Contacts of the helix formed by residues 485 - 498 (chain B) in PDB entry 1JQI
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 CYS 485 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B LEU* 4.3 13.0 - - + +
433B ALA* 4.4 14.4 - - + -
436B LEU* 4.0 22.0 - - + -
481B ILE 3.0 11.0 + - - +
482B SER* 3.5 5.4 - - - -
483B ARG 3.5 0.8 - - - -
484B GLY* 1.3 79.8 - - - +
486B ALA* 1.3 66.4 + - - +
487B SER* 3.6 14.4 - - - -
488B THR* 3.4 36.0 - - - +
489B GLY 3.2 15.9 + - - -
611B ALA* 5.1 0.2 - - - -
756B ARG* 4.9 4.3 - - - +
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Residues in contact with ALA 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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482B SER* 3.6 12.0 + - - +
485B CYS* 1.3 74.1 - - - +
487B SER* 1.3 62.1 + - - +
489B GLY* 3.4 1.0 + - - -
490B VAL 3.2 7.3 + - - -
609B ILE* 4.1 5.8 - - + -
654B GLN* 2.8 25.7 + - - +
658B ILE* 3.9 23.1 - - + -
756B ARG* 5.2 2.4 - - - +
760B ASP* 3.5 39.2 + - + +
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Residues in contact with SER 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B CYS* 3.3 8.3 - - - -
486B ALA* 1.3 75.5 - - - +
488B THR* 1.3 67.3 + - - +
490B VAL* 3.0 14.9 - - - +
491B ILE* 3.0 25.7 + - - +
609B ILE* 3.1 33.4 - - - +
610B ARG 3.6 0.2 + - - -
611B ALA* 3.2 31.2 + - - +
612B SER* 4.0 8.1 - - - -
760B ASP* 5.2 0.6 + - - -
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Residues in contact with THR 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 4.1 17.0 - - + +
436B LEU* 4.5 0.5 - - - +
443B PRO* 3.6 22.6 - - + +
446B GLN* 5.5 0.9 - - + -
447B VAL* 5.2 4.3 - - + -
450B MET* 3.3 35.2 - - + +
481B ILE* 3.9 9.2 - - + -
485B CYS* 3.4 27.7 - - - +
487B SER* 1.3 77.4 - - - +
489B GLY* 1.3 62.1 + - - +
491B ILE* 3.3 13.2 + - - +
492B MET* 3.1 22.0 + - - +
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Residues in contact with GLY 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 3.2 20.7 - - - +
481B ILE* 4.1 8.5 - - - +
482B SER* 3.6 22.2 - - - -
485B CYS 3.2 8.8 + - - -
486B ALA 3.4 2.9 + - - -
487B SER 3.1 1.0 - - - -
488B THR* 1.3 80.5 - - - +
490B VAL* 1.3 56.5 + - - +
492B MET* 3.3 1.1 + - - +
493B SER* 2.9 24.7 + - - -
654B GLN* 4.7 2.5 - - - -
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Residues in contact with VAL 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ALA 3.2 9.6 + - - +
487B SER* 3.0 29.2 + - - +
489B GLY* 1.3 72.7 - - - +
491B ILE* 1.3 66.7 + - - +
493B SER* 4.2 5.4 - - - -
494B VAL* 3.0 36.9 + - + +
563B THR* 4.5 6.5 - - + -
609B ILE* 4.5 9.4 - - + -
612B SER* 4.2 19.3 - - - +
651B ILE* 4.6 7.4 - - + -
654B GLN* 3.5 17.8 - - - +
767B TYR* 3.5 28.5 - - + +
800B CAA 4.4 5.8 - - + -
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Residues in contact with ILE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PHE* 3.4 38.6 - - + -
443B PRO* 4.0 18.8 - - + -
447B VAL* 4.3 15.5 - - + -
456B LEU* 5.2 2.4 - - + +
487B SER* 3.0 21.9 + - - +
488B THR* 3.5 13.0 - - - +
490B VAL* 1.3 77.0 - - - +
492B MET* 1.3 62.5 + - - +
495B ASN* 3.4 18.9 + - - +
525B ILE* 4.1 10.7 - - + +
564B ASN* 3.5 35.2 + - - +
611B ALA 4.6 6.5 - - - +
612B SER* 4.3 11.4 - - - -
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Residues in contact with MET 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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450B MET* 3.5 29.6 - - + -
