Contacts of the helix formed by residues 510 - 527 (chain C) 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 PRO 510 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C LEU 5.8 0.9 - - - +
441C MET* 5.7 3.8 - - - +
446C LEU* 4.5 9.4 - - + -
458C LEU 3.3 15.9 - - - +
459C SER* 3.6 24.0 - - - +
460C ALA 3.5 8.7 - - - +
461C GLN* 4.0 13.9 - - + +
509C PHE* 1.4 99.2 - - + +
511C SER* 1.3 66.8 + - - +
512C GLY 4.2 1.8 - - - +
513C LEU* 3.1 29.5 + - + +
514C VAL* 3.4 11.4 + - - +
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Residues in contact with SER 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ILE* 4.9 2.2 - - - +
457C ASP 4.0 15.5 + - - -
458C LEU* 3.4 14.1 + - - -
460C ALA* 2.9 23.5 + - - +
465C TYR* 3.9 24.4 - - - -
467C LEU* 3.9 18.0 - - - +
468C PRO* 5.9 1.0 - - - +
510C PRO* 1.3 71.7 - - - +
512C GLY* 1.3 51.1 + - - +
514C VAL* 3.3 10.4 + - - +
515C LEU* 2.7 37.4 + - - +
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Residues in contact with GLY 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ILE* 5.7 0.7 - - - +
440C LEU* 3.9 14.2 - - - +
446C LEU* 4.0 13.7 - - - -
458C LEU* 3.0 28.4 + - - +
511C SER* 1.3 73.6 - - - +
513C LEU* 1.4 60.9 + - - +
515C LEU* 4.1 8.1 - - - +
516C TYR* 3.3 23.0 + - - +
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Residues in contact with LEU 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C TYR* 3.9 10.1 - - + +
440C LEU* 3.6 31.6 - - + +
441C MET* 3.6 52.5 - - + +
446C LEU* 4.5 1.8 - - - +
509C PHE* 3.9 4.7 - - + -
510C PRO* 3.1 40.1 + - + +
512C GLY* 1.4 70.0 - - - +
514C VAL* 1.3 65.3 + - + +
516C TYR* 3.4 14.3 + - + +
517C TYR* 3.1 41.0 + - + +
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Residues in contact with VAL 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C LEU* 3.6 37.2 - - + +
468C PRO* 4.1 14.1 - - + -
471C MET* 3.7 19.2 - - + +
506C PHE* 3.5 25.8 - - + +
509C PHE 4.5 2.9 - - - +
510C PRO 3.6 15.7 - - - +
511C SER* 3.3 10.9 + - - +
513C LEU* 1.3 75.4 - - + +
515C LEU* 1.4 56.0 + - - +
517C TYR* 3.0 30.4 + - + +
518C ILE* 3.3 13.7 + - + +
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Residues in contact with LEU 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ILE* 4.8 12.1 - - + -
453C LEU* 4.8 9.4 - - + -
454C TRP* 5.3 10.1 - - + +
455C ILE* 3.8 18.8 - - + -
458C LEU* 3.8 32.1 - - + -
467C LEU* 4.5 20.4 - - + +
511C SER 2.7 19.8 + - - +
512C GLY* 4.1 6.1 - - - +
513C LEU 3.5 0.2 - - - -
514C VAL* 1.4 67.1 - - - +
516C TYR* 1.3 65.8 - - - +
518C ILE* 3.0 24.7 + - + +
519C VAL* 3.1 27.5 + - + +
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Residues in contact with TYR 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ILE* 4.8 2.2 - - + -
359C ILE* 4.3 16.7 - - + +
362C THR* 3.6 33.3 - - + +
433C PHE* 3.2 42.7 + + - +
436C LEU* 3.6 21.3 - - + -
437C TYR* 4.3 11.9 - - + -
440C LEU* 3.3 35.9 - - + -
512C GLY 3.3 6.9 + - - +
513C LEU* 3.4 16.6 + - + +
515C LEU* 1.3 79.0 - - - +
517C TYR* 1.4 90.0 + + - +
519C VAL* 3.4 1.0 + - - +
520C SER* 3.0 28.7 + - - -
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Residues in contact with TYR 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C TYR* 3.8 21.0 - + + -
441C MET* 5.6 0.2 - - - +
471C MET* 4.2 11.2 - - + -
475C MET* 3.8 21.8 - - + -
506C PHE* 3.5 58.2 - + + -
513C LEU* 3.1 40.7 + - + +
514C VAL* 3.0 19.3 + - + +
516C TYR* 1.4 103.2 - + - +
518C ILE* 1.4 58.6 + - - +
520C SER* 3.6 6.5 - - - -
521C ASN* 2.8 37.9 + - - +
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Residues in contact with ILE 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C LEU* 3.7 31.0 - - + +
470C LEU* 4.2 22.0 - - + -
471C MET* 4.4 22.7 - - + +
474C THR* 4.1 21.8 - - + +
514C VAL 3.5 15.3 - - - +
515C LEU* 3.0 14.4 + - + +
517C TYR* 1.4 78.4 - - - +
519C VAL* 1.4 61.3 + - + +
521C ASN* 3.2 4.2 + - - +
522C LEU* 3.0 29.6 + - + +
525C ILE* 5.0 2.3 - - + +
