD 4.5 4.0 - - - -
483B ASP* 3.0 13.9 + - - +
484B ALA* 1.3 77.6 - - - +
486B ARG* 1.3 61.8 + - - +
488B CYS* 3.2 5.0 + - - +
489B GLN* 3.0 30.0 + - + +
496B SER 4.0 1.3 - - - +
497B LYS* 3.5 14.0 - - + +
498B HIS* 2.7 40.8 + - - +
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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
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276A SER* 3.1 22.6 + - - -
277A GLY* 3.4 24.8 - - - +
280A HIS* 3.7 33.3 - - + +
1557A CD 4.6 0.4 - - - -
274B HIS* 5.3 2.6 + - - +
277B GLY* 6.2 2.6 - - - -
481B SER 5.2 0.7 - - - +
482B TYR* 4.0 33.9 - - + -
483B ASP* 3.0 32.8 + - - +
485B ASN* 1.3 74.4 - - - +
487B GLN* 1.3 57.8 + - - +
489B GLN* 2.9 34.0 + - - +
490B PHE* 2.9 63.1 + - + -
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Residues in contact with GLN 487 (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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392B GLY* 5.4 0.3 - - - -
393B LEU* 3.6 20.9 - - + +
482B TYR* 2.9 18.7 - - + +
483B ASP 3.0 12.8 + - - +
484B ALA* 3.5 10.5 - - - +
486B ARG* 1.3 72.5 - - - +
488B CYS* 1.3 64.6 + - - +
490B PHE* 3.4 11.1 + - + +
491B THR* 3.1 26.7 + - - -
509B LEU* 3.5 18.6 - - + +
527B PRO 4.7 1.2 + - - -
528B TRP* 3.7 11.5 - - - +
529B ALA* 3.0 34.1 - - - +
532B THR* 2.6 28.7 + - - +
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Residues in contact with CYS 488 (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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484B ALA 2.9 16.6 + - - -
485B ASN 3.5 7.9 - - - +
487B GLN* 1.3 76.6 - - - +
489B GLN* 1.3 56.3 + - - +
491B THR* 3.2 1.1 + - - -
492B PHE* 2.8 34.5 + - - +
496B SER* 3.7 5.7 - - - +
497B LYS* 3.5 22.0 - - - -
498B HIS* 3.7 2.9 - - - -
509B LEU* 3.9 7.2 - - - -
510B TRP 3.6 7.0 - - - -
511B CYS* 2.0 58.3 - - + -
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Residues in contact with GLN 489 (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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276A SER* 3.0 25.9 + - - +
279A LYS* 4.1 16.3 - - - +
280A HIS* 5.7 1.0 + - - +
273B PHE* 3.3 9.8 - - - -
485B ASN* 3.0 19.4 + - + +
486B ARG* 2.9 45.6 + - - +
488B CYS* 1.3 72.9 - - - +
490B PHE* 1.3 65.1 + - - +
493B GLY* 2.9 35.2 + - - +
494B GLU* 2.8 29.6 + - - +
496B SER 3.3 15.2 + - - +
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Residues in contact with PHE 490 (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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276A SER* 4.1 2.5 - - - -
273B PHE* 4.0 6.3 - + - -
274B HIS* 3.7 24.9 - + - -
281B TYR* 3.4 32.3 - + - +
358B ARG* 2.9 32.4 + - - +
391B ASP* 4.0 2.1 - - - -
392B GLY* 3.5 22.0 + - - +
393B LEU* 4.1 14.1 - - + -
482B TYR* 3.6 47.3 - + + -
486B ARG* 2.9 46.1 + - - -
487B GLN* 3.7 12.6 - - - +
488B CYS 3.4 0.2 - - - -
489B GLN* 1.3 75.4 - - - +
491B THR* 1.3 60.5 + - - +
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Residues in contact with THR 491 (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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358B ARG* 5.1 1.5 + - - -
391B ASP* 3.2 26.8 + - + +
392B GLY* 4.3 3.1 - - - -
487B GLN 3.1 15.7 + - - -
488B CYS* 3.2 1.1 + - - -
490B PHE* 1.3 80.8 - - - +
492B PHE* 1.3 82.1 + - + +
493B GLY 3.7 0.2 - - - -
509B LEU* 5.1 4.9 - - - +
511B CYS* 5.4 0.9 - - - -
524B LYS* 3.5 39.9 - - + -
526B PHE* 4.8 6.3 - - + -
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Residues in contact with PHE 492 (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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488B CYS 2.8 12.8 + - - +
491B THR* 1.3 94.3 - - + +
493B GLY* 1.3 61.1 + - - +
496B SER* 3.6 18.2 + - - +
509B LEU 5.3 0.9 - - - -
511B CYS* 3.7 24.2 - - + -
522B GLN* 3.4 51.6 + - + +
523B THR* 3.8 20.9 - - - -
524B LYS* 3.7 38.1 - - + -
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Residues in contact with GLY 493 (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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273B PHE* 4.5 7.6 - - - -
358B ARG* 4.8 3.9 - - - +
489B GLN* 2.9 27.6 + - - -
490B PHE 4.7 0.2 + - - -
491B THR 3.7 1.0 - - - -
492B PHE* 1.3 79.3 - - - +
494B GLU* 1.3 65.2 + - - -
495B ASP 3.2 3.1 - - - -
496B SER* 3.0 14.8 + - - -
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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
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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