Contacts of the helix formed by residues 489 - 507 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478I TRP* 5.0 2.9 - - + -
481I TRP* 4.2 11.4 - - + +
482I ALA* 3.7 31.6 - - + -
485I VAL* 3.8 14.4 - - + +
487I PRO* 3.0 1.6 - - - +
488I ASP* 1.3 77.3 - - - +
490I GLN* 1.3 63.7 + - - +
491I ASP 3.3 2.7 - - - -
492I ILE* 3.2 21.5 + - + +
493I LEU* 3.0 23.0 + - - +
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Residues in contact with GLN 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482I ALA* 5.2 2.7 - - - +
486I HIS* 4.7 10.2 + - - -
487I PRO* 2.9 31.9 + - + +
488I ASP 3.3 0.6 - - - -
489I ALA* 1.3 78.1 - - - +
491I ASP* 1.3 65.0 + - - +
493I LEU* 3.4 20.4 + - - +
494I ASP* 3.1 42.9 + - - +
497I GLU* 5.5 0.6 + - - -
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Residues in contact with ASP 491 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488I ASP 4.8 4.1 + - - +
489I ALA 3.3 0.4 - - - -
490I GLN* 1.3 75.4 - - - +
492I ILE* 1.3 70.2 + - + +
494I ASP* 3.1 14.0 + - - +
495I THR* 2.9 28.6 + - - +
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Residues in contact with ILE 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I TRP* 3.8 44.0 - - + +
271I VAL* 6.2 0.9 - - + -
272I LEU* 4.5 7.2 - - + -
420I THR* 3.3 33.3 - - + +
478I TRP* 3.8 30.3 - - + -
488I ASP 5.4 2.7 - - - +
489I ALA* 3.2 19.2 + - + +
491I ASP* 1.3 78.3 - - + +
493I LEU* 1.3 63.8 + - - +
495I THR* 3.2 7.7 + - - -
496I LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 493 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475I HIS* 3.6 33.0 - - + +
478I TRP* 4.4 8.0 - - + +
479I GLU* 4.3 19.7 - - + +
482I ALA* 3.8 26.9 - - + -
489I ALA 3.0 11.4 + - - +
490I GLN* 3.6 24.7 - - - +
492I ILE* 1.3 77.2 - - - +
494I ASP* 1.3 62.0 + - - +
496I LEU* 3.2 15.2 + - + +
497I GLU* 3.0 38.1 + - - +
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Residues in contact with ASP 494 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490I GLN* 3.1 42.3 + - - +
491I ASP* 3.1 15.9 + - - +
493I LEU* 1.3 76.7 - - - +
495I THR* 1.3 57.9 + - - +
497I GLU* 3.2 18.8 + - - +
498I ASP* 2.9 39.1 + - - +
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Residues in contact with THR 495 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I TRP* 6.1 0.2 - - - -
420I THR 3.4 22.6 + - - +
421I LYS 3.7 9.2 - - - +
422I PRO* 4.5 6.3 - - + -
491I ASP* 2.9 17.0 + - - +
492I ILE* 3.5 8.3 - - - -
494I ASP* 1.3 75.3 - - - +
496I LEU* 1.3 58.4 + - - +
498I ASP* 3.2 10.7 + - + +
499I ASN* 2.8 50.9 + - - +
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Residues in contact with LEU 496 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I PRO* 3.5 43.7 - - + +
420I THR* 3.9 8.4 - - + +
470I ILE* 3.9 16.4 - - + -
474I VAL* 3.8 17.7 - - + -
475I HIS* 3.7 38.6 - - + -
478I TRP* 4.0 16.6 - - + -
492I ILE 2.9 13.0 + - - +
493I LEU* 3.3 13.2 - - + +
495I THR* 1.3 76.7 - - - +
497I GLU* 1.3 58.2 + - - +
499I ASN* 3.2 4.0 + - - +
500I ARG* 2.9 27.0 + - - +
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Residues in contact with GLU 497 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470I ILE* 6.1 0.2 - - - -
475I HIS* 3.1 35.6 + - + +
490I GLN* 5.5 0.5 + - - -
493I LEU* 3.0 27.1 + - - +
494I ASP* 3.6 21.6 - - - +
496I LEU* 1.3 72.1 - - - +
498I ASP* 1.3 65.7 + - - +
500I ARG* 3.4 9.5 + - - +
501I GLU* 3.3 27.9 + - - +
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Residues in contact with ASP 498 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494I ASP* 2.9 25.2 + - - +
495I THR* 3.2 11.5 + - + +
497I GLU* 1.3 76.2 - - - +
499I ASN* 1.3 66.1 + - - +
501I GLU* 3.1 10.7 + - - +
