Contacts of the helix formed by residues 491 - 507 (chain G) in PDB entry 4MNE
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 491 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489G ALA 4.4 6.3 - - - +
490G PRO* 1.3 73.2 - - - +
492G PRO* 1.3 63.9 - - + +
493G GLN* 2.7 12.9 + - - +
494G GLN* 2.6 66.1 + - - +
495G LEU* 3.2 5.4 + - - -
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Residues in contact with PRO 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490G PRO 4.3 2.9 - - - +
491G THR* 1.3 86.1 - - - -
493G GLN* 1.3 57.7 + - - +
495G LEU* 4.1 14.7 - - + +
496G GLN* 3.8 15.2 + - - +
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Residues in contact with GLN 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491G THR* 2.7 17.7 + - - +
492G PRO* 1.3 74.0 - - - +
494G GLN* 1.3 65.2 + - + +
495G LEU 3.2 1.1 - - - -
496G GLN* 3.4 9.5 + - + +
497G ALA* 3.1 24.4 + - - +
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Residues in contact with GLN 494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485G LEU* 4.3 19.8 - - + +
487G VAL* 4.2 19.9 - - - +
489G ALA 4.3 0.7 - - - +
490G PRO* 3.1 18.0 - - + +
491G THR* 2.6 50.7 + - - +
493G GLN* 1.3 77.4 - - + +
495G LEU* 1.3 61.2 + - - +
497G ALA* 3.5 8.8 + - - +
498G PHE* 3.2 21.0 + - - +
525G LEU* 4.9 0.6 - - - +
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Residues in contact with LEU 495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D LEU* 4.4 22.4 - - + -
490G PRO* 3.5 46.2 - - + +
491G THR 3.2 8.2 + - - +
492G PRO* 4.2 12.1 - - + +
493G GLN 3.2 0.2 - - - -
494G GLN* 1.3 74.2 - - - +
496G GLN* 1.3 65.4 + - - +
497G ALA 3.0 1.8 - - - -
498G PHE* 3.0 8.8 + - + +
499G LYS* 2.9 45.1 + - - +
525G LEU* 4.1 11.4 - - + -
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Residues in contact with GLN 496 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492G PRO 3.8 11.5 + - - +
493G GLN* 3.4 14.0 + - + +
495G LEU* 1.3 79.5 - - - +
497G ALA* 1.3 60.6 + - - +
499G LYS* 4.6 18.5 + - - +
500G ASN* 2.7 64.0 + - - +
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Residues in contact with ALA 497 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485G LEU* 6.1 1.6 - - + -
493G GLN 3.1 13.7 + - - +
494G GLN* 3.5 13.0 - - - +
495G LEU 3.0 0.6 - - - -
496G GLN* 1.3 77.8 - - - +
498G PHE* 1.3 57.7 + - - +
500G ASN* 3.2 8.5 + - - +
501G GLU* 2.9 33.6 + - - +
596G GLY 5.9 2.7 - - - +
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Residues in contact with PHE 498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483G LYS 5.5 0.4 - - - -
485G LEU* 5.2 8.5 - - + +
494G GLN 3.2 10.4 + - - +
495G LEU* 3.0 13.6 + - + +
497G ALA* 1.3 79.5 - - - +
499G LYS* 1.3 68.3 + - + +
501G GLU* 3.5 5.2 + - - +
502G VAL* 3.1 32.9 + - + +
519G TYR* 3.7 31.6 - + + -
520G SER 3.5 12.1 - - - -
521G THR* 5.5 0.7 - - - -
525G LEU* 3.8 36.6 - - + -
526G ALA* 3.3 38.4 - - - -
527G ILE* 3.7 19.5 - - + -
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Residues in contact with LYS 499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D GLY* 6.4 0.2 - - - -
332D LEU* 6.6 0.2 - - - -
495G LEU* 2.9 34.8 + - - +
496G GLN* 4.2 22.7 + - - +
498G PHE* 1.3 80.7 - - + +
500G ASN* 1.3 55.9 + - - +
502G VAL* 3.8 4.3 - - - +
503G GLY* 2.7 35.5 + - - -
