Contacts of the helix formed by residues 16 - 25 (chain E) in PDB entry 5NC5
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 16 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A PRO* 5.7 3.6 - - - +
586A ARG* 5.7 1.9 - - - +
660A ASP* 3.0 36.7 + - - +
15E GLY* 1.3 75.8 - - - +
17E LYS* 1.3 62.8 - - - +
19E LEU* 3.5 14.3 + - + +
20E GLU* 3.3 42.6 + - + +
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Residues in contact with LYS 17 (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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15E GLY 4.0 6.7 - - - +
16E LYS* 1.3 81.5 - - - +
18E LEU* 1.3 56.1 + - - +
20E GLU* 4.0 8.2 - - - +
21E ALA* 3.0 31.2 + - - +
26E ARG* 4.7 3.9 + - - +
29E GLU* 3.7 21.1 - - - +
33E LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 18 (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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15E GLY* 3.3 15.9 + - - +
16E LYS 3.2 0.6 - - - -
17E LYS* 1.3 76.9 - - - +
19E LEU* 1.3 61.0 + - - +
22E ALA* 2.8 33.7 + - + +
30E VAL* 3.8 38.4 - - + +
33E LEU* 3.7 15.3 - - + +
34E MET* 3.8 25.4 - - + -
38E ALA* 4.4 8.5 - - + -
39E ASP 3.1 28.9 - - - +
40E VAL* 4.1 3.1 - - - -
42E ALA* 5.2 0.2 - - + -
50E PRO* 3.8 20.9 - - + -
66E LEU* 4.8 4.5 - - + -
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Residues in contact with LEU 19 (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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15E GLY 3.2 15.1 + - - +
16E LYS* 3.5 14.8 + - + +
18E LEU* 1.3 76.9 - - - +
20E GLU* 1.3 64.5 + - + +
22E ALA* 3.5 0.7 - - - +
23E ARG* 3.1 17.8 + - - +
42E ALA* 3.5 18.8 - - + +
43E ALA 4.1 6.5 - - - +
44E ASP* 4.0 30.3 - - + +
48E TRP 3.5 23.3 - - - +
50E PRO* 3.5 22.2 - - + -
53E LEU* 3.1 29.5 - - + +
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Residues in contact with GLU 20 (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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660A ASP* 4.8 2.1 - - - +
16E LYS* 3.3 46.4 + - + +
17E LYS* 4.0 7.4 - - - +
18E LEU 3.2 0.6 - - - -
19E LEU* 1.3 75.9 - - + +
21E ALA* 1.3 66.2 + - - +
23E ARG* 3.1 11.5 + - - +
24E ALA* 3.0 22.7 + - - +
26E ARG* 4.4 10.9 + - - +
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Residues in contact with ALA 21 (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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17E LYS 3.0 19.8 + - - +
18E LEU 3.9 2.7 - - - +
20E GLU* 1.3 76.3 - - - +
22E ALA* 1.3 62.4 + - - +
24E ALA 3.3 1.7 + - - -
25E GLY 3.1 4.3 + - - -
26E ARG* 3.0 40.7 + - - +
29E GLU* 3.6 36.6 - - + +
30E VAL* 4.3 7.6 - - + -
33E LEU* 4.2 7.2 - - + -
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Residues in contact with ALA 22 (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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18E LEU* 2.8 22.5 + - + +
19E LEU 3.5 4.9 - - - +
21E ALA* 1.3 75.8 - - - +
23E ARG* 1.3 64.3 + - - +
25E GLY* 3.3 8.1 + - - -
30E VAL* 4.3 12.7 - - + +
50E PRO* 4.0 33.2 - - + +
53E LEU* 4.8 2.5 - - + -
54E ALA* 4.4 6.2 - - - +
59E HIS* 3.5 11.4 - - - -
62E ILE* 4.1 15.8 - - + +
66E LEU* 5.1 0.4 - - + -
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Residues in contact with ARG 23 (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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722A GLU* 4.3 9.5 - - - +
723A ASP* 2.6 41.8 + - - +
724A THR* 5.2 1.2 - - - +
811A TYR* 3.6 26.5 + - - -
19E LEU 3.1 10.3 + - - +
20E GLU* 3.1 15.3 + - - +
22E ALA* 1.3 79.1 - - - +
24E ALA* 1.3 58.6 + - - +
53E LEU* 4.2 20.0 - - + -
57E TRP* 3.8 44.3 - - + +
59E HIS* 2.8 28.2 + - - -
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Residues in contact with ALA 24 (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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20E GLU 3.0 14.7 + - - +
21E ALA 3.3 0.4 + - - -
23E ARG* 1.3 76.9 - - - +
25E GLY* 1.3 62.6 + - - +
26E ARG* 3.9 34.0 - - + +
59E HIS* 4.0 6.2 - - - -
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Residues in contact with GLY 25 (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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21E ALA 3.1 2.0 + - - -
22E ALA 3.3 2.9 + - - -
23E ARG 3.0 6.7 + - - -
24E ALA* 1.3 80.2 - - - +
26E ARG* 1.3 59.0 + - - +
27E ASP* 3.3 14.2 + - - +
59E HIS* 3.9 19.7 - - - -
62E ILE* 3.4 19.3 - - - -
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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