Contacts of the helix formed by residues 45 - 51 (chain E) in PDB entry 1NUE
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 GLU 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E ALA 4.0 0.2 + - - -
44E SER* 1.3 71.3 - - - +
46E GLU* 1.3 64.0 + - + +
48E LEU* 3.2 3.6 + - - +
49E LYS* 2.8 59.4 + - - +
65E VAL* 3.9 19.2 - - + +
66E LYS* 3.8 32.9 + - + +
69E ASN* 4.1 25.2 - - + +
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Residues in contact with GLU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E SER* 3.2 20.2 + - - -
45E GLU* 1.3 78.7 - - + +
47E HIS* 1.3 61.1 + - - +
49E LYS* 3.3 11.6 + - - +
50E GLN* 3.1 26.4 + - - +
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Residues in contact with HIS 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 5.2 4.5 - - + +
43E ALA* 3.6 26.5 - - + -
44E SER* 3.2 22.0 + - - +
45E GLU 3.2 0.2 - - - -
46E GLU* 1.3 80.7 - - - +
48E LEU* 1.3 55.9 + - - +
50E GLN* 3.4 7.7 + - - +
51E HIS* 3.1 25.3 + - - +
132E LEU* 3.4 49.3 - - + +
133E TRP* 3.4 34.5 - + - -
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ALA* 3.4 35.9 - - + +
44E SER 2.9 20.4 + - - +
45E GLU* 3.7 5.4 - - - +
47E HIS* 1.3 74.4 - - - +
49E LYS* 1.3 58.8 + - - +
50E GLN 3.2 0.2 - - - -
51E HIS* 3.2 7.1 + - + +
52E TYR* 3.0 37.7 + - + +
65E VAL* 3.9 15.9 - - + +
68E MET* 3.6 32.5 - - + +
69E ASN* 3.5 33.9 - - + +
73E VAL* 6.0 0.7 - - + -
133E TRP* 4.2 15.9 - - + -
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Residues in contact with LYS 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLU* 2.8 49.8 + - - +
46E GLU* 3.3 9.4 + - - +
48E LEU* 1.3 70.4 - - - +
50E GLN* 1.3 60.4 + - - +
52E TYR 3.4 0.7 - - - -
53E ILE* 2.8 39.2 + - + +
61E PHE* 4.0 22.2 - - + -
65E VAL* 4.0 24.7 - - + -
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Residues in contact with GLN 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E GLU 3.1 14.3 + - - +
47E HIS* 3.5 12.3 - - - +
48E LEU 3.2 0.2 - - - -
49E LYS* 1.3 78.3 - - - +
51E HIS* 1.3 62.3 + - - +
53E ILE* 3.2 35.0 - - - +
128E LYS* 3.3 22.7 + - - +
132E LEU* 4.2 21.3 - - + +
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Residues in contact with HIS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E PHE* 3.7 8.3 - + - -
10E ALA* 6.1 0.2 - - - +
47E HIS 3.1 11.3 + - - +
48E LEU* 3.2 12.1 + - + +
50E GLN* 1.3 82.4 - - - +
52E TYR* 1.3 85.5 + + - +
53E ILE* 3.6 1.9 + - - +
54E ASP* 5.2 1.6 + - - +
68E MET* 5.6 3.1 - - + +
118E HIS* 3.5 42.0 + - - -
128E LYS* 3.8 11.2 + - - +
129E GLU* 3.7 26.4 - - + +
132E LEU* 3.7 13.2 - - + +
133E TRP* 2.9 37.9 + + + +
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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