Contacts of the helix formed by residues 480 - 497 (chain D) in PDB entry 5MG3
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 THR 480 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465D ILE* 4.0 39.1 - - + +
468D MET* 5.2 8.0 - - - +
477D LEU* 3.2 28.1 + - + +
479D ALA* 1.3 78.6 - - - +
481D SER* 1.4 62.9 + - - +
482D ALA 3.4 3.1 + - - -
483D LEU* 3.5 20.8 + - + +
484D ILE* 3.7 24.7 + - + +
521D ASN* 4.9 2.5 - - - +
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Residues in contact with SER 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D TYR* 3.6 33.0 + - - -
10D TYR* 5.6 5.6 - - - -
13D LEU* 4.2 13.8 - - - +
477D LEU* 3.3 11.3 + - - -
478D ILE* 2.7 23.4 + - - +
479D ALA 3.5 0.4 - - - -
480D THR* 1.4 77.7 - - - +
482D ALA* 1.4 64.3 + - - +
484D ILE* 3.2 25.6 - - - +
485D ALA* 3.7 9.0 + - - +
596D GLY 4.2 3.8 + - - -
600D ILE* 5.7 0.2 - - - +
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Residues in contact with ALA 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D TYR* 4.6 3.4 - - - -
478D ILE 4.8 0.2 + - - -
479D ALA 5.4 0.6 + - - -
480D THR 3.5 0.6 - - - -
481D SER* 1.4 80.7 + - - +
483D LEU* 1.3 56.7 + - - +
485D ALA* 3.8 2.4 + - - -
486D ASN* 3.1 27.5 + - - +
521D ASN* 6.4 1.3 - - + -
592D THR* 3.4 17.3 - - + +
593D ALA* 4.9 2.2 - - + -
596D GLY* 3.7 21.3 - - - +
597D THR* 3.5 32.3 - - + -
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Residues in contact with LEU 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D LEU* 4.2 27.8 - - + +
464D SER 6.4 0.2 - - - -
465D ILE* 4.8 14.8 - - + -
480D THR* 3.7 16.2 - - + +
481D SER 3.4 0.2 - - - -
482D ALA* 1.3 75.7 - - - +
484D ILE* 1.3 60.3 + - + +
486D ASN* 3.1 7.3 + - - +
487D LEU* 3.0 36.8 + - + +
514D LEU* 4.9 3.4 - - + -
517D ALA* 3.7 39.3 - - + +
518D VAL* 4.1 22.2 - - + -
521D ASN* 5.2 14.6 - - + +
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Residues in contact with ILE 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.5 19.3 - - + -
17D ILE* 3.9 52.3 - - + +
461D LEU* 6.3 1.1 - - + -
465D ILE* 5.9 3.4 - - + -
477D LEU* 4.5 14.6 - - + -
480D THR* 3.7 21.5 - - + +
481D SER* 3.2 29.8 - - - +
483D LEU* 1.3 77.4 - - + +
485D ALA* 1.4 60.3 + - - +
487D LEU* 3.7 10.9 + - + +
488D ILE* 3.3 31.3 + - + +
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Residues in contact with ALA 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D TYR* 5.7 2.2 - - - +
13D LEU* 4.9 16.8 - - + +
481D SER 3.7 8.9 + - - +
482D ALA* 3.8 9.2 - - - +
483D LEU 3.4 0.4 - - - -
484D ILE* 1.4 81.2 - - - +
486D ASN* 1.4 61.1 + - - +
488D ILE* 3.6 7.6 + - - +
489D LEU* 3.1 30.2 + - + +
592D THR* 4.1 12.3 - - + -
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Residues in contact with ASN 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ALA 3.1 19.5 + - - +
483D LEU* 3.1 6.9 + - - +
485D ALA* 1.4 75.1 - - - +
487D LEU* 1.4 64.0 + - - +
489D LEU* 3.3 5.2 + - - +
490D ILE* 3.0 41.7 + - - +
513D THR 4.9 0.3 - - - +
517D ALA* 3.3 19.2 - - - +
588D THR* 3.9 4.8 - - - +
589D SER* 2.7 47.4 + - - +
592D THR* 3.9 15.2 - - + +
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Residues in contact with LEU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D LEU* 3.7 41.5 - - + -
483D LEU* 3.0 29.5 + - + +
484D ILE* 3.8 10.8 - - + +
486D ASN* 1.4 75.3 - - - +
488D ILE* 1.3 60.0 + - + +
490D ILE* 2.9 17.7 + - + +
491D VAL* 2.9 37.3 + - + +
510D ILE* 6.2 3.6 - - + -
513D THR* 6.5 1.1 - - + -
514D LEU* 5.2 14.6 - - + -
