Contacts of the helix formed by residues 50 - 55 (chain 4) in PDB entry 1AR9
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 PRO 50 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721 ARG* 6.2 0.2 - - - +
453 GLU* 4.3 32.1 - - + +
483 GLU* 3.6 32.5 - - - +
484 GLN 3.9 4.0 - - - +
494 ASP* 1.3 94.5 - - - +
514 SER* 1.3 50.7 + - - +
524 LYS 3.3 1.1 - - - -
534 PHE* 2.8 35.3 + - + +
544 THR* 2.9 29.3 + - + +
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Residues in contact with SER 51 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494 ASP* 2.8 31.5 + - - -
504 PRO* 1.3 75.5 - - - +
524 LYS* 1.3 60.6 + - - +
544 THR* 3.3 9.9 + - - -
554 GLU* 2.8 52.3 + - - +
564 PRO* 4.1 0.2 - - - +
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Residues in contact with LYS 52 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352 TYR* 3.5 43.5 + - - +
362 GLY* 4.5 4.7 - - - +
383 GLY* 4.1 12.5 - - - +
393 GLU* 3.0 33.4 + - - +
484 GLN* 3.5 21.2 + - - +
494 ASP 4.5 3.2 + - - +
504 PRO 3.0 5.2 + - - +
514 SER* 1.3 73.5 - - - +
534 PHE* 1.3 96.1 + - + +
564 PRO* 3.7 15.2 - - - +
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Residues in contact with PHE 53 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501 GLY 4.7 3.5 - - - +
521 THR* 5.3 0.2 + - - -
2711 PRO* 3.5 26.5 - - + -
352 TYR* 3.6 31.4 - + - -
1912 PHE 5.3 2.3 - - - +
1922 VAL 4.8 6.1 - - - +
1952 HIS* 5.8 1.4 - - - -
383 GLY 3.6 4.5 - - - -
393 GLU 3.6 4.5 - - - -
403 VAL* 3.5 28.7 - - + -
453 GLU* 3.6 32.5 - - + -
463 LEU* 4.8 1.6 - - + -
493 ILE* 3.6 36.9 - - + +
504 PRO* 2.8 13.5 + - + +
524 LYS* 1.3 103.5 - - + +
544 THR* 1.3 61.3 + - + +
554 GLU 3.6 0.7 - - - -
564 PRO* 3.4 12.9 - - - +
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Residues in contact with THR 54 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501 GLY 5.1 0.2 - - - -
511 ALA* 3.4 3.5 - - - -
521 THR* 2.8 41.1 + - - +
483 GLU* 3.5 33.7 - - + +
493 ILE* 4.0 10.5 - - + +
504 PRO* 2.9 41.6 + - + +
514 SER* 3.3 4.3 + - - -
534 PHE* 1.3 77.8 - - - +
554 GLU* 1.3 73.9 + - - +
564 PRO* 3.4 1.6 - - - -
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Residues in contact with GLU 55 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511 ALA* 4.2 4.9 - - - -
521 THR 4.3 3.7 - - - +
541 PRO* 3.7 23.4 - - - +
514 SER* 2.8 35.3 + - - +
544 THR* 1.3 88.2 + - - +
564 PRO* 1.4 56.0 - - - +
574 ILE* 2.8 23.1 + - + +
614 LEU* 3.4 46.8 + - + +
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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