Contacts of the helix formed by residues 491 - 506 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487F VAL* 5.7 0.2 - - + -
489F ALA* 3.2 11.0 + - + +
490F PRO* 1.3 75.1 - - - +
492F PRO* 1.3 67.9 - - - +
493F GLN* 3.0 35.4 - - - +
494F GLN* 3.1 30.7 + - - +
495F LEU* 2.9 24.0 + - - +
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Residues in contact with PRO 492 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490F PRO 4.3 2.2 - - - +
491F THR* 1.3 86.5 - - - +
493F GLN* 1.3 58.6 + - - +
495F LEU* 3.7 9.5 - - + +
496F GLN* 2.9 29.8 + - - +
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Residues in contact with GLN 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491F THR* 3.0 30.2 + - - +
492F PRO* 1.3 79.4 - - - +
494F GLN* 1.3 71.7 + - + +
496F GLN* 3.5 5.0 + - - +
497F ALA* 3.0 27.5 + - - +
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Residues in contact with GLN 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485F LEU* 3.9 31.7 - - + +
487F VAL* 3.4 24.6 - - - +
489F ALA 3.4 9.2 - - - +
490F PRO* 5.0 0.4 - - + -
491F THR* 3.1 42.1 + - - +
493F GLN* 1.3 83.3 - - + +
495F LEU* 1.3 62.7 + - - +
497F ALA* 3.8 6.4 - - - +
498F PHE* 3.2 22.5 + - - +
525F LEU* 4.4 3.9 - - - +
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Residues in contact with LEU 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490F PRO* 5.0 15.5 - - + +
491F THR 2.9 15.9 + - - +
492F PRO* 3.7 9.6 - - + +
493F GLN 3.2 0.2 - - - -
494F GLN* 1.3 76.3 - - - +
496F GLN* 1.3 65.6 + - - +
498F PHE* 3.1 17.6 + - + +
499F LYS* 3.0 55.5 + - + +
525F LEU* 4.4 16.6 - - + -
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Residues in contact with GLN 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D LYS* 4.7 15.2 + - - +
492F PRO 2.9 19.0 + - - +
493F GLN* 4.0 4.9 - - - +
495F LEU* 1.3 76.6 - - - +
497F ALA* 1.3 57.0 + - - +
499F LYS* 3.6 22.3 + - - +
500F ASN* 3.1 60.4 + - - +
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Residues in contact with ALA 497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493F GLN 3.0 18.8 + - - +
494F GLN* 3.8 8.5 - - - +
495F LEU 3.1 0.2 - - - -
496F GLN* 1.3 75.1 - - - +
498F PHE* 1.3 59.7 + - - +
500F ASN* 3.2 11.1 + - - +
501F GLU* 2.9 30.6 + - - +
596F GLY 5.5 5.5 - - - +
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Residues in contact with PHE 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485F LEU* 6.0 2.0 - - + -
494F GLN 3.2 11.6 + - - +
495F LEU* 3.1 17.7 + - + +
497F ALA* 1.3 76.2 - - - +
499F LYS* 1.3 74.5 + - + +
501F GLU* 3.1 6.8 + - - +
502F VAL* 2.9 37.9 + - + +
519F TYR* 3.7 28.5 - + + -
520F SER 3.7 16.6 - - - -
521F THR* 5.5 1.8 - - - -
525F LEU* 3.8 33.9 - - + -
526F ALA 3.6 27.6 - - - -
527F ILE* 4.0 18.2 - - + -
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Residues in contact with LYS 499 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495F LEU* 3.0 50.9 + - + +
496F GLN* 3.8 27.5 + - - +
498F PHE* 1.3 84.2 - - + +
500F ASN* 1.3 57.5 + - - +
502F VAL* 3.5 5.9 + - - +
503F GLY* 2.9 26.2 + - - -
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Residues in contact with ASN 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496F GLN* 3.1 49.6 + - - +
497F ALA* 3.4 11.4 - - - +
499F LYS* 1.3 76.9 - - - +
501F GLU* 1.3 62.3 + - - +
503F GLY* 3.2 2.8 + - - -
504F VAL* 3.1 27.3 + - - +
598F ALA 5.4 8.1 - - - +
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Residues in contact with GLU 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483F LYS* 2.7 37.5 + - - +
497F ALA 2.9 16.9 + - - +
498F PHE* 3.9 5.6 - - - +
500F ASN* 1.3 75.4 - - - +
502F VAL* 1.3 63.9 + - - +
504F VAL* 3.3 4.4 + - - +
505F LEU* 3.0 36.0 + - + +
527F ILE* 4.1 20.0 - - + +
595F PHE* 3.2 38.8 + - + +
596F GLY* 3.6 12.5 + - - +
598F ALA 5.9 1.1 - - - -
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Residues in contact with VAL 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498F PHE* 2.9 32.3 + - + +
499F LYS* 3.9 5.8 - - - +
501F GLU* 1.3 75.7 - - - +
503F GLY* 1.3 61.9 + - - +
505F LEU* 4.1 6.0 - - - +
506F ARG* 3.2 35.5 + - - +
516F PHE* 4.2 8.7 - - + -
519F TYR* 3.6 50.5 - - + -
527F ILE* 3.9 19.7 - - + -
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Residues in contact with GLY 503 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499F LYS 2.9 17.2 + - - -
500F ASN* 3.2 3.1 + - - -
501F GLU 3.1 0.6 - - - -
502F VAL* 1.3 81.1 - - - +
504F VAL* 1.3 59.1 + - - +
506F ARG* 3.7 16.1 - - - +
507F LYS* 3.6 22.6 + - - +
600F VAL* 5.8 1.8 - - - -
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Residues in contact with VAL 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500F ASN* 3.1 17.4 + - + +
501F GLU* 3.8 5.4 - - - +
502F VAL 3.3 0.2 - - - -
503F GLY* 1.3 76.0 - - - +
505F LEU* 1.3 67.6 + - - +
507F LYS* 3.1 21.0 + - - +
508F THR* 3.9 6.4 - - - +
572F ILE* 4.0 15.9 - - + +
595F PHE* 3.6 32.1 - - + -
598F ALA* 3.9 14.8 - - + +
599F THR* 4.1 13.5 - - - +
600F VAL* 4.0 35.0 - - + +
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Residues in contact with LEU 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501F GLU* 3.0 34.7 + - + +
502F VAL 4.1 1.8 - - - +
504F VAL* 1.3 71.3 - - - +
506F ARG* 1.3 51.8 + - - +
507F LYS 2.8 14.6 + - - -
508F THR* 2.7 36.1 + - - +
514F LEU* 5.1 8.1 - - + +
516F PHE* 3.6 29.8 - - + +
527F ILE* 3.5 32.5 - - + -
529F THR* 4.7 8.3 - - + -
595F PHE* 3.7 40.4 - - + -
509G ARG* 4.0 3.6 + - - -
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Residues in contact with ARG 506 (chain F).
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* 4.3 14.3 + - - +
450F TRP* 3.3 34.6 + - + +
502F VAL* 3.2 36.3 + - + +
503F GLY* 3.7 12.5 + - - +
504F VAL 3.3 0.2 - - - -
505F LEU* 1.3 75.7 - - - +
507F LYS* 1.3 58.5 + - + +
508F THR 3.3 0.2 - - - -
516F PHE* 3.8 20.8 - - + -
519F TYR* 5.2 6.6 + - - -
450G TRP* 3.4 11.1 - - - -
506G ARG* 5.1 10.6 + - - +
509G ARG* 2.9 22.5 + - - +
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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