Contacts of the helix formed by residues 489 - 507 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C TRP* 5.0 2.9 - - + -
481C TRP* 4.1 12.1 - - + +
482C ALA* 3.7 32.3 - - + +
485C VAL* 3.8 13.3 - - + +
487C PRO* 3.0 1.6 - - - +
488C ASP* 1.3 77.4 - - - +
490C GLN* 1.3 62.7 + - - +
491C ASP 3.3 2.9 - - - -
492C ILE* 3.2 21.8 + - + +
493C LEU* 3.0 22.5 + - - +
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Residues in contact with GLN 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ALA* 5.1 2.6 - - - +
486C HIS* 4.8 9.5 + - - -
487C PRO* 2.9 31.5 + - + +
488C ASP 3.3 0.4 - - - -
489C ALA* 1.3 78.0 - - - +
491C ASP* 1.3 65.3 + - - +
493C LEU* 3.4 20.7 + - - +
494C ASP* 3.0 49.8 + - - +
497C GLU* 5.5 0.8 + - - -
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Residues in contact with ASP 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C ASP 4.8 3.5 + - - +
489C ALA 3.3 0.8 - - - -
490C GLN* 1.3 74.8 - - - +
492C ILE* 1.3 71.7 + - + +
494C ASP* 3.1 15.2 + - - +
495C THR* 2.9 28.0 + - - +
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Residues in contact with ILE 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TRP* 3.8 44.0 - - + +
271C VAL* 6.2 0.9 - - + -
272C LEU* 4.6 7.4 - - + -
420C THR* 3.4 33.3 - - + +
478C TRP* 3.8 29.8 - - + -
488C ASP 5.3 3.4 - - - +
489C ALA* 3.2 19.4 + - + +
491C ASP* 1.3 78.0 - - + +
493C LEU* 1.3 63.2 - - - +
495C THR* 3.2 8.3 + - - -
496C LEU* 2.9 22.1 + - - +
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Residues in contact with LEU 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C HIS* 3.6 33.4 - - + +
478C TRP* 4.4 8.0 - - + +
479C GLU* 4.3 20.0 - - + +
482C ALA* 3.8 27.6 - - + -
489C ALA 3.0 11.4 + - - +
490C GLN* 3.6 24.9 - - - +
492C ILE* 1.3 78.4 - - - +
494C ASP* 1.3 62.9 + - - +
496C LEU* 3.2 14.9 + - + +
497C GLU* 3.0 36.7 + - - +
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Residues in contact with ASP 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C GLN* 3.0 43.3 + - - +
491C ASP* 3.1 15.3 + - - +
493C LEU* 1.3 76.6 - - - +
495C THR* 1.3 61.9 + - - +
497C GLU* 3.1 18.5 + - - +
498C ASP* 2.9 32.0 + - - +
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Residues in contact with THR 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TRP* 6.0 0.5 - - - -
420C THR 3.4 21.5 + - - +
421C LYS 3.6 9.6 - - - +
422C PRO* 4.6 5.4 - - + -
491C ASP* 2.9 16.4 + - - +
492C ILE* 3.5 8.5 - - - -
494C ASP* 1.3 75.3 - - - +
496C LEU* 1.3 64.2 + - - +
498C ASP* 3.1 10.2 + - + +
499C ASN* 2.9 40.0 + - - +
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Residues in contact with LEU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C PRO* 3.4 43.3 + - + +
420C THR* 3.9 8.0 - - + +
470C ILE* 3.9 17.4 - - + +
474C VAL* 3.8 15.9 - - + -
475C HIS* 3.7 39.0 - - + -
478C TRP* 4.0 17.3 - - + -
492C ILE 2.9 13.0 + - - +
493C LEU* 3.3 12.1 - - + +
495C THR* 1.3 76.0 - - - +
497C GLU* 1.3 57.7 + - - +
499C ASN* 3.3 1.9 + - - +
500C ARG* 3.0 26.5 + - - +
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Residues in contact with GLU 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C ILE* 6.1 0.2 - - - -
475C HIS* 3.1 36.1 + - + +
490C GLN* 5.5 0.7 + - - -
493C LEU* 3.0 27.2 + - - +
494C ASP* 3.6 21.2 - - - +
496C LEU* 1.3 74.0 - - - +
498C ASP* 1.3 66.6 + - - +
500C ARG* 3.4 9.7 + - - +
501C GLU* 3.3 27.9 + - - +
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Residues in contact with ASP 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ASP* 2.9 24.8 + - - +
495C THR* 3.1 11.3 + - + +
497C GLU* 1.3 77.5 - - - +
499C ASN* 1.3 69.2 + - - +
501C GLU* 3.0 10.1 + - - +
502C TRP* 3.0 20.1 + - - +
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Residues in contact with ASN 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C PRO 2.8 23.8 + - - +