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Residues in contact with ILE 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 5.7 4.0 - - + -
16D VAL* 3.8 32.3 - - + +
17D ILE* 4.8 17.0 - - + -
20D GLY* 6.2 2.2 - - - -
484D ILE* 3.3 19.5 + - + +
485D ALA* 3.8 7.0 - - - +
486D ASN 3.3 0.2 - - - -
487D LEU* 1.3 81.7 - - + +
489D LEU* 1.3 75.1 + - + +
491D VAL* 3.5 5.3 + - - +
492D GLY* 2.9 22.2 + - - -
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Residues in contact with LEU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D ALA* 3.1 19.7 + - + +
486D ASN 3.9 0.2 - - - +
488D ILE* 1.3 89.0 - - + +
490D ILE* 1.4 52.4 + - - +
492D GLY* 4.8 1.1 - - - -
493D ILE* 2.8 45.1 + - + +
588D THR* 3.7 27.1 - - + +
592D THR* 4.1 13.7 - - + +
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Residues in contact with ILE 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D ASN* 3.0 35.9 + - - +
487D LEU* 2.9 20.4 + - + +
489D LEU* 1.4 74.3 - - - +
491D VAL* 1.3 63.2 - - + +
493D ILE* 3.6 4.0 + - - +
494D MET* 3.1 48.7 + - + +
510D ILE* 6.2 3.6 - - + -
513D THR* 3.8 25.4 - - + +
581D THR 5.5 1.3 - - - +
584D ILE* 4.5 7.3 - - + +
585D GLY* 3.4 33.2 - - - +
588D THR* 4.4 7.0 - - + +
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Residues in contact with VAL 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D LEU* 2.9 23.3 + - + +
488D ILE* 4.2 4.7 - - - +
490D ILE* 1.3 75.3 - - + +
492D GLY* 1.4 56.2 + - - +
494D MET* 3.5 9.8 + - + +
495D SER* 3.0 39.3 + - - +
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Residues in contact with GLY 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D ILE 2.9 16.1 + - - -
489D LEU* 3.6 4.5 - - - -
491D VAL* 1.4 72.1 - - - +
493D ILE* 1.4 64.1 + - - +
495D SER* 3.2 14.3 + - - -
496D LEU* 3.3 14.5 + - - +
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Residues in contact with ILE 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489D LEU* 2.8 27.2 + - + +
490D ILE* 4.2 2.9 - - - +
492D GLY* 1.4 69.3 - - - -
494D MET* 1.3 63.7 + - - +
496D LEU* 3.3 14.4 + - + +
497D LEU* 3.2 41.3 + - + +
584D ILE* 4.0 28.7 - - + +
588D THR* 3.4 28.5 - - + +
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Residues in contact with MET 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D ILE* 3.1 38.0 + - - +
491D VAL* 3.8 9.9 - - + +
492D GLY 3.2 0.4 - - - -
493D ILE* 1.3 78.7 - - - +
495D SER* 1.3 59.6 + - - +
497D LEU* 3.2 24.4 - - - +
498D PRO* 3.5 4.2 - - - +
502D LEU* 6.1 4.5 - - + -
510D ILE* 5.0 15.3 - - + -
581D THR* 4.4 26.5 - - + +
584D ILE* 3.4 21.8 - - + -
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Residues in contact with SER 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D VAL* 3.0 24.7 + - - +
492D GLY* 3.2 5.3 + - - -
494D MET* 1.3 73.9 - - - +
496D LEU* 1.3 58.1 + - - +
497D LEU 3.1 5.5 + - - -
498D PRO* 3.9 14.6 - - - +
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Residues in contact with LEU 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D GLY 3.3 14.4 + - - +
493D ILE* 3.3 13.7 + - + +
495D SER* 1.3 76.1 - - - +
497D LEU* 1.3 69.1 + - + +
498D PRO* 3.6 6.3 - - - +
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Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D ILE* 3.2 34.0 + - + +
494D MET* 3.2 12.1 - - - +
496D LEU* 1.3 91.9 - - + +
498D PRO* 1.3 57.8 - - - +
499D GLY 2.9 11.3 + - - -
500D ALA* 4.7 1.6 + - - +
584D ILE* 5.0 8.7 - - + -
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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