Contacts of the helix formed by residues 509 - 523 (chain F) in PDB entry 3HX0
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 SER 509 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420F ARG* 3.6 29.9 - - - +
508F GLY* 1.3 78.2 + - - -
510F ALA* 1.3 65.8 + - - +
511F ALA* 3.7 3.0 + - - +
512F PHE* 3.2 10.1 + - - +
513F ASN* 3.0 19.1 + - - -
573F ARG 2.7 21.4 + - - -
574F ASP 2.8 27.6 + - - -
702F D3T 4.5 1.8 - - - -
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Residues in contact with ALA 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F SER* 1.3 73.7 - - - +
511F ALA* 1.3 65.3 + - - +
513F ASN* 3.0 5.4 + - - +
514F ALA* 3.0 24.7 + - - +
702F D3T 3.6 54.9 + - + +
6G A 4.7 3.8 - - - +
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Residues in contact with ALA 511 (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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509F SER* 3.3 7.7 + - - +
510F ALA* 1.3 78.2 - - - +
512F PHE* 1.3 61.4 + - - +
514F ALA* 3.5 4.5 + - - +
515F SER* 2.7 36.3 + - - +
574F ASP 4.3 9.0 - - - +
575F TRP* 4.6 11.0 - - + +
5G A 5.1 16.2 - - + +
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Residues in contact with PHE 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504F LEU* 4.1 15.5 - - + -
508F GLY 3.7 10.5 - - - -
509F SER* 3.2 11.1 + - - +
511F ALA* 1.3 79.3 - - - +
513F ASN* 1.3 66.3 + - - +
515F SER* 3.7 3.9 - - - -
516F MET* 2.8 71.9 + - + +
560F PHE* 3.8 14.6 - + - -
568F ARG* 4.0 24.0 - - - -
573F ARG* 3.4 53.8 - - + +
575F TRP* 4.1 18.3 - - - +
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Residues in contact with ASN 513 (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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504F LEU* 3.6 19.9 - - - +
505F TYR* 3.0 31.7 + - - +
508F GLY* 3.5 1.6 - - - -
509F SER 3.0 20.3 + - - -
510F ALA 3.5 4.9 - - - +
512F PHE* 1.3 83.3 - - - +
514F ALA* 1.3 57.7 + - - +
515F SER 2.8 4.7 + - - -
516F MET* 2.9 4.6 + - - +
517F ARG* 2.6 49.6 + - + +
527F LEU* 6.4 0.2 - - - -
702F D3T 3.2 27.0 + - - +
6G A 4.3 6.3 - - + -
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Residues in contact with ALA 514 (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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510F ALA 3.0 13.1 + - - +
511F ALA* 4.0 2.7 - - - +
513F ASN* 1.3 78.4 - - - +
515F SER* 1.3 58.4 + - - +
518F ALA* 3.3 7.4 + - - +
5G A 3.7 27.3 - - - +
6G A 3.1 67.8 + - + +
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Residues in contact with SER 515 (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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511F ALA* 2.7 26.4 + - - +
512F PHE* 3.7 4.7 - - - -
513F ASN 2.8 0.8 + - - -
514F ALA* 1.3 76.1 - - - +
516F MET* 1.3 64.3 + - - +
517F ARG 3.2 0.2 - - - -
518F ALA* 3.2 4.9 + - - +
519F LEU* 3.0 21.3 + - - +
575F TRP* 5.7 2.8 + - - -
5G A 4.0 27.6 + - - -
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Residues in contact with MET 516 (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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504F LEU* 4.2 21.8 - - - -
512F PHE* 2.8 49.2 + - + +
513F ASN* 3.7 3.6 - - - +
515F SER* 1.3 69.7 - - - +
517F ARG* 1.3 65.9 + - - +
519F LEU* 3.2 10.5 + - - +
520F ALA* 3.0 20.8 + - - +
527F LEU* 4.1 14.1 - - + -
559F VAL* 5.0 1.1 - - - -
560F PHE* 3.3 35.9 - - + -
563F LEU* 4.2 14.0 - - + +
565F LEU* 3.6 24.9 - - + -
568F ARG* 6.1 0.7 - - - -
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Residues in contact with ARG 517 (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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505F TYR* 3.3 33.8 - - - +
513F ASN* 2.6 29.3 + - + +
516F MET* 1.3 71.6 - - - +
518F ALA* 1.3 63.2 + - - +
520F ALA* 2.9 12.2 + - - +
521F LYS* 2.9 20.3 + - - +
526F SER* 5.8 0.2 - - - -
527F LEU* 3.3 43.9 + - + +
528F SER* 3.8 4.0 - - - +
529F GLU* 3.6 24.9 + - - +
6G A 3.0 42.6 + - - +
7G A 2.8 56.5 + - - -
8G T 5.2 0.2 + - - -
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Residues in contact with ALA 518 (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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514F ALA 3.3 19.2 + - - +
515F SER 3.2 6.4 + - - +
517F ARG* 1.3 79.4 - - - +
519F LEU* 1.3 61.9 - - - +
521F LYS* 2.9 25.8 + - - +
522F THR* 3.3 11.5 + - - +
5G A 4.0 24.9 - - - +
6G A 3.7 18.8 - - - -
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Residues in contact with LEU 519 (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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515F SER 3.0 12.4 + - - +
516F MET* 3.4 10.5 - - - +
518F ALA* 1.3 74.9 - - - +
520F ALA* 1.3 64.2 + - - +
522F THR* 2.6 35.6 + - + +
523F LYS* 3.2 26.7 + - + +
563F LEU* 5.0 4.5 - - + +
565F LEU* 3.4 48.0 - - + -
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Residues in contact with ALA 520 (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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516F MET 3.0 11.5 + - - +
517F ARG 2.9 12.2 + - - +
519F LEU* 1.3 77.0 - - - +
521F LYS* 1.3 58.3 + - - +
523F LYS* 3.4 5.2 + - - +
525F MET* 2.9 35.3 + - + +
526F SER 4.7 0.9 - - - +
527F LEU* 4.2 25.8 - - + +
532F LEU* 4.8 0.7 - - + -
563F LEU* 3.6 31.2 - - + -
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Residues in contact with LYS 521 (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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517F ARG 2.9 8.7 + - - +
518F ALA* 2.9 18.0 + - - +
520F ALA* 1.3 75.1 - - - +
522F THR* 1.3 61.5 + - + +
524F GLY* 2.9 20.3 + - - -
525F MET 3.5 9.4 - - - +
526F SER* 5.4 0.4 - - - +
538F ARG* 3.3 45.4 + - - +
542F GLY* 4.4 15.1 + - - -
6G A 5.2 3.1 - - - +
7G A 4.1 20.9 + - - +
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Residues in contact with THR 522 (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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518F ALA 3.8 10.8 - - - +
519F LEU* 2.6 32.3 + - + +
521F LYS* 1.3 74.4 - - + +
523F LYS* 1.3 60.5 + - - +
524F GLY* 2.8 12.1 + - - -
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Residues in contact with LYS 523 (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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519F LEU* 3.2 29.1 + - + +
520F ALA* 3.5 11.9 - - - +
521F LYS 3.2 0.6 - - - -
522F THR* 1.3 83.0 + - - +
524F GLY* 1.3 58.5 + - - +
525F MET* 3.2 23.3 + - + +
563F LEU* 3.8 33.2 - - + +
564F GLY* 5.4 2.5 - - - -
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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