Contacts of the helix formed by residues 9 - 27 (chain C) in PDB entry 3G65
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 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.8 1.5 - - - +
8C VAL* 1.3 78.6 - - - +
10C GLY* 1.3 67.8 + - - +
11C ALA* 3.5 14.7 + - - +
12C CYS* 3.5 31.6 - - + +
13C LEU* 2.9 29.7 + - - +
63C PHE 5.2 0.9 - - - +
65C ASN* 4.4 11.3 + - - +
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Residues in contact with GLY 10 (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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8C VAL 3.3 5.8 + - - -
9C ASP* 1.3 75.7 + - - +
11C ALA* 1.3 63.6 + - - +
13C LEU* 3.1 9.1 + - - +
14C ASN* 2.9 26.5 + - - +
98C ALA 6.1 0.9 - - - -
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Residues in contact with ALA 11 (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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9C ASP* 3.4 13.2 + - - +
10C GLY* 1.3 75.0 - - - +
12C CYS* 1.3 58.7 + - - +
14C ASN* 3.6 4.2 + - - +
15C HIS* 3.0 30.9 + - - +
18C ARG* 5.1 3.6 + - - +
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Residues in contact with CYS 12 (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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7C ILE* 4.4 2.7 - - + -
9C ASP* 3.4 30.8 + - + +
10C GLY 3.2 0.6 - - - -
11C ALA* 1.3 77.9 - - - +
13C LEU* 1.3 56.9 + - - +
15C HIS* 3.2 6.3 + - - +
16C PHE* 2.8 36.4 + - - +
62C ASN* 3.4 25.6 - - - -
63C PHE* 3.8 32.3 - - + +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.8 16.9 - - + +
8C VAL 5.5 2.0 - - - +
9C ASP 2.9 17.5 + - - +
10C GLY* 3.5 9.2 - - - +
12C CYS* 1.3 77.3 - - - +
14C ASN* 1.3 61.5 + - - +
16C PHE* 3.3 7.3 + - + +
17C THR* 3.2 22.0 + - - +
92C LEU* 5.6 0.2 - - + -
95C ALA* 3.2 33.2 - - + +
96C GLN 4.7 3.4 - - - +
98C ALA* 4.0 27.4 - - + +
99C ARG 4.9 7.0 - - - +
101C LEU* 3.6 43.1 - - + +
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Residues in contact with ASN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLY 2.9 14.4 + - - +
11C ALA* 4.1 3.8 - - - +
13C LEU* 1.3 77.0 - - - +
15C HIS* 1.3 63.4 - - - +
17C THR* 3.0 22.5 + - - +
18C ARG* 3.1 42.4 + - - +
95C ALA 5.6 1.8 - - - -
96C GLN* 5.0 20.4 + - - +
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Residues in contact with HIS 15 (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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11C ALA 3.0 20.4 + - - +
12C CYS* 3.6 5.6 - - - +
14C ASN* 1.3 76.6 - - - +
16C PHE* 1.3 61.5 + - - +
18C ARG* 3.3 37.6 + - + +
19C ILE* 3.2 30.5 + - + +
63C PHE* 3.1 27.0 - + - -
267C HIS* 5.1 7.4 - + - -
268C GLU* 3.4 30.2 + - - +
270C VAL* 3.4 33.8 - - + +
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Residues in contact with PHE 16 (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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7C ILE* 4.2 21.1 - - + -
12C CYS 2.8 16.6 + - - +
13C LEU* 3.4 6.7 - - + +
14C ASN 3.1 0.2 - - - -
15C HIS* 1.3 76.0 + - - +
17C THR* 1.3 64.5 + - - +
19C ILE* 3.2 14.9 + - + +
20C SER* 3.3 10.6 + - - -
32C LEU* 6.5 0.7 - - + -
39C LEU* 4.7 9.2 - - + -
41C PHE* 5.1 14.1 - + - -
58C LEU* 4.2 20.6 - - + -
63C PHE* 4.0 26.7 - + + -
64C PHE* 4.2 22.2 - + - -
88C LEU* 5.2 7.0 - - + -
92C LEU* 3.6 37.7 - - + -
101C LEU* 4.7 3.6 - - + -
103C ILE* 5.8 11.2 - - + -
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Residues in contact with THR 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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13C LEU* 3.2 10.7 + - - +
14C ASN* 3.0 18.0 + - - +
16C PHE* 1.3 76.7 - - - +
18C ARG* 1.3 65.5 + - + +
20C SER* 3.0 3.5 + - - -
21C ASN* 3.0 41.2 + - - +
92C LEU* 3.2 48.7 + - + +
93C LYS* 4.8 5.4 - - - +
95C ALA* 4.9 6.8 + - - +
96C GLN* 5.1 12.3 - - + +
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Residues in contact with ARG 18 (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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11C ALA* 5.1 4.0 + - - +
14C ASN* 3.1 40.8 + - - +
15C HIS* 3.4 43.1 - - + +
17C THR* 1.3 75.3 - - + +
19C ILE* 1.3 63.1 + - + +
21C ASN* 3.3 12.8 + - - +
22C MET* 3.1 22.7 + - - +
268C GLU* 5.3 4.4 + - - -
