Contacts of the helix formed by residues 12 - 26 (chain C) in PDB entry 4H7Y
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 ASN 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ALA* 3.1 19.2 + - - +
11C ASN* 1.3 74.4 - - - +
13C PRO* 1.3 74.8 - - + +
14C GLU* 3.2 13.4 + - - +
15C ASP* 2.8 53.2 + - - +
16C TRP* 3.1 21.9 + - - -
49C LEU* 3.7 6.7 - - - +
54C TYR* 4.0 5.8 - - + +
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Residues in contact with PRO 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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12C ASN* 1.3 88.6 - - + +
14C GLU* 1.3 64.0 + - - +
17C LEU* 2.8 33.1 + - - +
49C LEU* 3.9 16.4 - - + -
54C TYR* 3.4 47.8 - - + -
57C ASN* 3.5 24.9 - - - +
59C SER* 3.9 2.2 - - - -
60C PHE* 3.6 21.1 - - + +
63C ILE* 3.6 4.7 - - + +
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Residues in contact with GLU 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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12C ASN* 3.4 13.3 - - - +
13C PRO* 1.3 84.2 - - - +
15C ASP* 1.3 65.5 + - - +
17C LEU* 3.4 3.1 + - - +
18C SER* 3.0 29.4 + - - -
57C ASN* 2.9 27.9 + - - +
59C SER* 3.7 20.3 + - - +
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Residues in contact with ASP 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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10C ALA* 3.6 33.1 + - - +
12C ASN* 2.8 35.0 + - - +
14C GLU* 1.3 74.9 - - - +
16C TRP* 1.3 62.3 + - - +
18C SER* 3.5 7.1 + - - -
19C LEU* 3.3 22.4 + - - +
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Residues in contact with TRP 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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10C ALA 4.5 3.0 + - - -
11C ASN* 3.0 28.8 + - - +
12C ASN 3.1 29.5 + - - +
13C PRO 3.8 3.1 - - - +
15C ASP* 1.3 77.2 - - - +
17C LEU* 1.3 62.6 + - - +
19C LEU* 3.2 20.3 + - + +
20C LEU* 2.9 34.5 + - + +
41C ARG* 3.8 38.8 - - - -
44C GLN* 4.0 11.9 - - + -
45C ALA* 3.4 41.3 - - + -
48C ALA* 4.0 9.1 - - + +
49C LEU* 3.9 12.8 - - + -
63C ILE* 4.0 13.2 - - + -
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Residues in contact with LEU 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 PRO 2.8 22.9 + - - +
14C GLU* 3.8 3.4 - - - +
16C TRP* 1.3 72.4 - - - +
18C SER* 1.3 58.2 + - - +
20C LEU* 3.2 3.0 + - + -
21C LEU* 2.8 55.3 + - + +
42C TYR* 4.7 11.0 - - - +
59C SER* 3.9 25.6 - - - +
62C ARG* 3.6 46.0 - - + +
63C ILE* 4.0 23.5 - - + +
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Residues in contact with SER 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 GLU 3.0 19.0 + - - -
15C ASP* 3.7 8.1 + - - -
17C LEU* 1.3 75.1 - - - +
19C LEU* 1.3 62.7 + - - +
21C LEU* 3.5 8.9 + - - +
22C LYS* 3.2 25.5 + - - +
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Residues in contact with LEU 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 ASP 3.3 9.7 + - - +
16C TRP* 3.2 22.8 + - + +
18C SER* 1.3 80.4 - - - +
20C LEU* 1.3 63.3 + - + +
22C LYS* 3.3 10.7 + - - +
23C LEU* 3.0 29.1 + - + +
41C ARG* 3.8 52.5 - - + +
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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
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16C TRP* 2.9 27.5 + - + +
17C LEU* 3.8 4.0 - - + +
19C LEU* 1.3 77.9 - - + +
21C LEU* 1.3 64.7 + - - +
23C LEU* 3.8 4.1 - - - +
24C GLU* 3.1 24.4 + - - +
38C LEU* 4.1 5.0 - - + +
41C ARG* 3.6 49.4 - - + +
42C TYR* 3.7 48.5 + - + +
45C ALA* 4.0 20.6 - - + -
63C ILE* 4.1 11.7 - - + -
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Residues in contact with LEU 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 LEU* 2.8 44.6 + - + +
18C SER* 3.8 8.1 - - - +
20C LEU* 1.3 76.3 - - - +
22C LYS* 1.3 63.4 + - - +
24C GLU* 3.4 12.2 + - + +
25C LYS* 3.0 22.8 + - - +
42C TYR* 4.9 6.3 - - - +
62C ARG* 4.0 29.4 - - - +
66C ARG* 6.4 0.4 - - + -
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Residues in contact with LYS 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 SER 3.2 12.3 + - - +
19C LEU* 3.6 12.7 - - - +
21C LEU* 1.3 78.7 - - - +
23C LEU* 1.3 58.0 + - - +
25C LYS* 3.0 10.2 + - + +
26C ASN* 2.9 46.1 + - - +
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Residues in contact with LEU 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 LEU* 3.0 19.0 + - + +
20C LEU* 3.8 7.0 - - + +
21C LEU 3.3 0.2 - - - -
22C LYS* 1.3 77.3 - - - +
24C GLU* 1.3 56.1 + - - +
26C ASN* 3.2 16.1 + - + +
27C SER* 2.6 36.6 + - - +
37C LYS* 4.4 6.7 - - + +
38C LEU* 3.7 28.7 - - + +
41C ARG* 3.7 35.0 - - + +
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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 3.1 16.0 + - - +
21C LEU* 3.8 10.6 - - + +
23C LEU* 1.3 76.5 - - - +
25C LYS* 1.3 62.5 + - - +
27C SER* 3.2 18.4 + - - -
28C VAL* 4.0 8.8 - - + +
30C LEU* 5.3 8.6 - - + +
38C LEU* 3.7 31.9 - - + +
42C TYR* 4.1 6.8 + - - -
66C ARG* 2.8 50.3 + - - +
70C LEU* 4.7 0.3 - - - +
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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 LEU 3.0 14.2 + - - +
22C LYS* 3.0 14.2 + - + +
24C GLU* 1.3 77.6 - - - +
26C ASN* 1.3 65.4 + - - +
27C SER 3.3 0.4 - - - -
28C VAL* 3.2 27.2 - - + +
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Residues in contact with ASN 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 LYS* 2.9 39.3 + - - +
23C LEU* 3.2 8.7 + - + +
25C LYS* 1.3 86.6 - - - +
27C SER* 1.3 62.8 + - - +
28C VAL* 3.6 3.1 - - - -
34C LEU* 4.8 4.5 - - - +
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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
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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