Contacts of the helix formed by residues 491 - 502 (chain O) in PDB entry 5MQF
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 TYR 491 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490O ASN* 1.3 74.5 - - - +
492O ASP* 1.3 59.4 + - - +
493O ALA 3.3 0.2 - - - -
494O TRP* 3.4 10.7 + - + +
495O PHE* 2.9 28.4 + - - +
521O VAL* 5.1 6.1 - - + +
532O ARG* 5.3 14.8 - - + -
535O TYR* 5.3 11.7 - - + -
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Residues in contact with ASP 492 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610M ARG* 4.5 22.7 - - + -
490O ASN* 3.3 7.2 - - + +
491O TYR* 1.3 79.0 - - - +
493O ALA* 1.3 57.6 + - - +
495O PHE* 3.2 8.2 + - - +
496O ASP* 2.9 27.4 + - - +
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Residues in contact with ALA 493 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483O GLU 5.1 1.0 - - - +
486O ALA* 3.6 31.8 - - + +
488O PRO* 4.9 12.1 - - + -
489O HIS 5.1 2.2 - - - +
490O ASN* 3.7 11.0 + - - +
491O TYR 3.3 0.4 - - - -
492O ASP* 1.3 78.7 - - - +
494O TRP* 1.3 57.8 + - - +
496O ASP* 3.3 7.5 + - - +
497O TYR* 2.9 28.3 + - - +
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Residues in contact with TRP 494 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488O PRO* 6.3 1.5 - - + +
490O ASN 4.0 4.0 + - - +
491O TYR* 3.4 16.6 + - + +
492O ASP 3.3 0.4 - - - -
493O ALA* 1.3 78.3 - - - +
495O PHE* 1.3 57.8 + - - +
497O TYR* 3.4 7.6 + - - +
498O LEU* 2.9 27.9 + - - +
517O ALA* 3.8 29.2 - - + +
520O ASN* 6.2 1.6 - - + -
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Residues in contact with PHE 495 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610M ARG* 6.2 2.5 - - + -
491O TYR 2.9 17.0 + - - +
492O ASP* 3.2 8.7 + - - +
494O TRP* 1.3 75.4 - - - +
496O ASP* 1.3 59.0 + - - +
498O LEU* 3.4 7.4 + - - +
499O ARG* 2.9 27.7 + - - +
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Residues in contact with ASP 496 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483O GLU* 4.9 12.9 - - + +
492O ASP 2.9 12.5 + - - +
493O ALA* 3.3 11.0 + - - +
495O PHE* 1.3 74.4 - - - +
497O TYR* 1.3 58.9 + - - +
499O ARG* 3.2 7.3 + - - +
500O LEU* 2.9 30.5 + - - +
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Residues in contact with TYR 497 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483O GLU* 4.0 19.6 + - - +
484O VAL* 5.5 3.4 - - - +
493O ALA 2.9 16.5 + - - +
494O TRP* 3.7 9.0 - - - +
495O PHE 3.4 0.2 - - - -
496O ASP* 1.3 75.9 - - - +
498O LEU* 1.3 56.7 + - - +
500O LEU* 3.8 5.3 + - - +
501O VAL* 2.9 29.6 + - - +
513O VAL* 5.5 5.6 - - + +
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Residues in contact with LEU 498 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494O TRP 2.9 17.6 + - - +
495O PHE* 3.7 8.1 - - - +
496O ASP 3.2 0.2 - - - -
497O TYR* 1.3 74.8 - - - +
499O ARG* 1.3 58.8 - - - +
501O VAL* 3.1 8.6 + - - -
502O GLU* 2.9 27.0 + - - +
513O VAL* 5.9 3.8 - - + -
539O ASN* 6.0 6.3 - - + -
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Residues in contact with ARG 499 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574M GLU* 6.3 3.4 - - + -
495O PHE 2.9 17.8 + - - +
496O ASP* 3.2 8.5 + - - +
498O LEU* 1.3 75.5 - - - +
500O LEU* 1.3 60.7 + - - +
502O GLU* 3.2 21.4 + - - +
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Residues in contact with LEU 500 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475O LYS* 5.7 9.7 - - + +
479O GLN 6.4 0.2 - - - -
480O TYR* 5.8 5.6 - - + -
483O GLU* 4.6 16.8 - - + -
496O ASP 2.9 16.3 + - - +
497O TYR* 3.8 5.2 - - - +
499O ARG* 1.3 75.9 - - - +
501O VAL* 1.3 55.6 + - - +
502O GLU 3.3 1.6 + - - -
503O SER 4.1 12.2 + - - +
504O ASP* 4.5 4.0 - - - +
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Residues in contact with VAL 501 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497O TYR 2.9 21.1 + - - +
498O LEU* 3.1 10.9 + - - +
500O LEU* 1.3 75.3 - - - +
502O GLU* 1.3 67.4 + - - +
503O SER 3.4 2.7 - - - -
504O ASP* 4.1 17.4 + - + +
509O ALA* 5.7 3.4 - - + +
510O VAL* 5.4 10.3 - - - +
513O VAL* 4.8 15.9 - - + -
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Residues in contact with GLU 502 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498O LEU 2.9 9.6 + - - +
499O ARG* 3.2 18.4 + - - +
500O LEU 3.3 0.4 - - - -
501O VAL* 1.3 79.3 - - - +
503O SER* 1.3 60.1 + - - +
504O ASP 4.1 0.5 + - - -
505O ALA 5.8 0.2 - - - +
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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