Contacts of the helix formed by residues 505 - 517 (chain T) 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 LYS 505 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210A LYS 5.5 7.4 - - - +
503T TYR 4.2 1.4 + - - -
504T GLU* 1.3 70.5 - - - +
506T PHE* 1.3 60.1 + - - +
507T PHE 3.1 0.2 - - - -
508T GLY* 3.1 5.4 + - - +
509T LEU* 2.9 28.3 + - - +
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Residues in contact with PHE 506 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A LYS 5.7 2.7 - - - -
468T ASP* 5.6 2.9 - - - +
469T PHE* 4.0 27.6 - - + +
504T GLU* 3.2 8.5 - - + +
505T LYS* 1.3 79.0 - - - +
507T PHE* 1.3 56.3 + - - +
509T LEU* 3.8 6.6 - - - +
510T LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 507 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497T CYS* 3.7 35.7 - - + +
504T GLU* 3.3 18.5 + - + +
505T LYS 3.1 0.8 - - - -
506T PHE* 1.3 78.8 - - - +
508T GLY* 1.3 58.4 + - - +
510T LEU* 3.8 4.8 - - - +
511T ALA* 2.9 30.1 + - - +
550T MET* 5.4 7.6 - - + -
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Residues in contact with GLY 508 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504T GLU 3.9 2.8 + - - -
505T LYS* 3.1 10.3 + - - -
507T PHE* 1.3 79.3 - - - +
509T LEU* 1.3 56.1 + - - +
511T ALA* 3.5 5.3 + - - +
512T GLY* 2.9 23.9 + - - -
550T MET* 5.0 13.6 - - - +
553T HIS* 4.6 20.8 - - - +
554T LEU* 5.6 5.8 + - - +
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Residues in contact with LEU 509 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209A HIS 5.2 4.5 - - - +
1210A LYS* 4.8 20.0 - - + +
470T GLU* 5.1 18.1 - - + +
505T LYS 2.9 16.2 + - - +
506T PHE* 3.9 7.6 - - - +
507T PHE 3.3 0.2 - - - -
508T GLY* 1.3 74.8 - - - +
510T LEU* 1.3 59.6 + - - +
512T GLY* 3.2 1.4 + - - -
513T ARG* 2.9 32.9 + - - +
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Residues in contact with LEU 510 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469T PHE* 4.3 21.7 - - + +
470T GLU* 5.5 1.5 - - - +
473T ALA* 6.0 5.2 - - + +
506T PHE 2.9 19.8 + - - +
507T PHE* 3.9 6.1 - - - +
509T LEU* 1.3 76.5 - - - +
511T ALA* 1.3 49.8 + - - +
513T ARG* 5.1 1.8 - - - -
514T PHE* 2.6 42.2 + - + +
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Residues in contact with ALA 511 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507T PHE 2.9 18.8 + - - +
508T GLY* 3.9 6.5 - - - +
509T LEU 3.2 0.2 - - - -
510T LEU* 1.3 76.4 - - - +
512T GLY* 1.3 59.7 + - - +
514T PHE* 4.2 3.8 - - - -
515T CYS* 2.9 35.5 + - + +
550T MET* 6.3 1.8 - - + -
554T LEU* 5.7 8.7 - - + -
560T LEU* 5.2 0.3 - - - +
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Residues in contact with GLY 512 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508T GLY 2.9 17.6 + - - -
509T LEU* 3.2 2.4 + - - -
511T ALA* 1.3 77.9 - - - +
513T ARG* 1.3 49.7 + - - +
515T CYS* 4.6 1.0 - - - +
516T MET* 2.6 41.0 + - - +
554T LEU* 5.9 6.7 - - - +
560T LEU* 5.7 2.8 - - - +
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Residues in contact with ARG 513 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S SER* 4.7 20.6 - - - +
27S ARG* 4.0 11.1 - - + +
470T GLU* 5.9 7.2 - - + -
473T ALA* 5.3 5.6 - - + -
509T LEU 2.9 14.3 + - - +
510T LEU* 4.7 2.5 - - - +
512T GLY* 1.3 72.6 - - - +
514T PHE* 1.3 67.7 + - - +
516T MET* 3.2 5.0 + - - -
517T LEU* 2.9 24.8 + - - +
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Residues in contact with PHE 514 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473T ALA* 5.8 6.8 - - + +
510T LEU* 2.6 25.6 + - + +
511T ALA* 4.2 3.1 - - - +
513T ARG* 1.3 76.6 - - - +
515T CYS* 1.3 63.0 + - - +
517T LEU* 3.0 19.6 + - - +
521T TYR* 3.2 13.5 - - - +
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Residues in contact with CYS 515 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511T ALA* 2.9 25.4 + - + +
514T PHE* 1.3 73.6 - - - +
516T MET* 1.3 58.6 + - - +
517T LEU 3.2 0.4 - - - -
518T LYS 3.5 1.7 - - - +
521T TYR* 3.4 14.8 - - - +
522T MET* 2.8 30.1 + - - +
525T PHE* 3.7 20.2 - - + -
560T LEU* 3.7 24.0 - - + -
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Residues in contact with MET 516 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S ARG* 4.2 14.2 - - + +
30S ARG* 6.2 0.2 - - - +
512T GLY 2.6 24.6 + - - +
513T ARG* 3.4 7.0 - - - +
514T PHE 3.1 0.4 - - - -
515T CYS* 1.3 75.7 - - - +
517T LEU* 1.3 64.1 + - - +
518T LYS 4.6 0.7 - - - -
522T MET* 5.3 1.6 - - - -
559T SER* 5.4 12.1 - - - -
560T LEU* 5.0 3.1 - - + +
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Residues in contact with LEU 517 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S LEU 4.7 9.6 - - - +
27S ARG* 3.9 17.9 - - + +
30S ARG* 5.9 2.9 - - - +
513T ARG 2.9 10.6 + - - +
514T PHE* 3.0 17.2 + - - +
515T CYS 3.2 0.2 - - - -
516T MET* 1.3 81.1 - - - +
518T LYS* 1.3 63.6 + - + +
521T TYR* 4.8 0.7 - - + -
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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