Contacts of the helix formed by residues 18 - 24 (chain A) in PDB entry 2NUE
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 LYS 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.5 18.9 - - + +
5A GLU* 4.4 17.3 - - + -
8A GLU* 2.9 33.8 + - - +
14A THR* 5.0 4.9 - - - +
15A PHE* 2.7 31.1 + - + +
16A LYS 5.8 0.4 - - - -
17A ASP* 1.3 71.8 - - - +
19A SER* 1.3 62.2 + - - +
20A LEU 3.2 0.4 + - - -
21A LEU* 3.4 7.9 + - + +
22A GLU* 3.1 20.3 + - - +
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Residues in contact with SER 19 (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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17A ASP* 2.5 17.2 + - - +
18A LYS* 1.3 73.9 - - - +
20A LEU* 1.3 69.4 + - - +
22A GLU* 2.9 22.6 - - - +
23A LYS* 3.2 9.2 + - - +
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Residues in contact with LEU 20 (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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15A PHE* 4.3 3.1 - - + -
17A ASP* 2.7 31.9 + - + +
19A SER* 1.3 69.8 + - - +
21A LEU* 1.3 65.1 + - - +
22A GLU 2.7 5.7 + - - -
23A LYS* 2.7 28.2 + - - +
24A ALA* 3.0 10.4 + - - +
39A LEU* 4.6 10.2 - - + +
115A ALA* 3.7 22.0 - - + +
118A ILE* 4.4 15.7 - - + -
119A ASP* 3.5 43.7 - - + +
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Residues in contact with LEU 21 (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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4A LEU* 3.5 37.2 - - + +
7A LEU* 3.7 29.6 - - + -
8A GLU* 3.9 20.4 - - + +
11A LEU* 4.9 0.4 - - + -
15A PHE* 3.4 31.3 - - + -
18A LYS* 3.4 9.7 + - + +
20A LEU* 1.3 77.7 - - - +
22A GLU* 1.3 64.1 + - - +
24A ALA* 3.6 6.1 + - + +
25A LEU* 3.2 37.1 + - + +
112A LEU* 3.7 23.8 - - + -
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Residues in contact with GLU 22 (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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4A LEU* 4.0 22.5 - - + +
18A LYS 3.1 12.5 + - - +
19A SER* 2.9 19.7 - - - +
20A LEU 2.7 4.2 + - - -
21A LEU* 1.3 74.5 - - - +
23A LYS* 1.3 55.1 + - - +
25A LEU* 3.2 4.9 + - - +
26A THR* 2.6 33.4 + - - +
94A ARG* 2.7 58.7 + - - +
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Residues in contact with LYS 23 (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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19A SER 3.2 6.7 + - - +
20A LEU* 2.7 22.3 + - - +
22A GLU* 1.3 73.2 - - - +
24A ALA* 1.3 55.1 + - - +
25A LEU 2.7 15.8 + - - -
26A THR* 2.8 19.5 + - - +
34A GLU* 3.1 42.1 + - + +
35A HIS 2.7 32.1 - - - +
36A TYR* 3.4 11.9 - - - +
38A THR* 6.2 3.1 - - - -
39A LEU* 4.1 20.3 - - + +
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Residues in contact with ALA 24 (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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20A LEU 3.0 12.0 + - - +
21A LEU* 3.9 7.6 - - - +
22A GLU 3.4 0.2 - - - -
23A LYS* 1.3 75.7 - - - +
25A LEU* 1.3 59.1 + - + +
36A TYR* 3.8 13.6 - - - +
39A LEU* 4.0 6.6 - - + +
108A VAL* 3.3 20.6 - - - +
111A ALA* 3.4 37.1 - - - +
112A LEU* 4.0 8.1 - - + -
115A ALA* 4.0 14.1 - - + -
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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