421C LYS 2.9 23.4 + - - -
423C LEU* 3.5 27.1 + - + +
426C TYR* 3.7 25.1 - - + -
470C ILE* 4.7 2.2 - - + -
495C THR* 2.9 25.7 + - - +
496C LEU 3.7 4.3 - - - +
498C ASP* 1.3 78.1 - - - +
500C ARG* 1.3 61.5 + - - +
502C TRP* 3.2 7.9 + - - +
503C TYR* 3.1 27.5 + - - +
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Residues in contact with ARG 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C VAL* 3.2 23.5 - - + +
470C ILE* 3.9 29.8 - - + +
471C ASP* 2.7 42.2 + - - +
475C HIS* 6.2 3.1 - - - -
496C LEU 3.0 13.3 + - - +
497C GLU* 3.6 13.0 - - - +
498C ASP 3.1 0.4 - - - -
499C ASN* 1.3 77.6 - - - +
501C GLU* 1.3 86.2 + - - +
503C TYR* 3.4 3.9 + - - +
504C GLN* 2.9 57.4 + - - +
486F HIS* 4.4 13.0 - - - -
487F PRO* 5.0 6.3 - - - +
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Residues in contact with GLU 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C GLU 3.3 12.6 + - - +
498C ASP* 3.0 10.4 + - - +
500C ARG* 1.3 108.8 + - - +
502C TRP* 1.3 62.8 + - - +
504C GLN* 3.3 11.5 - - - +
505C SER* 2.8 31.7 + - - +
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Residues in contact with TRP 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B TRP* 3.4 47.3 + + - +
505B SER* 3.5 27.1 - - - +
506B THR* 3.6 16.2 + - - -
423C LEU* 3.6 21.9 - - + +
427C ARG* 3.1 49.4 - - - -
498C ASP 3.0 12.2 + - - +
499C ASN* 3.2 12.1 + - - +
501C GLU* 1.3 76.3 - - - +
503C TYR* 1.3 108.8 + + - +
505C SER* 3.1 9.3 + - - -
506C THR* 3.0 38.3 + - + -
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Residues in contact with TYR 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C LEU* 4.6 1.1 - - + -
426C TYR* 3.5 47.1 - + - -
427C ARG* 3.6 19.7 + - + +
430C THR* 3.2 31.1 + - + +
431C ASP* 5.5 0.7 + - - -
462C VAL* 4.7 5.2 - - + -
463C GLU* 3.6 34.4 - - + +
466C GLN* 3.9 15.7 - - + -
467C VAL* 4.0 13.5 - - + +
470C ILE* 5.5 0.9 - - + -
499C ASN 3.1 13.1 + - - +
500C ARG* 3.9 4.7 - - - +
502C TRP* 1.3 107.0 - + - +
504C GLN* 1.3 63.5 + - - +
506C THR* 3.2 13.2 + - + -
507C ILE* 3.3 14.4 + - - +
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Residues in contact with GLN 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C VAL* 3.8 11.1 - - + +
500C ARG* 2.9 53.1 + - - +
501C GLU* 3.3 19.0 + - - +
503C TYR* 1.3 76.5 - - - +
505C SER* 1.3 63.3 + - - +
507C ILE* 3.0 53.5 + - - +
509C GLN* 5.0 2.6 + - - -
487F PRO* 5.7 4.8 - - - +
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Residues in contact with SER 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 4.7 9.4 - - - +
502B TRP* 4.1 18.4 - - - -
501C GLU* 2.8 15.4 + - - +
502C TRP* 3.4 9.6 - - - -
504C GLN* 1.3 78.6 - - - +
506C THR* 1.3 62.2 + - - +
507C ILE 3.1 7.3 + - - +
509C GLN* 5.3 2.1 + - - +
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Residues in contact with THR 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 5.1 4.9 - - + -
427B ARG* 4.7 17.3 - - - +
502B TRP* 3.4 19.1 + - + +
463C GLU* 3.5 25.8 - - + +
502C TRP* 3.0 33.0 + - + -
503C TYR* 3.2 10.9 + - + -
505C SER* 1.3 75.4 - - - +
507C ILE* 1.3 64.1 + - - +
508C PRO* 3.1 12.8 - - - +
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Residues in contact with ILE 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C GLU* 3.5 14.4 - - + -
464C LYS* 3.7 53.2 - - + +
467C VAL* 3.8 12.3 - - + -
503C TYR 3.3 10.0 + - - +
504C GLN* 3.0 37.2 + - - +
505C SER 3.1 5.9 - - - +
506C THR* 1.3 74.4 - - - +
508C PRO* 1.3 69.3 - - + +
509C GLN* 2.7 36.8 + - - +
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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
------------------------------------------------------------
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