502I TRP* 3.0 20.7 + - - +
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Residues in contact with ASN 499 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I PRO 2.8 24.1 + - - +
421I LYS 2.9 23.2 + - - -
423I LEU* 3.5 27.2 + - + +
426I TYR* 3.7 24.9 - - + -
470I ILE* 4.7 1.6 - - + -
495I THR* 2.8 25.7 + - - +
496I LEU 3.6 4.3 - - - +
498I ASP* 1.3 78.5 - - - +
500I ARG* 1.3 62.2 + - - +
502I TRP* 3.3 7.9 + - - +
503I TYR* 3.1 26.9 + - - +
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Residues in contact with ARG 500 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486H HIS* 5.2 4.9 - - - -
487H PRO* 6.0 2.4 - - - +
467I VAL* 3.3 22.8 - - + +
470I ILE* 3.9 29.6 - - + +
471I ASP* 2.7 41.8 + - - +
475I HIS* 6.2 2.9 - - - -
496I LEU 2.9 13.7 + - - +
497I GLU* 3.5 13.7 - - - +
498I ASP 3.1 0.2 - - - -
499I ASN* 1.3 79.9 - - - +
501I GLU* 1.3 86.3 + - - +
503I TYR* 3.3 3.8 + - - +
504I GLN* 2.8 60.6 + - - +
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Residues in contact with GLU 501 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497I GLU 3.3 11.6 + - - +
498I ASP* 3.1 11.5 + - - +
500I ARG* 1.3 108.6 + - - +
502I TRP* 1.3 65.7 + - - +
504I GLN* 3.3 11.9 + - - +
505I SER* 2.9 30.3 + - - +
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Residues in contact with TRP 502 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I LEU* 3.6 30.5 - - + +
427I ARG* 3.2 48.0 - - - -
498I ASP 3.0 12.6 + - - +
499I ASN* 3.6 12.1 - - - +
500I ARG 3.2 0.2 - - - -
501I GLU* 1.3 79.8 - - - +
503I TYR* 1.3 105.5 + + - +
505I SER* 3.2 7.0 + - - -
506I THR* 2.9 44.8 + - + -
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Residues in contact with TYR 503 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I LEU* 4.6 0.9 - - + -
426I TYR* 3.5 46.9 - + - -
427I ARG* 3.6 19.3 + - + +
430I THR* 3.2 30.1 + - + +
431I ASP* 5.5 0.9 + - - -
462I VAL* 4.7 5.8 - - + -
463I GLU* 3.5 37.4 - - + +
466I GLN* 3.9 16.6 - - + -
467I VAL* 4.0 13.7 - - + -
470I ILE* 5.5 0.7 - - + -
499I ASN 3.1 14.5 + - - +
500I ARG* 3.8 4.0 - - - +
502I TRP* 1.3 107.4 - + - +
504I GLN* 1.3 62.7 + - - +
506I THR* 3.3 9.5 + - + -
507I ILE* 3.3 16.3 + - - +
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Residues in contact with GLN 504 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467I VAL* 3.8 11.4 - - + +
500I ARG* 2.8 52.9 + - - +
501I GLU* 3.3 18.2 - - - +
502I TRP 3.2 0.2 - - - -
503I TYR* 1.3 77.2 - - - +
505I SER* 1.3 64.3 + - - +
507I ILE* 3.0 54.0 + - - +
509I GLN* 4.9 2.8 + - - -
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Residues in contact with SER 505 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501I GLU* 2.9 15.6 + - - +
502I TRP* 3.2 10.5 + - - -
504I GLN* 1.3 78.5 - - - +
506I THR* 1.3 62.0 - - - +
507I ILE 3.1 7.6 + - - +
509I GLN* 5.2 2.3 + - - +
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Residues in contact with THR 506 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463I GLU* 3.4 30.6 - - + +
502I TRP* 2.9 44.0 + - + -
503I TYR* 3.5 6.3 - - + -
504I GLN 3.2 0.6 - - - -
505I SER* 1.3 74.3 - - - +
507I ILE* 1.3 64.6 + - - +
508I PRO* 3.1 13.2 - - - +
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Residues in contact with ILE 507 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463I GLU* 3.5 14.4 - - + -
464I LYS* 3.7 46.2 - - + +
467I VAL* 3.8 18.4 - - + -
503I TYR 3.3 9.8 + - - +
504I GLN* 3.0 37.1 + - - +
505I SER 3.7 6.1 - - - +
506I THR* 1.3 75.3 - - - +
508I PRO* 1.3 68.7 - - + +
509I GLN* 2.7 35.4 + - - +
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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