Contacts of the helix formed by residues 489 - 507 (chain B) in PDB entry 1MKD
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 ALA 489 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 6.4 0.2 - - + -
478B TRP* 5.0 3.1 - - + -
481B TRP* 4.1 11.7 - - + +
482B ALA* 3.7 31.2 - - + -
485B VAL* 3.8 13.9 - - + +
487B PRO 3.0 1.2 - - - -
488B ASP* 1.3 77.7 - - - +
490B GLN* 1.3 63.6 + - - +
491B ASP 3.3 2.9 - - - -
492B ILE* 3.2 21.9 + - + +
493B LEU* 3.0 22.3 + - - +
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Residues in contact with GLN 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ALA* 5.1 3.3 - - - +
486B HIS* 4.7 9.5 + - - -
487B PRO* 2.9 32.4 + - + +
488B ASP 3.3 0.6 - - - -
489B ALA* 1.3 77.6 - - - +
491B ASP* 1.3 64.4 + - - +
493B LEU* 3.4 20.7 + - - +
494B ASP* 3.1 42.9 + - - +
497B GLU* 5.5 0.8 + - - -
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Residues in contact with ASP 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ASP 4.8 3.9 + - - +
489B ALA 3.3 0.8 - - - -
490B GLN* 1.3 75.4 - - - +
492B ILE* 1.3 70.1 + - + +
494B ASP* 3.1 13.9 + - - +
495B THR* 2.9 29.1 + - - +
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 3.8 43.7 - - + +
271B VAL* 6.2 0.9 - - + -
272B LEU* 4.6 7.2 - - + -
420B THR* 3.4 31.7 - - + +
478B TRP* 3.8 30.7 - - + -
488B ASP 5.3 2.9 - - - +
489B ALA* 3.2 20.3 + - + +
491B ASP* 1.3 77.4 - - + +
493B LEU* 1.3 64.1 + - - +
495B THR* 3.3 8.0 + - - -
496B LEU* 3.0 22.2 + - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B HIS* 3.6 34.3 - - + +
478B TRP* 4.4 9.1 - - + +
479B GLU* 4.3 19.3 - - + +
482B ALA* 3.8 26.9 - - + -
489B ALA 3.0 11.6 + - - +
490B GLN* 3.6 25.4 - - - +
492B ILE* 1.3 77.8 - - - +
494B ASP* 1.3 63.1 + - - +
496B LEU* 3.2 14.6 + - + +
497B GLU* 3.0 37.3 + - - +
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Residues in contact with ASP 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B GLN* 3.1 42.5 + - - +
491B ASP* 3.1 15.8 + - - +
493B LEU* 1.3 76.9 - - - +
495B THR* 1.3 55.5 + - - +
497B GLU* 3.2 17.9 + - - +
498B ASP* 2.9 38.6 + - - +
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Residues in contact with THR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 6.0 0.3 - - - -
420B THR 3.4 21.0 + - - +
421B LYS 3.6 9.6 - - - +
422B PRO* 4.5 6.3 - - + -
423B LEU 5.4 0.2 - - - +
491B ASP* 2.9 15.7 + - - +
492B ILE* 3.6 8.7 - - - -
494B ASP* 1.3 72.4 - - - +
496B LEU* 1.3 66.1 + - - +
498B ASP* 3.1 10.5 + - + +
499B ASN* 2.8 45.4 + - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B PRO* 3.4 44.2 - - + +
420B THR* 3.9 8.5 - - + +
470B ILE* 3.9 15.7 - - + -
474B VAL* 3.8 16.8 - - + -
475B HIS* 3.7 39.0 - - + -
478B TRP* 4.0 17.0 - - + -
492B ILE 3.0 13.4 + - - +
493B LEU* 3.3 12.6 - - + +
495B THR* 1.3 77.2 - - - +
497B GLU* 1.3 56.7 + - - +
499B ASN* 3.2 2.9 + - - +
500B ARG* 2.9 27.0 + - - +
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Residues in contact with GLU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ILE* 6.1 0.2 - - - -
475B HIS* 3.1 37.0 + - + +
490B GLN* 5.5 0.7 + - - -
493B LEU* 3.0 26.7 + - - +
494B ASP* 3.2 21.1 + - - +
496B LEU* 1.3 72.2 - - - +
498B ASP* 1.3 66.7 + - - +
500B ARG* 3.4 9.7 + - - +
501B GLU* 3.3 27.0 + - - +
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Residues in contact with ASP 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ASP* 2.9 25.5 + - - +
495B THR* 3.1 10.6 + - + +
497B GLU* 1.3 74.4 - - - +
499B ASN* 1.3 70.9 + - - +
501B GLU* 3.0 10.5 + - - +
502B TRP* 3.0 20.9 + - - +
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Residues in contact with ASN 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B PRO 2.8 23.3 + - - +
421B LYS 2.9 23.6 + - - -