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Residues in contact with ASN 500 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496G GLN* 2.7 52.9 + - - +
497G ALA* 3.2 6.0 + - - +
499G LYS* 1.3 75.5 - - - +
501G GLU* 1.3 59.1 + - - +
503G GLY* 3.3 2.0 + - - -
504G VAL* 2.9 35.8 + - + +
598G ALA 5.1 9.2 - - - +
599G THR* 6.3 0.9 - - - -
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Residues in contact with GLU 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483G LYS* 2.6 34.3 + - - +
497G ALA* 2.9 17.8 + - - +
498G PHE* 3.9 5.3 - - - +
500G ASN* 1.3 75.2 - - - +
502G VAL* 1.3 53.3 + - - +
504G VAL* 2.9 7.2 + - - +
505G LEU* 2.8 43.6 + - + +
527G ILE* 3.6 22.9 - - + +
595G PHE* 3.3 25.0 + - + +
596G GLY* 3.5 25.6 + - - +
598G ALA 5.7 0.7 - - - -
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Residues in contact with VAL 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450G TRP* 6.1 0.2 - - + -
498G PHE* 3.1 24.5 + - + +
499G LYS* 3.8 4.7 - - - +
501G GLU* 1.3 78.0 - - - +
503G GLY* 1.3 57.8 + - - +
505G LEU* 3.3 8.7 + - - +
506G ARG* 2.8 39.7 + - + +
516G PHE* 4.2 12.7 - - + -
519G TYR* 3.9 48.0 - - + -
527G ILE* 4.0 17.3 - - + -
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Residues in contact with GLY 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499G LYS 2.7 22.4 + - - -
500G ASN* 3.6 2.2 - - - -
502G VAL* 1.3 75.2 - - - +
504G VAL* 1.3 62.4 + - - +
506G ARG* 3.6 11.7 - - - +
507G LYS* 3.2 26.8 + - - +
600G VAL* 6.2 0.2 - - - -
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Residues in contact with VAL 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500G ASN* 2.9 19.8 + - + +
501G GLU* 3.5 7.9 - - - +
503G GLY* 1.3 74.4 - - - +
505G LEU* 1.3 60.9 + - - +
507G LYS* 2.8 34.5 + - - +
508G THR* 3.7 5.1 - - + +
572G ILE* 3.7 33.0 - - + -
595G PHE* 3.7 23.3 - - + -
598G ALA* 4.0 26.9 - - + +
599G THR* 4.2 13.2 - - - -
600G VAL* 4.6 9.4 - - + -
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Residues in contact with LEU 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F ARG* 3.8 2.3 + - - -
501G GLU* 2.8 35.6 + - + +
502G VAL* 3.8 3.6 - - - +
504G VAL* 1.3 73.5 - - - +
506G ARG* 1.3 60.9 + - - +
508G THR* 2.7 31.7 + - - +
513G ILE* 5.2 0.2 - - + -
514G LEU* 4.5 12.8 - - + +
516G PHE* 3.8 34.9 - - + +
527G ILE* 3.6 32.1 - - + -
529G THR* 4.8 7.0 - - + -
595G PHE* 3.8 38.4 - - + -
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Residues in contact with ARG 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F TRP* 3.3 21.9 - - - +
506F ARG* 5.1 10.9 + - - +
509F ARG* 2.9 23.6 + - - +
449G ASP* 3.8 15.9 + - - -
450G TRP* 3.3 43.1 - - + +
502G VAL* 2.8 32.8 + - + +
503G GLY* 3.6 10.3 - - - +
505G LEU* 1.3 72.4 - - - +
507G LYS* 1.3 58.8 + - + +
508G THR 3.2 0.2 - - - -
516G PHE* 4.2 13.8 - - + -
519G TYR* 6.6 0.4 - - - -
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Residues in contact with LYS 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449F ASP 5.2 12.3 - - - +
450F TRP* 3.4 18.6 - - - -
503G GLY 3.2 21.3 + - - +
504G VAL* 2.8 10.2 + - - +
506G ARG* 1.3 76.2 - - + +
508G THR* 1.3 60.4 + - - +
570G LYS* 3.5 32.4 + - + +
572G ILE* 4.3 15.7 - - + -
600G VAL* 4.2 27.1 - - + -
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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
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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