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Residues in contact with VAL 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ILE* 3.4 56.1 - - + +
360C ILE* 6.3 0.7 - - + -
362C THR* 4.7 3.2 - - + +
363C PHE* 4.4 17.6 - - + +
515C LEU* 3.1 25.5 + - + +
516C TYR 4.3 1.8 - - - +
518C ILE* 1.4 75.8 - - + +
520C SER* 1.3 65.7 + - - +
522C LEU* 3.2 35.7 + - + +
523C VAL* 4.0 5.0 + - - +
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Residues in contact with SER 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C THR* 3.7 23.1 - - - +
366C ARG* 3.0 55.0 + - - +
433C PHE* 4.2 5.5 - - - -
516C TYR* 3.0 24.3 + - - -
517C TYR* 3.6 11.2 - - - -
519C VAL* 1.3 78.7 - - - +
521C ASN* 1.4 62.8 + - - +
522C LEU 3.3 0.2 - - - -
523C VAL* 4.3 1.6 + - - +
524C THR* 5.1 1.7 + - - -
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Residues in contact with ASN 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ARG* 4.9 4.3 + - - -
471C MET* 5.7 0.6 - - - +
474C THR* 3.6 30.9 - - + +
475C MET* 3.4 31.2 - - - +
478C ILE* 3.5 28.0 - - + +
517C TYR* 2.8 25.6 + - - +
518C ILE 3.7 1.1 - - - +
519C VAL 3.2 0.4 - - - -
520C SER* 1.4 83.6 + - - +
522C LEU* 1.3 57.2 + - - +
523C VAL 3.3 1.8 - - - -
524C THR* 3.2 11.4 + - - +
525C ILE* 3.1 29.0 + - - +
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Residues in contact with LEU 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 4.3 15.9 - - + -
518C ILE* 3.0 15.6 + - + +
519C VAL* 3.2 35.6 + - + +
521C ASN* 1.3 72.3 - - - +
523C VAL* 1.4 64.4 + - - +
525C ILE* 3.9 24.0 - - + -
526C ILE* 3.1 29.4 + - + +
531C ILE* 4.5 20.4 - - + -
532C TYR 6.4 0.9 - - - -
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Residues in contact with VAL 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 3.7 40.8 - - + +
366C ARG* 3.6 47.8 - - + +
367C GLY* 4.8 5.4 - - - +
370C TYR* 5.8 5.4 - - + -
519C VAL 4.0 3.1 + - - +
520C SER 4.6 0.4 - - - +
521C ASN 3.3 0.2 - - - -
522C LEU* 1.4 78.3 - - - +
524C THR* 1.4 61.7 + - - +
525C ILE 3.5 0.2 + - - -
526C ILE 3.6 1.0 + - - -
527C GLN* 3.0 33.6 + - - +
33F LEU* 3.7 21.3 - - + +
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Residues in contact with THR 524 (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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366C ARG* 5.6 1.0 - - - -
373C THR* 4.1 20.6 - - - +
374C LYS* 5.7 8.1 - - + +
478C ILE* 4.1 24.0 - - + +
520C SER 5.1 1.8 + - - -
521C ASN* 3.2 13.1 + - - -
523C VAL* 1.4 75.7 - - - +
525C ILE* 1.3 56.6 + - - +
527C GLN* 3.0 39.2 + - + +
528C GLN* 3.3 23.9 + - + +
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Residues in contact with ILE 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C THR* 3.8 30.3 - - + +
477C PHE* 3.8 23.6 - - + -
478C ILE* 3.8 14.6 - - + -
518C ILE* 5.0 3.1 - - + +
521C ASN 3.1 18.9 + - - +
522C LEU* 3.9 18.6 - - + +
523C VAL 3.4 0.2 - - - -
524C THR* 1.3 71.9 - - - +
526C ILE* 1.3 57.9 + - - +
527C GLN 3.1 1.3 - - - -
528C GLN* 2.7 25.9 + - + -
529C GLN* 3.0 41.8 + - - +
531C ILE* 4.2 11.9 - - + -
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Residues in contact with ILE 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 3.6 31.2 - - + -
522C LEU* 3.1 24.3 + - + +
524C THR 3.5 0.4 - - - -
525C ILE* 1.3 73.8 - - - +
527C GLN* 1.4 55.2 + - - +
528C GLN 3.4 2.3 + - - -
529C GLN 4.0 7.4 + - - -
531C ILE* 4.0 19.1 - - + +
29F ILE* 4.1 1.0 - - - +
32F LEU* 3.4 38.5 - - + +
33F LEU* 3.6 42.6 - - + +
36F ALA* 4.3 14.1 - - + -
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Residues in contact with GLN 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C TYR* 3.4 10.6 - - - -
374C LYS* 2.7 41.7 + - + +
523C VAL* 3.0 31.7 + - - +
524C THR* 3.0 18.7 + - + +
526C ILE* 1.4 74.5 - - - +
528C GLN* 1.3 60.7 + - - +
29F ILE* 3.1 36.0 - - + +
30F SER* 4.0 15.4 + - - +
33F LEU* 3.9 33.9 - - + +
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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