Contacts of the helix formed by residues 42 - 46 (chain A) in PDB entry 2R2N
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 ASN 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU 3.8 0.8 + - - -
41A PRO* 1.3 70.1 - - - +
43A PRO* 1.4 67.5 - - - +
44A ASN* 2.8 50.8 + - - +
45A MET* 3.4 20.2 + - + +
46A PHE* 4.3 7.8 - - - -
263B LYS 5.1 0.2 - - - +
325B PHE* 3.3 26.1 - - + -
326B TYR* 2.8 17.3 + - + +
403B SER* 2.9 29.7 + - - +
404B SER* 3.8 18.0 + - - +
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Residues in contact with PRO 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO 3.2 8.0 - - - +
42A ASN* 1.4 87.4 - - - +
44A ASN* 1.3 56.4 + - - +
45A MET 3.1 6.4 + - - -
46A PHE* 3.2 31.7 + - + +
69A LYS* 4.1 37.7 - - + +
73A GLN* 4.0 13.9 - - + +
429A GOL 2.7 29.8 + - - -
404B SER* 5.1 3.6 - - - +
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN* 2.8 27.0 + - - +
43A PRO* 1.3 82.2 - - - +
45A MET* 1.3 69.5 + - + +
46A PHE 3.3 0.2 - - - -
49A LYS* 3.1 22.0 + - - -
69A LYS* 3.3 32.3 + - - +
429A GOL 3.3 6.7 + - - -
56B GLU* 5.4 1.2 - - - +
325B PHE* 6.4 0.4 - - + -
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN* 3.6 17.9 - - + +
43A PRO 3.1 0.6 - - - -
44A ASN* 1.3 90.4 - - + +
46A PHE* 1.3 69.7 + - + +
47A PRO* 4.4 0.2 - - - +
263B LYS 5.0 3.4 - - - +
264B ILE 3.9 1.7 - - - +
318B HIS* 3.2 24.6 - - - -
321B ARG 4.7 1.6 - - - +
322B VAL* 3.9 28.0 - - + -
325B PHE* 3.6 49.8 - - + -
326B TYR* 4.0 20.4 - - + -
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO* 3.8 13.5 - - + -
42A ASN 4.3 7.0 - - - -
43A PRO* 3.2 33.1 + - + +
45A MET* 1.3 77.8 - - - +
47A PRO* 1.4 63.4 - - + +
48A PHE 3.5 0.4 - - - -
49A LYS* 3.2 9.5 + - - -
72A LEU* 3.3 48.9 - - + -
73A GLN* 4.7 2.0 - - - -
429A GOL 3.1 21.8 - - - -
262B SER 3.3 28.0 - - - -
263B LYS 3.6 17.5 - - - -
264B ILE 3.8 2.5 - - - -
265B ILE 3.1 26.9 - - - +
266B SER 3.7 6.1 - - - -
267B SER* 3.6 12.1 - - - -
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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