Contacts of the helix formed by residues 507 - 518 (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 ALA 507 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506O GLU* 1.3 75.2 - - - +
508O GLU* 1.3 56.8 + - - +
509O ALA 3.4 0.2 - - - -
510O VAL* 3.8 10.6 - - - +
511O ARG* 2.9 31.4 + - - +
543O TYR* 4.5 16.1 - - - +
546O LEU* 5.6 4.0 - - + -
547O GLU* 4.9 15.9 - - + -
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Residues in contact with GLU 508 (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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506O GLU* 2.9 7.4 + - + +
507O ALA* 1.3 78.4 - - - +
509O ALA* 1.3 58.1 + - - +
511O ARG* 3.4 5.4 + - - +
512O GLU* 2.9 28.8 + - - +
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Residues in contact with ALA 509 (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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501O VAL* 5.7 3.5 - - + +
504O ASP* 5.2 6.7 - - + -
505O ALA* 4.1 22.6 - - + +
506O GLU 3.2 9.6 + - - +
508O GLU* 1.3 76.4 - - - +
510O VAL* 1.3 60.1 + - - +
512O GLU* 3.3 6.7 + - - +
513O VAL* 2.9 29.8 + - - +
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Residues in contact with VAL 510 (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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501O VAL* 5.4 10.8 - - - +
506O GLU 3.7 4.1 + - - +
507O ALA* 3.4 14.5 + - - +
508O GLU 3.3 0.8 - - - -
509O ALA* 1.3 79.7 - - - +
511O ARG* 1.3 56.8 + - - +
513O VAL* 3.4 5.3 + - - +
514O TYR* 2.9 29.5 + - - +
543O TYR* 3.7 26.9 - - + +
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Residues in contact with ARG 511 (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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507O ALA 2.9 18.5 + - - +
508O GLU* 3.9 5.2 - - - +
510O VAL* 1.3 76.9 - - - +
512O GLU* 1.3 56.9 + - - +
514O TYR* 4.0 5.3 - - - +
515O GLU* 2.9 32.2 + - - +
543O TYR* 4.3 5.8 - - + +
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Residues in contact with GLU 512 (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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508O GLU 2.9 18.9 + - - +
509O ALA* 3.7 7.9 - - - +
510O VAL 3.3 0.4 - - - -
511O ARG* 1.3 78.0 - - - +
513O VAL* 1.3 56.6 + - - +
515O GLU* 4.3 3.3 - - - +
516O ARG* 2.9 31.0 + - - +
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Residues in contact with VAL 513 (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* 5.5 5.6 - - + +
498O LEU* 5.9 4.3 - - + -
501O VAL* 4.8 16.2 - - + -
509O ALA 2.9 17.0 + - - +
510O VAL* 3.9 5.4 - - - +
512O GLU* 1.3 73.9 - - - +
514O TYR* 1.3 62.7 + - - +
516O ARG* 3.9 4.8 - - - +
517O ALA* 2.9 32.7 + - - +
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Residues in contact with TYR 514 (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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510O VAL 2.9 18.4 + - - +
511O ARG* 4.0 5.8 - - - +
513O VAL* 1.3 78.5 - - - +
515O GLU* 1.3 57.3 + - - +
517O ALA* 3.8 1.6 - - - -
518O ILE* 2.9 31.4 + - - +
536O LEU* 5.4 2.4 - - - +
539O ASN* 3.9 40.8 - - + +
540O TYR* 4.3 8.7 - - + +
543O TYR* 4.8 1.6 - - + -
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Residues in contact with GLU 515 (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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511O ARG 2.9 19.4 + - - +
512O GLU* 4.3 3.6 - - - +
514O TYR* 1.3 76.1 - - - +
516O ARG* 1.3 63.0 + - - +
518O ILE* 3.7 12.0 + - - +
519O ALA* 3.9 12.0 + - - +
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Residues in contact with ARG 516 (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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512O GLU 2.9 21.6 + - - +
513O VAL* 3.9 6.1 - - - +
514O TYR 3.3 0.4 - - - -
515O GLU* 1.3 78.7 - - - +
517O ALA* 1.3 57.1 + - - +
519O ALA* 4.2 0.9 + - - +
520O ASN* 3.2 22.5 + - - +
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Residues in contact with ALA 517 (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* 3.8 30.3 - - + +
513O VAL 2.9 17.8 + - - +
514O TYR* 3.8 2.5 - - - +
516O ARG* 1.3 75.2 - - - +
518O ILE* 1.3 64.3 + - - +
519O ALA 3.5 0.2 - - - -
520O ASN* 3.7 15.2 + - - +
521O VAL* 4.3 4.5 + - - +
536O LEU* 5.5 1.4 - - - +
539O ASN* 6.3 2.2 - - + -
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Residues in contact with ILE 518 (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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514O TYR 2.9 20.4 + - - +
515O GLU* 4.0 8.1 - - - +
516O ARG 3.4 0.8 - - - -
517O ALA* 1.3 80.4 - - - +
519O ALA* 1.3 59.8 + - + +
520O ASN 3.3 0.7 + - - -
521O VAL 4.4 2.1 + - - +
522O PRO* 4.0 13.5 - - - +
536O LEU* 4.1 27.7 - - + +
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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
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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