Contacts of the helix formed by residues 51 - 59 (chain H) in PDB entry 5FNA
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 ASP 51 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E ASN* 5.9 1.3 + - - -
45H GLU* 3.1 28.1 - - + +
46H ASN* 2.5 27.1 + - - +
47H ALA* 3.6 10.0 - - - +
48H THR* 2.8 13.4 + - - -
50H MET* 1.3 78.5 - - - +
52H LYS* 1.3 51.8 + - - +
53H THR* 2.6 3.5 + - - -
54H ARG* 2.4 66.2 + - - +
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Residues in contact with LYS 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H GLU* 6.4 0.2 - - + -
21H ILE* 5.4 13.0 - - + -
22H ASN* 5.3 8.1 + - - +
25H LEU* 5.6 4.9 - - + +
42H VAL* 3.6 47.3 - - + +
43H LYS* 4.3 16.4 - - - +
45H GLU* 3.6 26.9 - - + -
49H VAL* 2.5 54.6 + - + +
50H MET 2.4 3.0 + - - -
51H ASP* 1.3 79.2 - - - +
53H THR* 1.3 55.4 + - - +
54H ARG 3.1 0.2 - - - -
55H ALA* 2.9 7.9 + - - +
56H LEU* 2.8 29.7 + - + +
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Residues in contact with THR 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ILE* 3.3 40.0 + - - +
16H MET* 3.8 36.3 - - + +
21H ILE* 3.8 14.8 - - + -
50H MET* 2.6 20.6 + - + +
51H ASP* 2.6 3.1 + - - -
52H LYS* 1.3 79.2 - - - +
54H ARG* 1.3 61.3 + - - +
56H LEU* 3.2 11.3 + - + +
57H ILE* 3.1 27.7 + - - +
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Residues in contact with ARG 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASN* 3.6 34.7 - - - +
23E GLY* 4.4 1.8 - - - +
26E ASP* 2.9 34.9 + - - -
43E LYS* 6.3 0.7 - - - +
13H ILE* 4.6 10.1 - - + +
45H GLU* 4.7 9.6 - - - +
51H ASP* 2.4 56.3 + - + +
53H THR* 1.3 76.0 + - - +
55H ALA* 1.3 59.6 + - - +
57H ILE* 3.3 15.6 + - + +
58H ASP* 3.1 26.3 + - - +
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Residues in contact with ALA 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H VAL* 4.2 21.5 - - + -
45H GLU* 3.8 16.5 + - - +
51H ASP 3.8 0.2 + - - -
52H LYS 2.9 13.2 + - - +
54H ARG* 1.3 77.4 - - - +
56H LEU* 1.3 59.8 + - + +
58H ASP* 3.1 13.5 + - - +
59H SER* 2.9 28.3 + - - -
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Residues in contact with LEU 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H MET* 3.8 30.5 - - + -
21H ILE* 4.0 22.9 - - + -
24H LEU* 4.4 17.7 - - + -
25H LEU* 4.0 27.6 - - + -
28H LEU* 4.9 4.5 - - + -
34H LEU* 6.0 0.2 - - + -
42H VAL* 6.0 3.1 - - + -
52H LYS* 2.8 14.5 + - + +
53H THR* 3.2 19.3 + - - +
55H ALA* 1.3 72.5 - - + +
57H ILE* 1.3 65.5 + - + +
59H SER* 2.6 26.7 + - - +
60H VAL* 3.2 13.2 + - - +
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Residues in contact with ILE 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ASP* 6.5 1.3 - - - -
29E LEU* 5.6 7.6 - - + -
36E LYS* 4.5 20.4 - - - -
6H LYS* 6.5 0.4 - - + -
10H LYS* 3.7 47.6 - - + +
13H ILE* 3.8 20.6 - - + -
53H THR 3.1 16.3 + - - +
54H ARG* 3.4 13.0 - - + +
55H ALA 3.2 0.2 - - - -
56H LEU* 1.3 76.1 - - + +
58H ASP* 1.3 63.8 + - - +
60H VAL* 2.9 29.8 + - + +
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Residues in contact with ASP 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D MET* 6.5 0.4 - - - -
36E LYS* 2.8 32.4 + - - +
40E GLU* 4.0 10.9 - - - +
43E LYS* 4.9 5.4 + - - -
54H ARG* 3.1 13.7 + - - +
55H ALA* 3.1 15.2 + - - +
57H ILE* 1.3 78.2 - - - +
59H SER* 1.3 58.1 + - - +
60H VAL 3.0 13.5 + - - +
61H ILE* 3.8 10.3 + - - +
62H PRO* 5.0 2.8 - - - +
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Residues in contact with SER 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H LEU* 5.1 3.3 - - - +
33H VAL* 5.4 5.4 - - - +
34H LEU* 4.2 31.3 - - - +
55H ALA 2.9 11.1 + - - -
56H LEU* 2.6 34.2 + - - +
58H ASP* 1.3 73.0 - - - +
60H VAL* 1.3 58.9 + - - +
61H ILE* 3.1 20.3 + - - +
64H GLY 5.6 0.7 - - - +
68H CYS* 4.5 6.3 - - - -
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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