423B LEU* 3.5 27.2 + - + +
426B TYR* 3.7 24.6 - - + -
470B ILE* 4.7 1.8 - - + -
495B THR* 2.8 25.4 + - - +
496B LEU 3.6 4.3 - - - +
498B ASP* 1.3 78.3 - - - +
500B ARG* 1.3 62.8 + - - +
502B TRP* 3.3 7.7 + - - +
503B TYR* 3.1 27.4 + - - +
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Residues in contact with ARG 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL* 3.3 22.5 - - + +
470B ILE* 3.9 30.0 - - + +
471B ASP* 2.7 40.4 + - - +
475B HIS* 6.2 2.7 - - - -
496B LEU 2.9 13.9 + - - +
497B GLU* 3.6 13.2 - - - +
498B ASP 3.1 0.4 - - - -
499B ASN* 1.3 77.1 - - - +
501B GLU* 1.3 88.1 + - - +
503B TYR* 3.4 3.8 + - - +
504B GLN* 2.8 57.4 + - - +
486E HIS* 4.8 7.5 - - - -
487E PRO* 5.4 6.1 - - - +
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Residues in contact with GLU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B GLU 3.3 12.6 + - - +
498B ASP* 3.0 11.3 + - - +
500B ARG* 1.3 110.7 + - - +
502B TRP* 1.3 64.3 + - - +
504B GLN* 3.3 12.0 - - - +
505B SER* 2.9 29.4 + - - +
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Residues in contact with TRP 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 3.6 29.2 - - + +
427B ARG* 3.2 49.4 - - - -
498B ASP 3.0 12.2 + - - +
499B ASN* 3.6 11.7 - - - +
500B ARG 3.2 0.2 - - - -
501B GLU* 1.3 78.3 - - - +
503B TYR* 1.3 106.8 + + - +
505B SER* 3.2 6.9 + - - -
506B THR* 3.0 38.5 + - + -
427C ARG* 5.9 1.6 - - - -
502C TRP* 3.4 41.8 + + - +
505C SER* 4.1 19.3 - - - -
506C THR* 3.4 21.6 + - + -
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Residues in contact with TYR 503 (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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423B LEU* 4.6 0.9 - - + -
426B TYR* 3.5 47.6 - + - -
427B ARG* 3.7 19.3 + - + +
430B THR* 3.2 31.1 + - + +
431B ASP* 5.5 0.5 + - - -
462B VAL* 4.7 5.2 - - + -
463B GLU* 3.6 34.7 - - + +
466B GLN* 3.9 16.2 - - + -
467B VAL* 4.0 13.5 - - + -
470B ILE* 5.6 0.7 - - + -
499B ASN 3.1 14.0 + - - +
500B ARG* 3.9 4.5 - - - +
502B TRP* 1.3 109.2 - + - +
504B GLN* 1.3 62.9 + - - +
506B THR* 3.2 13.2 + - + -
507B ILE* 3.3 15.4 + - - +
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Residues in contact with GLN 504 (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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467B VAL* 3.8 10.2 - - + +
500B ARG* 2.8 52.5 + - - +
501B GLU* 3.3 18.4 + - - +
502B TRP 3.1 0.2 - - - -
503B TYR* 1.3 77.1 - - - +
505B SER* 1.3 64.7 + - - +
507B ILE* 3.0 53.5 + - - +
509B GLN* 4.9 2.4 + - - -
487E PRO* 6.3 0.8 - - - +
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Residues in contact with SER 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B GLU* 2.9 15.4 + - - +
502B TRP* 3.2 8.4 + - - -
504B GLN* 1.3 77.5 - - - +
506B THR* 1.3 60.7 + - - +
507B ILE 3.1 7.5 + - - +
509B GLN* 5.3 2.1 + - - +
423C LEU* 3.9 18.7 - - - +
502C TRP* 3.5 24.5 - - - +
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Residues in contact with THR 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B GLU* 3.5 26.0 - - + +
502B TRP* 3.0 34.7 + - + -
503B TYR* 3.2 11.2 + - + -
505B SER* 1.3 73.9 - - - +
507B ILE* 1.3 63.4 + - - +
508B PRO* 3.1 12.3 - - - +
423C LEU* 4.7 6.7 - - - -
427C ARG* 3.9 24.6 + - - +
502C TRP* 3.6 12.5 + - - -
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Residues in contact with ILE 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B GLU* 3.5 13.9 - - + -
464B LYS* 3.7 52.7 - - + +
467B VAL* 3.9 11.7 - - + -
503B TYR 3.3 9.6 + - - +
504B GLN* 3.0 37.6 + - - +
505B SER 3.8 5.0 - - - +
506B THR* 1.3 74.8 - - - +
508B PRO* 1.3 69.3 - - + +
509B GLN* 2.7 37.4 + - - +
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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