Contacts of the helix formed by residues 12 - 25 (chain C) in PDB entry 6BZE
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 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 GLU* 2.8 47.3 + - + +
11C GLU* 1.3 79.0 - - - +
13C LEU* 1.3 65.8 + - - +
14C THR* 3.2 4.0 - - - -
15C GLU* 3.0 26.6 + - - +
16C VAL* 3.6 7.6 - - - +
113C HIS* 4.1 26.2 - - + +
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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
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10C GLU* 5.5 7.1 + - - +
11C GLU* 4.8 18.6 - - - +
12C ASP* 1.3 79.1 - - - +
14C THR* 1.3 80.4 + - + +
15C GLU 2.9 6.8 + - - -
16C VAL* 3.0 23.0 + - + +
17C LYS* 2.5 44.8 + - - +
76C PRO 5.3 1.6 - - - +
110C LYS* 5.3 12.1 - - + -
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Residues in contact with THR 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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11C GLU* 3.5 30.7 - - - +
13C LEU* 1.3 84.5 - - - +
15C GLU* 1.3 80.6 + - + +
17C LYS* 3.6 24.7 - - - +
18C LYS* 4.0 8.8 - - - +
73C GLN 4.7 2.9 + - - +
74C GLU 4.8 2.6 + - - -
75C ASN 4.1 3.5 + - - +
76C PRO* 3.3 37.2 + - + +
94G PHE* 4.8 4.9 - - + -
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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 GLU 5.1 0.9 - - - +
12C ASP* 3.3 16.4 - - + +
13C LEU 2.9 0.2 - - - -
14C THR* 1.3 95.0 + - + +
16C VAL* 1.3 60.5 + - + +
17C LYS 3.0 2.0 - - - -
18C LYS* 2.3 63.3 + - - +
19C ASP* 3.5 4.6 + - - -
73C GLN 5.4 0.9 - - - +
27G TYR* 5.5 3.0 + - - -
30G GLU* 5.4 3.3 - - - +
94G PHE* 5.7 5.5 - - - -
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Residues in contact with VAL 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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12C ASP 3.6 14.4 - - - +
13C LEU* 3.0 17.0 + - + +
15C GLU* 1.3 74.3 - - + +
17C LYS* 1.3 59.7 + - - +
19C ASP* 3.1 15.8 + - - +
20C ALA* 2.7 35.6 + - - +
106C LEU* 3.6 20.0 - - + -
109C ILE* 3.6 21.0 - - + +
110C LYS* 4.0 14.1 - - + -
113C HIS* 4.1 27.8 - - + +
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Residues in contact with LYS 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* 2.5 65.3 + - - +
14C THR* 3.6 17.7 - - - +
15C GLU 3.0 0.2 - - - -
16C VAL* 1.3 79.2 - - - +
18C LYS* 1.3 52.1 + - + +
20C ALA* 3.3 8.5 - - - +
21C LEU* 2.5 38.2 + - - +
76C PRO 3.9 11.9 - - - +
77C LYS 4.2 15.3 - - - +
78C GLY* 5.0 11.2 - - - +
79C LEU* 4.8 5.8 - - - -
106C LEU* 3.5 35.1 - - + +
110C LYS* 5.8 1.0 - - - +
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Residues in contact with LYS 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 THR 4.0 5.8 - - - +
15C GLU* 2.3 75.8 + - - +
17C LYS* 1.3 74.6 - - + +
19C ASP* 1.3 55.3 + - - +
21C LEU* 2.8 9.0 + - - +
22C GLU* 2.3 45.5 + - + +
73C GLN* 3.5 51.6 - - + +
30G GLU* 5.6 5.8 - - - +
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Residues in contact with ASP 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 3.5 3.7 + - - +
16C VAL* 3.1 23.4 + - - +
18C LYS* 1.3 80.4 + - - +
20C ALA* 1.3 51.3 + - - +
22C GLU* 2.7 12.5 + - - +
23C ASN* 2.4 50.8 + - - +
109C ILE* 3.9 15.4 - - + +
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Residues in contact with ALA 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 VAL 2.7 15.6 + - - +
17C LYS* 3.3 12.3 - - - +
19C ASP* 1.3 72.2 - - - +
21C LEU* 1.3 51.3 + - - +
23C ASN* 3.2 12.2 + - - +
24C LEU* 2.6 36.7 + - - +
102C GLU* 4.9 3.8 - - + +
105C LYS* 3.7 10.3 - - + +
106C LEU* 3.5 37.5 - - + +
109C ILE* 4.4 1.7 - - + +
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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 LYS 2.5 21.5 + - - +
18C LYS* 3.1 9.6 - - - +
20C ALA* 1.3 72.0 - - - +
22C GLU* 1.3 54.7 + - - +
24C LEU* 3.1 12.6 - - + +
25C ARG* 2.4 39.6 + - - +
69C LEU* 3.7 41.5 - - + +
72C LEU* 4.7 8.5 - - + -
73C GLN* 3.5 37.0 - - + +
102C GLU* 4.7 13.0 - - + +
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Residues in contact with GLU 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 LYS* 2.3 40.4 + - + +
19C ASP* 2.7 15.0 + - - +
21C LEU* 1.3 68.8 - - - +
23C ASN* 1.3 62.7 + - - +
25C ARG* 3.6 23.6 - - - +
26C VAL* 4.8 4.0 + - - +
73C GLN* 2.2 36.4 + - - +
44F LYS* 3.3 34.0 + - - +
45F LYS* 4.9 19.8 - - - +
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Residues in contact with ASN 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 ASP* 2.4 46.7 + - - +
20C ALA 3.4 5.8 + - - +
22C GLU* 1.3 75.3 - - - +
24C LEU* 1.3 56.8 + - - +
26C VAL* 4.3 14.1 - - - +
105C LYS* 3.5 31.0 + - - +
109C ILE* 3.1 29.4 - - - +
45F LYS* 5.0 17.2 - - - +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA 2.6 20.8 + - - +
21C LEU* 3.0 12.5 + - + +
23C ASN* 1.3 74.1 - - - +
25C ARG* 1.3 59.8 + - - +
26C VAL 3.0 3.1 - - - +
27C TYR* 2.9 51.8 + - + +
69C LEU* 4.9 4.9 - - + +
95C LEU* 5.8 4.9 - - + -
98C LYS 4.9 0.9 - - - +
101C ASP* 3.8 13.2 - - - +
102C GLU* 3.4 45.5 - - + +
105C LYS* 3.7 26.5 - - + -
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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 LEU* 2.4 25.9 + - - +
22C GLU* 3.6 28.9 - - - +
23C ASN 3.4 0.4 - - - -
24C LEU* 1.3 70.0 - - - +
26C VAL* 1.3 61.9 + - + +
27C TYR 3.3 0.9 + - - -
28C LEU* 3.3 14.8 + - + +
66C GLY* 3.5 37.0 + - - -
69C LEU* 4.9 14.5 - - - +
70C ASP* 4.6 10.9 + - - +
73C GLN* 5.0 2.5 - - - +
40F HIS* 5.2 4.6 + - - +
41F LEU* 3.1 49.7 + - + +
44F LYS* 3.0 48.4 - - + +
49F ARG* 5.2 1.4 - - - +
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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