455B LEU* 3.5 32.5 - - + +
456B LEU* 4.1 13.0 - - + -
458B MET* 3.9 21.3 - - - -
474B TYR* 4.3 3.8 - - + -
477B ALA* 4.3 3.6 - - + -
478B LEU* 4.0 38.1 - - + +
481B ILE* 4.1 11.4 - - + -
488B THR 3.1 16.3 + - - +
489B GLY 3.5 4.0 - - - +
491B ILE* 1.3 75.7 - - - +
493B SER* 1.3 65.2 + - - +
495B ASN* 3.4 2.4 + - - +
496B ASN* 3.0 33.5 + - - +
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Residues in contact with SER 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B TYR* 2.9 24.2 + - - -
478B LEU* 3.7 11.4 - - - +
489B GLY 2.9 16.5 + - - -
490B VAL* 3.8 9.4 - - - -
492B MET* 1.3 77.0 - - - +
494B VAL* 1.3 58.9 + - - +
497B SER* 2.9 33.6 + - - -
498B LEU* 5.0 1.0 - - - +
647B GLY* 4.4 4.0 + - - -
650B GLY* 3.6 19.0 - - - -
651B ILE* 4.2 11.3 + - - +
654B GLN* 6.0 0.9 - - - -
768B GLU* 4.8 3.2 + - - -
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B VAL* 3.0 22.9 + - + +
493B SER* 1.3 77.2 - - - +
495B ASN* 1.3 63.9 + - - +
498B LEU* 3.0 23.8 + - + -
499B TYR 3.0 21.5 + - - -
526B GLY 3.6 21.1 - - - +
527B CYS* 3.9 14.1 - - - -
528B PHE* 4.4 2.9 - - + +
563B THR* 4.0 17.3 - - + +
564B ASN* 3.6 12.1 - - - +
768B GLU* 5.1 0.9 - - - +
799B FAD 5.8 0.4 - - - +
800B CAA 3.5 31.4 - - + -
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Residues in contact with ASN 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LEU* 2.8 37.1 + - + +
491B ILE 3.4 10.3 + - - +
492B MET 3.9 6.3 - - - +
493B SER 3.4 0.4 - - - -
494B VAL* 1.3 80.3 - - - +
496B ASN* 1.3 57.5 + - - +
499B TYR* 3.6 9.9 - - - +
500B LEU* 3.1 41.3 + - - +
519B PHE* 3.2 22.0 + - - +
525B ILE* 3.2 21.1 - - + +
526B GLY* 2.9 31.7 + - - +
564B ASN* 4.7 0.4 - - - +
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Residues in contact with ASN 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU 2.9 25.0 + - - -
456B LEU 3.6 10.3 - - - -
457B ALA* 3.4 4.9 + - - -
458B MET* 3.0 30.8 + - - +
459B ASP* 4.4 3.1 + - - +
471B TYR* 4.6 5.2 + - + +
474B TYR* 3.4 30.9 - - + +
492B MET* 3.0 31.0 + - - +
495B ASN* 1.3 78.0 - - - +
497B SER* 1.3 59.1 + - - +
500B LEU* 3.7 6.9 - - - +
501B GLY* 3.1 23.4 + - - -
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Residues in contact with SER 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B TYR* 2.8 25.8 + - - -
474B TYR* 2.9 24.0 + - - -
493B SER* 2.9 15.8 + - - -
496B ASN* 1.3 72.5 - - - +
498B LEU* 1.3 61.8 + - - +
501B GLY* 3.5 5.3 - - - -
502B PRO* 3.3 19.6 - - - +
643B THR* 3.6 6.9 - - - +
646B MET* 3.7 7.8 + - - +
647B GLY* 3.5 28.2 - - - -
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Residues in contact with LEU 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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493B SER 3.9 1.0 + - - +
494B VAL* 3.0 23.2 + - + +
497B SER* 1.3 84.2 - - - +
499B TYR* 1.3 59.3 + - - +
502B PRO* 3.1 17.5 - - - +
528B PHE* 3.3 49.0 - - + +
572B VAL* 4.5 2.9 - - - +
643B THR* 3.9 15.0 - - + +
644B LEU* 4.6 6.7 - - + -
647B GLY* 3.9 24.7 - - - -
768B GLU* 3.4 24.5 - - - +
800B CAA 3.6 30.3 - - + -
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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
------------------------------------------------------------
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