Contacts of the helix formed by residues 18 - 28 (chain C) in PDB entry 3DEG
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 SER 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ASP* 5.9 4.3 - - - -
17C LYS* 1.4 91.1 - - - +
19C THR* 1.3 56.8 + - - +
21C SER* 2.9 16.6 + - - -
22C ASP* 2.6 39.7 + - - +
37C GLU* 5.0 6.9 + - - +
41C LEU* 4.1 13.2 - - - +
42C ASP* 4.6 8.5 + - - -
53C THR* 4.4 12.0 + - - -
77C ASP* 4.7 2.8 + - - -
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Residues in contact with THR 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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14C ASP* 6.1 0.8 - - - +
16C GLY* 4.2 7.7 - - - -
17C LYS 4.4 0.8 - - - +
18C SER* 1.3 76.1 + - - +
20C LEU* 1.4 66.2 + - - +
22C ASP* 3.9 8.2 + - + +
23C ARG* 2.7 59.1 + - + +
34C ARG* 4.1 15.5 - - - +
37C GLU* 3.8 27.1 + - - +
41C LEU* 4.8 1.0 - - - +
132C LYS* 5.0 5.6 + - - +
163C ALA* 4.9 6.7 - - + +
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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 GLY 2.6 28.3 + - - +
17C LYS* 3.1 11.9 - - - +
18C SER 2.7 10.1 - - - +
19C THR* 1.4 74.3 - - - +
21C SER* 1.3 60.3 + - - +
23C ARG* 3.1 6.5 + - - +
24C ILE* 3.0 36.9 + - + +
99C LEU* 4.0 22.2 - - + -
101C VAL* 3.5 22.2 - - + -
129C VAL* 4.2 8.3 - - + -
131C ASN* 4.5 0.2 - - - +
161C CYS* 4.1 22.7 - - - -
169C VAL* 3.9 26.7 - - + -
172C VAL* 4.2 14.4 - - + -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 4.1 11.7 - - - -
17C LYS* 2.5 14.9 + - - -
18C SER* 2.9 29.6 + - - -
20C LEU* 1.3 74.5 - - - +
22C ASP* 1.3 63.0 + - - +
24C ILE* 3.7 4.9 + - - +
25C ILE* 3.4 26.6 + - - +
41C LEU* 5.3 2.4 - - - +
59C VAL* 5.6 0.2 - - - +
75C PHE* 3.2 28.6 - - - -
77C ASP* 4.8 7.0 + - - -
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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 SER 2.6 19.3 + - - +
19C THR* 3.9 10.2 + - + +
20C LEU 3.2 0.2 - - - -
21C SER* 1.3 74.2 + - - +
23C ARG* 1.3 63.5 + - - +
25C ILE* 3.1 23.4 + - - +
26C GLN* 3.2 16.3 + - - +
34C ARG* 4.3 8.5 - - - +
35C GLU* 3.2 29.7 - - - +
36C MET* 4.2 1.4 + - - -
37C GLU 4.5 0.2 + - - -
41C LEU* 2.1 61.1 - - - +
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Residues in contact with ARG 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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16C GLY* 3.2 20.1 + - - -
19C THR* 2.7 56.0 + - - +
20C LEU* 3.1 9.1 + - - +
22C ASP* 1.3 77.7 - - - +
24C ILE* 1.3 61.8 + - - +
26C GLN* 3.3 12.0 + - - +
27C ILE* 3.2 28.0 + - + +
34C ARG* 3.8 18.6 - - - +
131C ASN* 2.6 33.7 + - - +
161C CYS* 4.2 5.7 - - - -
162C SER* 3.1 32.0 + - - +
163C ALA* 3.3 17.6 - - - +
166C GLY* 5.1 7.2 - - - -
169C VAL* 4.1 22.2 - - + +
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Residues in contact with ILE 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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7C PHE* 4.8 9.4 - - + -
9C ILE* 4.0 21.8 - - + -
20C LEU* 3.0 39.9 + - + +
21C SER* 3.8 5.2 - - - +
23C ARG* 1.3 76.7 - - - +
25C ILE* 1.3 62.2 + - - +
27C ILE* 3.3 12.0 + - - +
28C CYS* 3.2 20.1 + - - -
61C LEU* 3.9 17.9 - - + -
73C LEU* 5.1 4.5 - - + -
75C PHE* 5.0 8.7 - - + -
99C LEU* 4.3 9.4 - - + -
169C VAL* 4.1 9.6 - - + -
172C VAL* 5.3 0.7 - - + -
173C LEU* 3.7 36.8 - - + -
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Residues in contact with ILE 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 SER* 3.4 22.0 - - - +
22C ASP* 3.1 17.6 + - - +
24C ILE* 1.3 77.4 - - - +
26C GLN* 1.3 57.0 + - - +
28C CYS 3.2 7.8 + - - -
29C GLY 3.5 0.2 + - - -
30C GLY 2.7 62.7 + - - +
31C LEU 4.0 2.0 - - - +
34C ARG* 6.2 0.4 - - - -
35C GLU* 5.4 10.3 - - - +
41C LEU* 5.8 3.4 - - + -
59C VAL* 4.1 28.0 - - + -
61C LEU* 4.0 20.9 - - + -
75C PHE* 4.8 2.5 - - + -
242C PRO* 4.2 17.7 - - + -
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Residues in contact with GLN 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 ASP 3.2 5.0 + - - +
23C ARG* 3.3 19.9 + - - +
25C ILE* 1.3 78.0 - - - +
27C ILE* 1.3 64.1 + - + +
28C CYS 3.2 5.9 + - - +
30C GLY* 4.1 12.4 - - - +
32C SER 5.0 2.0 - - - +
34C ARG* 2.0 96.0 + - + +
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Residues in contact with ILE 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 ARG* 3.2 13.6 + - + +
24C ILE 3.3 13.9 - - - +
26C GLN* 1.3 78.2 - - + +
28C CYS* 1.3 59.4 + - - +
63C TYR* 5.1 7.5 - - + -
166C GLY* 5.1 7.0 - - - +
169C VAL* 3.9 15.3 - - + +
170C GLN* 3.6 39.3 - - + +
173C LEU* 3.5 29.8 - - + -
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Residues in contact with CYS 28 (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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24C ILE* 3.2 14.6 + - - +
25C ILE 3.2 2.2 + - - +
26C GLN 3.9 3.5 - - - +
27C ILE* 1.3 85.0 - - - +
29C GLY* 1.3 70.8 + - - +
30C GLY 3.3 1.6 + - - -
61C LEU* 3.8 28.7 - - + -
62C ASP 4.0 11.4 - - - +
63C TYR* 4.0 20.0 - - - -
73C LEU* 4.6 1.6 - - - -
173C LEU* 3.5 32.8 - - - -
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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