Contacts of the helix formed by residues 16 - 27 (chain C) in PDB entry 4NAT
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 THR 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PRO* 3.5 13.0 - - + +
15C ILE* 1.3 78.7 - - - +
17C TYR* 1.3 58.9 + - - +
18C GLY* 3.0 15.9 + - - -
19C HIS* 3.0 26.3 + - + +
20C LEU* 3.0 23.3 + - - +
128C ILE* 3.7 10.4 + - - +
129C SER* 4.2 5.6 - - - +
130C SER* 3.8 23.5 + - - +
133C VAL* 4.4 5.4 - - + -
146C PHE 3.6 12.3 - - - -
147C VAL* 4.1 13.0 - - + -
148C PRO* 4.5 6.1 - - - -
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Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C THR* 1.3 70.9 - - - +
18C GLY* 1.3 64.0 + - - +
19C HIS 3.2 0.2 - - - -
20C LEU* 3.7 15.9 - - + +
21C ASP* 3.0 25.3 + - - +
125C TYR* 3.7 32.0 - - + -
144C SER 3.8 9.5 + - - -
145C GLU* 3.3 24.7 - - - -
146C PHE 3.0 19.0 + - - +
147C VAL* 3.4 19.2 + - - +
148C PRO* 3.5 34.1 - - + +
149C PRO* 4.0 8.1 - - - +
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 3.0 9.6 + - - -
17C TYR* 1.3 76.9 - - - +
19C HIS* 1.3 62.4 + - - +
21C ASP* 3.6 12.5 - - - +
22C ILE* 3.7 14.0 + - - +
121C SER* 5.7 4.7 - - - -
125C TYR* 4.1 22.2 - - - -
128C ILE* 3.6 14.4 - - - +
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Residues in contact with HIS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 5.7 0.7 - - - +
12C PHE* 3.5 22.2 - + + -
14C PRO 3.9 1.0 + - - -
15C ILE* 3.6 17.0 - - + -
16C THR* 3.0 46.1 + - + +
18C GLY* 1.3 76.8 - - - +
20C LEU* 1.3 60.6 + - - +
22C ILE* 3.4 8.5 + - - +
23C ILE* 3.2 25.1 + - + +
92C ARG* 5.9 2.9 + - - -
129C SER* 5.7 1.0 - - - -
130C SER* 3.3 22.2 + - - -
202C ADP 2.8 42.2 + - - -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 3.9 11.7 - - + -
16C THR 3.0 15.0 + - - +
17C TYR* 4.0 18.8 - - + +
18C GLY 3.4 0.4 - - - -
19C HIS* 1.3 75.0 - - - +
21C ASP* 1.3 60.6 + - - +
23C ILE* 3.7 8.6 - - + +
24C GLU* 2.8 53.8 + - + +
59C SER* 3.6 29.4 - - - +
60C VAL* 3.8 20.0 - - + -
62C HIS* 4.6 3.4 - - + -
63C LEU* 4.7 0.7 - - + -
148C PRO* 3.5 33.2 - - + -
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Residues in contact with ASP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR 3.0 19.2 + - - +
18C GLY 3.6 6.7 - - - +
20C LEU* 1.3 76.2 - - - +
22C ILE* 1.3 58.8 + - - +
24C GLU* 3.7 7.1 - - - +
25C ARG* 2.9 74.1 + - - +
121C SER* 4.6 2.1 - - - -
122C SER* 3.5 20.5 + - - -
125C TYR* 4.1 21.9 - - + +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 4.5 14.4 - - + -
18C GLY 3.8 13.0 - - - +
19C HIS* 3.4 9.6 + - - +
20C LEU 3.4 0.4 - - - -
21C ASP* 1.3 80.0 - - - +
23C ILE* 1.3 58.9 + - - +
25C ARG* 3.4 5.0 + - - +
26C SER* 2.8 33.1 + - - -
88C ILE* 4.0 25.1 - - + -
89C ARG 4.8 0.2 - - - -
90C GLY* 3.0 39.5 - - - +
91C LEU 4.7 0.2 - - - +
119C MET* 4.0 25.1 - - + +
121C SER* 5.1 12.3 - - - -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.8 24.9 - - + -
12C PHE* 4.9 3.8 - - + -
15C ILE* 4.1 20.0 - - + -
19C HIS* 3.2 26.1 + - + +
20C LEU* 3.7 13.9 - - + +
22C ILE* 1.3 75.0 - - - +
24C GLU* 1.3 63.3 + - - +
26C SER* 3.2 11.3 + - - -
27C THR* 3.2 14.6 + - - +
33C ILE* 4.7 5.4 - - + +
35C VAL* 4.0 22.9 - - + -
60C VAL* 4.3 8.3 - - + -
63C LEU* 4.0 20.9 - - + -
66C VAL* 4.0 20.0 - - + -
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 2.8 34.5 + - + +
21C ASP* 3.7 7.6 - - - +
23C ILE* 1.3 72.9 - - - +
25C ARG* 1.3 63.7 + - + +
26C SER 3.1 0.2 - - - -
27C THR* 2.8 26.8 + - - -
28C ASP* 4.6 2.3 + - - +
62C HIS* 2.9 29.0 + - - -
63C LEU* 3.8 22.0 - - + -
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Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASP* 2.9 52.3 + - - +
22C ILE* 3.8 3.4 - - - +
23C ILE 3.3 0.2 - - - -
24C GLU* 1.3 76.5 - - + +
26C SER* 1.3 58.2 + - - +
27C THR 3.6 0.2 - - - -
28C ASP* 4.8 1.2 + - - -
29C ARG* 3.1 32.0 + - - +
119C MET* 3.6 44.8 - - + +
120C MET* 2.8 33.5 + - - +
121C SER* 3.9 1.2 - - - +
122C SER* 3.5 12.3 - - - +
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.9 5.6 - - - +
22C ILE 2.8 21.5 + - - -
23C ILE 3.5 5.2 - - - -
24C GLU 3.1 0.6 - - - -
25C ARG* 1.3 77.6 - - - +
27C THR* 1.3 62.8 + - - +
28C ASP 3.3 3.4 - - - -
29C ARG* 3.2 16.1 + - - +
30C PHE* 3.6 14.8 + - - -
33C ILE* 3.6 20.3 - - - +
88C ILE* 3.6 32.5 - - - +
119C MET* 4.2 7.5 - - - +
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE 3.2 15.8 + - - +
24C GLU* 2.8 16.3 + - - +
26C SER* 1.3 75.8 - - - +
28C ASP* 1.3 64.9 + - - +
29C ARG 3.3 1.1 - - - -
30C PHE 3.3 8.8 - - - +
33C ILE* 4.1 6.5 - - + -
63C LEU* 4.2 21.5 - - + +
65C ASN* 2.8 47.4 - - - +
66C VAL* 3.6 20.2 - - + -
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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