Contacts of the helix formed by residues 9 - 24 (chain C) in PDB entry 4A12
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 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LEU 5.3 2.9 - - - +
7C LYS 3.9 6.1 + - - +
8C LEU* 1.3 74.4 - - - +
10C LYS* 1.4 57.7 + - - +
11C ASP* 3.4 3.1 - - + +
12C LYS* 3.1 21.1 + - + +
13C ARG* 2.8 30.8 + - - +
19G C 5.2 1.1 - - - -
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Residues in contact with LYS 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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9C LYS* 1.4 70.8 - - - +
11C ASP* 1.3 86.2 + - - +
13C ARG* 3.5 17.1 + - - +
14C ARG* 3.1 66.8 + - - +
49C TYR* 6.2 0.4 - - - -
18G A 3.5 49.3 + - + +
19G C 3.8 25.1 + - - +
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Residues in contact with ASP 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 LYS* 3.4 2.2 - - + +
10C LYS* 1.3 105.5 + - - +
12C LYS* 1.4 63.3 + - + +
14C ARG* 3.5 12.0 + - - +
15C GLU* 3.2 22.7 + - - +
49C TYR* 5.8 2.3 - - - -
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Residues in contact with LYS 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 LYS 3.6 22.0 + - - -
8C LEU* 3.8 23.9 - - + +
9C LYS* 3.1 22.9 + - + +
11C ASP* 1.4 74.3 - - + +
13C ARG* 1.4 65.1 + - - +
15C GLU* 3.5 6.8 + - - +
16C ALA* 3.1 22.0 + - - +
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Residues in contact with ARG 13 (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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6C LEU* 6.0 3.5 - - + +
8C LEU* 4.1 22.6 + - + +
9C LYS 2.8 20.9 + - - +
10C LYS* 3.6 21.0 + - - +
12C LYS* 1.4 69.5 - - - +
14C ARG* 1.3 54.7 + - - +
16C ALA* 3.1 7.8 + - - +
17C ILE* 2.8 51.3 + - + +
36C PHE* 4.1 18.8 - - + +
38C VAL* 4.0 25.4 - - - +
42C THR* 3.4 12.8 - - - +
46C ASP* 2.9 40.3 + - - -
19G C 3.0 42.2 + - - -
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Residues in contact with ARG 14 (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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48B THR* 5.4 6.9 - - - +
10C LYS* 3.1 55.1 + - - +
11C ASP* 3.8 9.7 + - - +
13C ARG* 1.3 75.7 - - - +
15C GLU* 1.3 59.1 + - - +
17C ILE* 3.3 4.7 + - - -
18C ARG* 2.9 25.3 + - - +
45C LEU* 4.3 14.3 + - - +
46C ASP* 2.8 43.2 + - + +
49C TYR* 3.4 50.6 - - - +
50C LEU* 3.3 29.6 - - + +
19G C 5.5 1.2 + - - -
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Residues in contact with GLU 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 ASP 3.2 14.0 + - - +
12C LYS* 3.9 8.5 - - - +
13C ARG 3.3 0.2 - - - -
14C ARG* 1.3 74.8 - - - +
16C ALA* 1.3 58.0 + - - +
18C ARG* 3.0 50.1 + - - +
19C GLN* 3.0 47.8 + - - +
50C LEU* 5.2 3.0 - - - +
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Residues in contact with ALA 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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8C LEU* 4.4 10.5 - - + -
12C LYS 3.1 14.2 + - - +
13C ARG* 3.1 11.1 + - - +
15C GLU* 1.3 75.8 - - - +
17C ILE* 1.4 56.0 + - - +
19C GLN* 3.6 10.3 + - - +
20C GLN* 3.1 27.7 + - - +
36C PHE* 3.5 22.9 - - + -
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Residues in contact with ILE 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 ARG* 2.8 32.1 + - + +
14C ARG* 3.5 4.7 - - - +
16C ALA* 1.4 74.8 - - - +
18C ARG* 1.4 59.3 + - - +
20C GLN* 3.1 3.6 + - - +
21C ILE* 2.9 50.8 + - + +
32C LEU* 4.8 7.2 - - + -
36C PHE* 3.7 27.1 - - + -
43C ILE* 3.7 22.2 - - + +
46C ASP* 3.3 36.6 - - + +
47C ARG* 5.0 4.5 - - + -
50C LEU* 4.2 13.0 - - + -
52C ILE* 4.9 0.2 - - + -
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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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14C ARG 2.9 14.2 + - - +
15C GLU* 3.0 45.0 + - - +
17C ILE* 1.4 76.8 - - - +
19C GLN* 1.3 77.6 + - - +
21C ILE* 3.6 2.8 + - - +
22C ASP* 3.2 46.8 + - - +
50C LEU* 4.2 18.8 - - + +
52C ILE* 4.0 21.2 - - + +
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Residues in contact with GLN 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 GLU* 3.0 41.8 + - - +
16C ALA* 3.9 8.6 + - - +
18C ARG* 1.3 98.5 - - - +
20C GLN* 1.4 56.6 + - - +
22C ASP* 3.4 6.6 - - - +
23C SER* 3.0 30.5 + - - -
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Residues in contact with GLN 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 ALA 3.1 17.7 + - - +
17C ILE* 3.1 6.5 + - - +
19C GLN* 1.4 75.9 - - - +
21C ILE* 1.4 55.2 + - - +
23C SER* 3.4 9.4 + - - -
24C ASN* 2.9 35.3 + - - +
27C ILE* 4.0 19.3 - - + +
32C LEU* 3.9 24.2 - - + -
35C LEU* 4.5 12.2 - - + +
36C PHE* 4.4 8.6 - - + -
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Residues in contact with ILE 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 ILE* 2.9 37.0 + - + +
18C ARG 4.0 3.6 - - - +
20C GLN* 1.4 71.7 - - - +
22C ASP* 1.3 62.1 + - - +
24C ASN 3.6 4.9 - - - -
25C PRO* 3.0 34.6 - - + +
27C ILE* 3.9 18.8 - - + -
32C LEU* 3.9 11.9 - - + -
47C ARG* 3.8 15.7 - - + -
52C ILE* 3.7 32.3 - - + -
58C ARG* 3.6 32.8 - - - +
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Residues in contact with ASP 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* 3.2 32.3 + - - +
19C GLN* 3.4 12.1 - - - +
21C ILE* 1.3 77.7 - - - +
23C SER* 1.3 64.7 + - - +
24C ASN 3.3 0.7 + - - -
25C PRO* 3.9 11.8 - - - +
67D TYR* 4.8 1.0 + - - -
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Residues in contact with SER 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 GLN 3.0 14.8 + - - -
20C GLN* 3.8 12.8 + - - -
21C ILE 3.4 0.2 - - - -
22C ASP* 1.3 79.9 - - - +
24C ASN* 1.3 59.6 + - - +
67D TYR* 3.0 13.6 + - - -
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Residues in contact with ASN 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 GLN* 2.9 19.5 + - - +
21C ILE 3.0 7.0 - - - +
23C SER* 1.3 79.8 - - - +
25C PRO* 1.4 64.1 - - - +
26C PHE* 3.3 26.5 + - - +
27C ILE* 3.3 49.6 - - + +
31C GLU* 4.9 3.8 + - - -
67D TYR* 3.5 6.2 + - - +
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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