Contacts of the helix formed by residues 44 - 48 (chain 3) 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 MET 44 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721 ARG* 3.4 39.3 - - + +
751 SER* 3.5 17.9 - - - +
423 ASN* 2.9 10.9 + - - +
433 MET* 1.3 74.0 - - - +
453 GLU* 1.3 64.7 + - - +
463 LEU 3.2 0.2 - - - -
473 ALA* 3.2 13.9 + - + +
483 GLU* 3.0 26.2 + - - +
1033 ILE* 3.7 25.6 - - + -
1043 LEU* 4.9 1.8 - - + -
2163 ALA* 5.6 0.2 - - - -
2203 PHE* 3.7 33.0 - - + +
2213 SER* 4.2 3.8 - - - -
2223 VAL* 3.6 32.1 - - + -
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Residues in contact with GLU 45 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721 ARG* 4.5 4.2 - - - +
403 VAL* 3.9 5.6 - - + +
413 LYS* 2.9 27.9 + - - +
423 ASN* 2.9 26.7 + - + +
443 MET* 1.3 75.7 - - - +
463 LEU* 1.3 66.1 + - + +
483 GLU* 3.1 18.9 + - - +
493 ILE* 3.6 10.6 + - - +
484 GLN* 2.8 53.1 + - - +
504 PRO* 4.3 25.4 - - + +
534 PHE* 3.6 17.2 - - + -
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Residues in contact with LEU 46 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241 PHE* 4.4 7.2 - - + +
1251 PHE* 4.0 20.4 - - + -
2711 PRO* 3.6 41.1 - - + -
403 VAL* 3.9 22.4 - - + -
433 MET* 2.9 27.2 + - + +
453 GLU* 1.3 78.3 - - + +
473 ALA* 1.3 61.8 + - - +
493 ILE* 3.0 35.6 + - + +
993 MET* 4.1 27.3 - - + +
1033 ILE* 3.6 10.5 - - + -
534 PHE* 4.8 2.5 - - + -
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Residues in contact with ALA 47 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433 MET 3.3 3.2 + - - +
443 MET* 3.2 33.9 + - + +
463 LEU* 1.3 79.4 - - - +
483 GLU* 1.3 57.6 + - - +
493 ILE 3.4 3.7 + - - +
1003 LEU* 3.8 34.9 - - + +
1033 ILE* 3.8 9.7 - - + +
2153 SER* 3.6 5.2 - - - -
2163 ALA* 2.8 28.3 + - + -
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Residues in contact with GLU 48 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521 THR* 3.5 10.0 - - - +
721 ARG* 2.8 40.2 + - - +
443 MET 3.0 11.1 + - - +
453 GLU 3.1 9.3 + - - +
473 ALA* 1.3 76.1 - - - +
493 ILE* 1.3 59.8 + - - +
1153 LYS* 4.4 1.2 + - - -
2153 SER* 3.4 10.0 - - - -
2163 ALA* 3.5 24.5 - - + +
2173 CYS 4.2 5.3 - - - -
2183 ASN* 4.0 18.0 + - - +
504 PRO* 3.6 23.9 - - + +
544 THR* 3.5 19.8 - - + +
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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