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Residues in contact with ILE 19 (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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15C HIS* 3.2 29.6 - - + +
16C PHE* 3.4 9.9 - - + +
17C THR 3.1 0.4 - - - -
18C ARG* 1.3 77.9 - - + +
20C SER* 1.3 60.1 + - - +
22C MET* 3.4 24.6 + - + +
23C ILE* 3.2 22.8 + - + +
41C PHE* 4.1 25.6 - - + -
56C CYS* 4.3 10.8 - - - -
58C LEU* 3.6 25.8 - - + -
63C PHE* 3.8 20.0 - - + -
270C VAL* 3.9 12.3 - - + -
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Residues in contact with SER 20 (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 PHE 3.3 3.1 + - - -
17C THR 3.0 9.2 + - - -
19C ILE* 1.3 76.4 - - - +
21C ASN* 1.3 64.7 + - - +
23C ILE* 3.1 12.1 - - - +
24C ALA* 3.0 24.3 + - - +
41C PHE* 5.8 2.2 - - - -
85C SER 4.4 1.2 + - - +
88C LEU* 3.4 16.9 - - - +
89C SER* 3.1 31.5 + - - -
92C LEU* 3.5 24.7 - - - -
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Residues in contact with ASN 21 (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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17C THR* 3.0 33.6 + - - +
18C ARG* 3.6 10.3 - - - +
20C SER* 1.3 78.4 - - - +
22C MET* 1.3 61.9 + - - +
24C ALA* 3.6 9.8 + - - +
25C LYS* 3.3 32.0 + - - +
89C SER* 3.9 18.3 - - - +
93C LYS* 6.0 0.5 - - - +
96C GLN* 5.9 1.8 - - - +
245C GLN* 5.9 4.5 - - - +
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Residues in contact with MET 22 (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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18C ARG 3.1 13.0 + - - +
19C ILE* 3.6 33.9 - - + +
20C SER 3.2 0.4 - - - -
21C ASN* 1.3 75.1 - - - +
23C ILE* 1.3 63.7 + - + +
25C LYS* 3.0 21.0 + - - +
26C LEU* 3.2 25.6 + - + +
54C MET* 6.3 0.7 - - - -
56C CYS* 4.3 13.5 - - - -
243C GLY* 3.7 28.6 - - - +
244C GLN* 3.7 27.4 - - - +
270C VAL* 5.4 3.8 - - + -
272C LEU* 3.7 18.4 - - + -
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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
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19C ILE* 3.2 13.1 + - + +
20C SER* 3.1 23.1 - - - +
22C MET* 1.3 82.6 - - + +
24C ALA* 1.3 57.3 + - - +
25C LYS 3.1 0.7 - - - -
26C LEU* 3.6 8.3 - - - +
27C ALA* 3.0 28.7 + - + +
30C CYS* 3.3 35.9 - - + -
41C PHE* 3.3 43.7 - - + -
54C MET* 3.6 20.9 - - + -
56C CYS* 6.5 1.1 - - + -
85C SER* 3.9 10.1 - - - +
88C LEU* 5.7 2.7 - - + -
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Residues in contact with ALA 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 SER 3.0 18.7 + - - +
21C ASN* 3.7 8.1 - - - +
22C MET 3.1 0.4 - - - -
23C ILE* 1.3 77.5 - - - +
25C LYS* 1.3 60.9 + - + +
27C ALA 3.6 9.6 - - - +
28C LYS* 5.2 1.6 - - - -
85C SER* 3.6 21.7 - - - +
86C GLU* 4.6 4.1 + - - +
89C SER* 4.0 21.8 - - - +
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Residues in contact with LYS 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 ASN* 3.3 23.7 - - - +
22C MET* 3.0 8.8 + - - +
24C ALA* 1.3 81.6 - - + +
26C LEU* 1.3 63.7 + - + +
27C ALA 3.5 0.7 - - - -
239C GLN* 4.8 13.7 - - - +
242C ALA* 4.7 15.1 + - + +
243C GLY* 4.7 20.4 + - - +
245C GLN* 3.8 22.8 - - - +
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Residues in contact with LEU 26 (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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22C MET* 3.4 34.8 - - + +
23C ILE* 3.2 5.5 + - - +
25C LYS* 1.3 81.3 - - - +
27C ALA* 1.3 60.0 + - - +
43C LEU* 5.1 1.0 - - - +
52C VAL* 5.8 3.5 - - - +
54C MET* 4.0 30.2 - - + +
239C GLN* 3.3 41.2 - - + +
240C PHE* 4.0 12.6 - - + +
243C GLY* 4.6 5.4 - - - -
244C GLN* 5.2 2.7 - - - +
272C LEU* 4.4 15.3 - - + -
274C TYR* 4.2 27.5 + - + +
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Residues in contact with ALA 27 (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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23C ILE* 3.0 15.7 + - + +
24C ALA 3.6 9.1 - - - +
25C LYS 3.5 1.0 - - - -
26C LEU* 1.3 84.5 - - + +
28C LYS* 1.3 59.6 + - - +
29C THR 4.0 5.6 - - - +
30C CYS* 4.7 5.8 - - + -
43C LEU* 3.5 31.6 - - + -
54C MET* 5.0 5.2 - - + -
85C SER* 2.9 27.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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