Contacts of the helix formed by residues 22 - 34 (chain C) in PDB entry 2GBR
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 THR 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B SER* 2.5 42.0 + - - +
60B THR* 6.3 0.4 - - + -
20C SER 3.3 2.9 + - - +
21C ASP* 1.3 78.0 - - - +
23C ILE* 1.3 65.1 + - - +
24C GLU 3.8 0.2 + - - -
25C ASN* 3.1 19.4 + - - +
26C VAL* 3.0 20.8 + - - +
57C ASP 3.7 8.7 - - - +
58C GLY* 4.4 11.2 - - - +
59C ARG 3.2 13.0 - - - +
60C THR* 4.0 12.6 - - + +
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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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22C THR* 1.3 73.3 - - - +
24C GLU* 1.3 52.4 + - - +
26C VAL* 3.1 6.8 + - + +
27C LYS* 2.7 58.7 + - - +
48C LEU* 3.8 14.4 - - + -
55C LEU* 3.9 40.4 - - + +
56C GLU 3.3 24.2 - - - +
57C ASP* 3.4 3.3 + - - +
59C ARG 2.9 16.1 + - - +
61C LEU* 4.0 26.0 - - + +
64C TYR* 4.1 15.0 - - + -
72C LEU* 5.6 0.7 - - + -
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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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19B PRO* 3.6 28.7 - - + +
20B SER* 3.9 10.8 - - - +
62B SER* 4.6 12.3 + - - +
22C THR 3.2 0.4 - - - -
23C ILE* 1.3 75.6 - - - +
25C ASN* 1.3 55.7 + - - +
27C LYS* 3.3 13.7 + - - +
28C ALA* 3.0 28.9 + - - +
31C GLN* 4.9 5.0 + - - +
57C ASP* 3.0 42.7 + - + +
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Residues in contact with ASN 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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18B GLU* 3.4 26.5 + - - +
19B PRO* 3.2 16.7 - - - +
20B SER* 3.0 34.6 + - - +
21C ASP* 2.9 29.1 + - - +
22C THR* 3.1 30.6 + - - +
24C GLU* 1.3 73.2 - - - +
26C VAL* 1.3 65.9 + - - +
28C ALA* 3.6 3.5 + - - +
29C LYS* 3.4 27.3 + - - +
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 4.3 9.6 - - + -
5C VAL* 5.0 0.2 - - + -
15C LEU* 4.0 17.9 - - + -
17C VAL* 3.9 23.8 - - + -
21C ASP* 4.4 3.4 - - + -
22C THR 3.0 14.1 + - - +
23C ILE* 3.1 9.6 + - + +
25C ASN* 1.3 77.8 - - - +
27C LYS* 1.3 62.1 + - - +
29C LYS* 3.1 10.5 + - - +
30C ILE* 3.0 25.7 + - + +
48C LEU* 4.2 18.2 - - + -
61C LEU* 4.1 24.5 - - + -
72C LEU* 4.4 7.6 - - + -
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Residues in contact with LYS 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* 2.7 35.4 + - - +
24C GLU* 3.6 13.2 - - - +
25C ASN 3.3 0.2 - - - -
26C VAL* 1.3 72.9 - - - +
28C ALA* 1.3 63.4 + - - +
30C ILE* 3.3 11.4 + - + +
31C GLN* 3.0 38.1 + - - +
43C PRO 5.5 7.5 + - - +
44C ASP* 5.7 4.2 + - - +
46C GLN 5.5 4.6 + - - -
47C ARG* 5.9 1.0 - - - +
48C LEU* 3.8 26.7 - - + +
55C LEU 4.4 8.4 + - - -
57C ASP* 2.2 42.9 + - - +
74C LEU* 6.5 0.2 - - + -
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Residues in contact with ALA 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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1B MET 6.0 3.6 - - - +
19B PRO* 4.2 20.9 - - + -
24C GLU* 3.0 17.4 + - - +
25C ASN 3.7 8.7 - - - +
27C LYS* 1.3 76.7 - - - +
29C LYS* 1.3 57.1 + - + +
31C GLN* 3.4 16.7 + - - +
32C ASP* 3.1 32.5 + - - +
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Residues in contact with LYS 29 (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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18B GLU* 3.5 26.5 + - - -
303B CD 3.9 9.7 - - - -
15C LEU* 3.9 20.6 - - + -
16C GLU 3.3 25.6 + - - +
17C VAL* 4.1 13.2 - - + +
21C ASP* 4.2 6.7 - - - -
25C ASN 3.4 12.8 + - - +
26C VAL* 3.1 9.4 + - - +
28C ALA* 1.3 74.4 - - + +
30C ILE* 1.3 68.1 + - - +
32C ASP* 3.2 11.5 + - - +
33C LYS* 3.1 25.6 + - - +
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Residues in contact with ILE 30 (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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5C VAL* 3.8 27.1 - - + -
7C THR* 6.1 2.0 - - + -
13C ILE* 4.1 15.9 - - + -
15C LEU* 3.9 14.8 - - + +
26C VAL* 3.0 19.8 + - + +
27C LYS* 3.5 9.9 - - + +
29C LYS* 1.3 75.3 - - - +
31C GLN* 1.3 58.7 + - + +
33C LYS* 2.9 21.1 + - - +
34C GLU* 3.0 37.5 + - + +
48C LEU* 3.8 33.9 - - + -
74C LEU* 3.9 17.0 - - + -
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Residues in contact with GLN 31 (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 GLU* 4.9 5.1 + - - +
27C LYS* 3.0 34.2 + - - +
28C ALA* 3.4 14.2 - - - +
29C LYS 3.3 0.2 - - - -
30C ILE* 1.3 76.0 - - + +
32C ASP* 1.3 63.6 + - - +
34C GLU* 3.6 23.4 + - - +
39C LEU* 3.4 28.8 - - + +
43C PRO* 4.1 32.5 + - + +
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Residues in contact with ASP 32 (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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1B MET 5.9 1.4 + - - -
28C ALA* 3.1 18.8 + - - +
29C LYS* 3.2 13.7 + - - +
31C GLN* 1.3 77.7 - - - +
33C LYS* 1.3 61.5 + - + +
34C GLU 3.6 4.2 + - - +
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Residues in contact with LYS 33 (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 LYS* 5.5 4.3 + - - -
13C ILE* 3.4 38.1 - - + +
14C THR 3.7 21.8 + - - +
15C LEU* 4.0 7.6 - - + -
29C LYS 3.1 13.5 + - - +
30C ILE 2.9 3.8 + - - +
32C ASP* 1.3 78.5 - - + +
34C GLU* 1.3 62.7 + - - +
35C GLY 3.9 0.7 + - - -
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C THR* 5.6 9.3 - - + +
8C LEU* 4.8 0.2 - - - +
13C ILE* 5.8 2.2 - - + -
30C ILE* 3.0 27.4 + - + +
31C GLN* 3.7 27.2 - - - +
32C ASP 3.3 5.2 - - - +
33C LYS* 1.3 78.8 - - + +
35C GLY* 1.3 68.6 + - - +
38C ALA* 3.4 35.2 - - + +
39C LEU* 4.2 14.2 - - + +
46C GLN* 4.4 5.9 - - - +
74C LEU* 3.6 25.5 - - - +
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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