Contacts of the helix formed by residues 45 - 51 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA 3.9 0.2 + - - -
44A SER* 1.3 73.7 - - - +
46A GLU* 1.3 75.0 + - + +
48A LEU* 3.4 3.6 + - - +
49A LYS* 3.0 36.4 + - - +
65A VAL* 3.9 19.6 - - + +
66A LYS* 3.2 43.1 + - - +
69A ASN* 3.9 27.9 - - + +
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Residues in contact with GLU 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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44A SER* 3.1 7.4 + - - +
45A GLU* 1.3 82.6 - - + +
47A HIS* 1.3 65.1 + - - +
49A LYS* 2.8 43.7 + - - +
50A GLN* 3.2 25.6 + - - +
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 5.4 3.5 - - + +
43A ALA* 3.7 24.0 - - + -
44A SER* 3.1 24.8 + - - +
46A GLU* 1.3 76.6 - - - +
48A LEU* 1.3 56.3 - - - +
50A GLN* 3.2 10.3 + - - +
51A HIS* 3.0 25.8 + - - +
132A LEU* 3.3 51.7 + - + +
133A TRP* 3.1 39.1 - + - -
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Residues in contact with LEU 48 (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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43A ALA* 3.5 32.5 - - + +
44A SER 3.0 17.5 + - - +
45A GLU* 3.8 4.7 - - - +
46A GLU 3.3 0.2 - - - -
47A HIS* 1.3 73.9 - - - +
49A LYS* 1.3 58.9 + - - +
51A HIS* 3.2 7.0 + - + +
52A TYR* 2.9 37.6 + - + +
65A VAL* 3.9 16.8 - - + +
68A MET* 3.7 33.4 - - + +
69A ASN* 3.7 31.2 - - + +
73A VAL* 6.0 0.4 - - + -
133A TRP* 4.1 19.3 - - + -
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Residues in contact with LYS 49 (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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45A GLU* 3.0 26.1 + - - +
46A GLU* 2.8 42.3 + - - +
48A LEU* 1.3 74.9 - - - +
50A GLN* 1.3 61.7 + - - +
52A TYR 3.4 0.9 - - - -
53A ILE* 2.8 33.4 + - - +
61A PHE* 4.0 31.1 - - + -
65A VAL* 4.1 14.1 - - + -
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Residues in contact with GLN 50 (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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46A GLU 3.2 11.8 + - - +
47A HIS* 3.2 10.4 + - - +
49A LYS* 1.3 79.3 - - - +
51A HIS* 1.3 66.9 + - - +
53A ILE* 3.2 37.8 + - - +
128A LYS* 3.0 22.3 + - - +
132A LEU* 4.1 20.0 - - + -
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Residues in contact with HIS 51 (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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8A PHE* 3.8 9.0 - + - -
10A ALA* 6.1 0.2 - - - +
47A HIS 3.0 12.3 + - - +
48A LEU* 3.5 13.2 - - + +
50A GLN* 1.3 79.2 - - - +
52A TYR* 1.3 88.1 + + - +
53A ILE 3.6 0.7 + - - -
54A ASP* 4.3 4.7 - - - +
68A MET* 5.5 2.3 - - + +
118A HIS* 3.5 41.2 + - - -
128A LYS* 3.6 12.6 + - - +
129A GLU* 3.6 29.4 + - + +
132A LEU* 3.5 15.1 - - + +
133A TRP* 3.0 36.3 + + + +
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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