Contacts of the helix formed by residues 17 - 31 (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 GLY 17 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15H SER 4.1 0.2 + - - -
16H MET* 1.3 77.8 - - - +
18H GLU* 1.3 63.7 + - - -
19H GLY* 3.0 11.8 + - - -
20H THR* 3.0 19.9 + - - +
21H ILE* 3.0 19.3 + - - +
50H MET* 4.7 7.0 - - - -
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Residues in contact with GLU 18 (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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17H GLY* 1.3 68.0 - - - -
19H GLY* 1.3 68.6 + - - +
20H THR 3.0 4.0 + - - -
21H ILE* 3.7 13.7 - - - +
22H ASN* 3.1 46.3 + - - +
49H VAL* 3.6 38.7 - - + +
50H MET* 4.6 4.5 - - - +
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Residues in contact with GLY 19 (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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17H GLY 3.0 2.8 + - - -
18H GLU* 1.3 86.2 + - - +
20H THR* 1.3 64.5 + - - +
22H ASN* 5.4 0.7 - - - +
23H GLY 5.2 1.7 + - - -
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Residues in contact with THR 20 (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* 5.6 1.2 - - - +
17H GLY 3.0 11.9 + - - -
19H GLY* 1.3 82.6 - - - +
21H ILE* 1.3 71.2 + - - +
22H ASN 3.2 2.5 - - - -
23H GLY 3.1 2.0 + - - +
24H LEU 3.0 6.2 + - - -
74H TYR* 2.7 30.7 + - - +
78H GLU* 2.6 48.0 + - + +
79H ASP* 5.7 2.5 - - + -
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Residues in contact with ILE 21 (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* 3.9 20.9 - - + -
17H GLY* 3.0 36.2 + - - +
18H GLU* 4.0 6.7 - - - +
20H THR* 1.3 76.9 - - - +
22H ASN* 1.3 61.5 + - - +
24H LEU* 2.9 9.2 + - + +
25H LEU* 2.8 46.3 + - + +
49H VAL 5.3 3.1 - - - +
50H MET* 5.1 7.4 - - - +
52H LYS* 5.4 9.6 - - + -
53H THR* 3.8 29.8 - - + +
56H LEU* 4.0 19.3 - - + -
78H GLU* 5.4 0.7 - - - -
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Residues in contact with ASN 22 (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* 3.1 38.2 + - - +
19H GLY* 5.4 1.5 - - - +
21H ILE* 1.3 77.5 - - - +
23H GLY* 1.3 56.0 + - - +
25H LEU* 3.3 18.7 + - - +
26H ASP* 2.9 37.1 + - - +
52H LYS* 5.3 7.8 + - - +
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Residues in contact with GLY 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H GLY 5.2 1.0 + - - -
20H THR* 3.1 5.4 + - - +
21H ILE 3.1 0.6 - - - -
22H ASN* 1.3 76.7 - - - +
24H LEU* 1.3 64.2 + - - +
26H ASP* 3.1 12.4 + - - +
27H GLU* 3.0 21.8 + - - +
74H TYR* 3.3 21.9 - - - -
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Residues in contact with LEU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H MET* 4.8 11.4 - - + -
20H THR 3.0 7.8 + - - +
21H ILE* 2.9 10.9 + - - +
23H GLY* 1.3 73.7 - - - +
25H LEU* 1.3 59.0 + - - +
27H GLU* 3.0 8.7 + - + +
28H LEU* 2.8 33.2 + - + +
56H LEU* 4.4 31.2 - - + -
70H ILE* 6.2 0.7 - - + -
71H CYS* 3.8 37.5 - - + +
74H TYR* 3.3 45.4 + - + -
75H ILE* 6.0 3.1 - - + -
78H GLU* 5.6 2.2 - - - +
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Residues in contact with LEU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ILE* 2.8 30.8 + - + +
22H ASN* 3.4 19.3 - - - +
24H LEU* 1.3 76.3 - - - +
26H ASP* 1.3 66.0 + - - +
28H LEU* 3.0 14.4 + - + +
29H LEU* 2.9 19.6 + - - +
34H LEU* 4.8 4.7 - - + -
39H MET* 3.1 39.3 - - + +
42H VAL* 4.4 28.9 - - + -
52H LYS* 5.6 3.6 - - + +
56H LEU* 4.0 25.1 - - + -
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Residues in contact with ASP 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ASN* 2.9 23.8 + - - +
23H GLY* 3.1 11.7 + - - +
25H LEU* 1.3 78.4 - - - +
27H GLU* 1.3 58.2 + - - +
29H LEU* 3.3 14.0 + - - +
30H GLN* 3.0 32.3 + - + +
39H MET* 6.2 0.2 - - - +
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Residues in contact with GLU 27 (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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23H GLY 3.0 11.7 + - - +
24H LEU* 3.0 13.9 + - + +
26H ASP* 1.3 76.0 - - - +
28H LEU* 1.3 63.7 + - + +
30H GLN* 3.0 14.2 + - - +
31H THR* 2.7 48.6 + - + +
70H ILE* 4.2 15.9 - - + +
74H TYR* 4.6 17.5 - - + -
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Residues in contact with LEU 28 (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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24H LEU* 2.8 28.5 + - + +
25H LEU* 3.0 21.5 + - + +
27H GLU* 1.3 76.5 - - + +
29H LEU* 1.3 57.8 + - - +
31H THR* 3.4 4.0 - - - +
32H ARG 3.1 4.0 + - - -
33H VAL* 2.7 59.9 + - + -
34H LEU* 3.3 28.7 + - + -
39H MET* 4.0 6.7 - - + -
56H LEU* 4.9 7.0 - - + -
59H SER* 5.1 4.3 - - - +
67H ALA 5.0 2.9 - - - +
70H ILE* 5.1 6.1 - - + -
71H CYS* 3.7 28.3 - - - -
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Residues in contact with LEU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU 2.9 11.0 + - - +
26H ASP* 3.3 16.2 - - - +
28H LEU* 1.3 76.0 - - - +
30H GLN* 1.3 70.1 + - - +
32H ARG* 3.0 14.0 + - - +
34H LEU 3.9 17.0 - - - +
35H ASN* 4.6 0.4 - - - -
36H LYS* 3.9 49.6 - - + +
39H MET* 3.8 10.7 - - + +
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Residues in contact with GLN 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ASP* 3.0 19.0 + - + +
27H GLU* 3.0 25.1 + - - +
29H LEU* 1.3 83.7 - - - +
31H THR* 1.3 58.6 + - + +
32H ARG* 3.1 4.2 + - - +
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Residues in contact with THR 31 (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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81D TYR* 2.9 19.2 + - - -
27H GLU* 2.7 44.3 + - - +
28H LEU* 3.3 4.3 + - - -
30H GLN* 1.3 77.3 - - + +
32H ARG* 1.3 69.0 + - - +
33H VAL* 3.0 17.8 + - - +
70H ILE* 3.9 30.1 - - + +
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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