Contacts of the helix formed by residues 22 - 34 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A SER 4.4 1.8 - - - +
21A ASP* 1.3 77.2 - - - +
23A ILE* 1.3 66.7 + - - +
24A GLU* 3.6 5.3 + - - +
25A ASN* 3.0 46.9 + - - +
26A VAL* 3.0 13.6 + - - +
57A ASP 3.7 8.3 - - - -
58A GLY* 4.3 11.2 - - - +
59A ARG 3.3 12.8 - - - +
60A THR* 4.0 12.6 - - + +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 1.3 71.8 - - - +
24A GLU* 1.3 58.6 + - - +
26A VAL* 3.1 6.5 + - + +
27A LYS* 2.9 35.3 + - + +
48A LEU* 4.2 17.7 - - + +
55A LEU* 3.8 41.3 - - + +
56A GLU 3.3 24.9 - - - +
57A ASP* 3.2 10.7 + - - +
59A ARG 2.9 16.2 + - - +
61A LEU* 3.7 33.0 - - + +
64A TYR* 4.1 13.2 - - + -
72A LEU* 5.2 1.6 - - + -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.8 6.5 - - - +
23A ILE* 1.3 77.8 - - - +
25A ASN* 1.3 64.2 + - - +
27A LYS* 3.4 14.0 + - - +
28A ALA* 3.2 21.3 + - - +
43A PRO* 5.3 5.5 - - - +
57A ASP* 2.7 32.7 + - + +
58A GLY* 5.5 0.4 - - - -
306A CD 2.3 30.8 - - - -
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 3.0 30.2 + - - +
22A THR* 3.0 33.0 + - - +
24A GLU* 1.3 77.0 - - - +
26A VAL* 1.3 61.6 + - - +
28A ALA* 3.4 7.7 + - - +
29A LYS* 3.3 30.6 + - - +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.4 9.2 - - + -
5A VAL* 4.9 0.2 - - + -
15A LEU* 3.9 12.6 - - + -
17A VAL* 4.1 14.8 - - + -
21A ASP* 4.5 4.7 - - + -
22A THR 3.0 15.0 + - - +
23A ILE* 3.1 10.5 + - - +
25A ASN* 1.3 73.4 - - - +
27A LYS* 1.3 64.4 + - - +
29A LYS* 3.1 10.8 + - - +
30A ILE* 3.0 29.6 + - + +
48A LEU* 3.8 19.7 - - + -
61A LEU* 4.1 33.2 - - + -
72A LEU* 4.5 5.6 - - + -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 2.9 27.3 + - + +
24A GLU* 3.7 14.4 - - - +
26A VAL* 1.3 76.3 - - - +
28A ALA* 1.3 56.7 + - - +
30A ILE* 3.4 9.8 + - + +
31A GLN* 3.0 27.5 + - - +
43A PRO* 2.8 26.9 + - + -
46A GLN* 2.4 40.2 + - - +
47A ARG* 4.5 1.0 - - - +
48A LEU* 3.6 24.0 - - + +
57A ASP* 3.5 20.1 + - - +
74A LEU* 5.1 4.9 - - + -
77A ARG* 3.3 11.9 - - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU 3.2 12.8 + - - +
25A ASN* 3.7 10.5 - - - +
26A VAL 3.3 0.2 - - - -
27A LYS* 1.3 72.2 - - - +
29A LYS* 1.3 66.4 + - + +
31A GLN* 3.3 7.7 + - - +
32A ASP* 3.2 29.6 + - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.9 20.0 - - + -
16A GLU 3.4 26.9 + - - +
17A VAL* 4.2 13.2 - - + -
21A ASP* 4.3 17.3 - - - -
25A ASN* 3.3 19.5 + - - +
26A VAL* 3.1 9.8 + - - +
28A ALA* 1.3 76.2 - - + +
30A ILE* 1.3 65.1 + - - +
32A ASP* 3.2 17.5 + - - +
33A LYS* 3.2 17.8 + - - +
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.8 29.6 - - + -
7A THR* 5.2 1.1 - - + -
13A ILE* 3.8 22.7 - - + -
15A LEU* 3.7 15.7 - - + +
26A VAL* 3.0 20.9 + - + +
27A LYS* 3.6 9.6 - - - +
29A LYS* 1.3 77.8 - - - +
31A GLN* 1.3 62.9 + - - +
33A LYS* 3.1 2.8 + - - +
34A GLU* 3.0 40.3 + - - +
46A GLN* 5.8 0.2 - - - +
48A LEU* 3.8 30.3 - - + -
74A LEU* 3.9 20.0 - - + -
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS 3.0 14.4 + - - +
28A ALA* 3.6 11.2 - - - +
29A LYS 3.2 0.4 - - - -
30A ILE* 1.3 77.9 - - - +
32A ASP* 1.3 66.1 + - - +
34A GLU* 3.4 35.2 + - + +
38A ALA 5.4 3.5 - - - +
39A LEU* 6.1 7.7 - - + +
41A ILE 4.5 12.3 - - - +
43A PRO* 4.8 17.0 - - - +
46A GLN* 4.8 5.4 - - - +
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.2 11.8 + - - +
29A LYS* 3.2 10.7 + - - +
30A ILE 3.2 0.8 - - - -
31A GLN* 1.3 80.2 - - - +
33A LYS* 1.3 60.5 + - + +
34A GLU 4.0 4.3 - - - +
313A CD 2.2 31.5 - - - -
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.0 27.8 - - + +
14A THR* 3.3 27.1 + - - +
15A LEU* 4.0 16.2 - - + +
29A LYS 3.2 12.7 + - - +
30A ILE 3.1 7.4 + - - +
32A ASP* 1.3 76.1 - - + +
34A GLU* 1.3 65.1 + - - +
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A THR* 4.7 17.0 - - + +
13A ILE* 5.5 2.9 - - + -
30A ILE* 3.0 32.3 + - + +
31A GLN* 3.5 34.4 - - + +
32A ASP 3.4 4.6 - - - +
33A LYS* 1.3 82.4 - - - +
35A GLY* 1.3 64.8 + - - +
38A ALA* 3.5 31.5 - - + +
39A LEU* 6.1 0.3 - - - +
41A ILE 5.7 0.2 - - - +
46A GLN* 3.7 19.9 + - - +
74A LEU* 3.8 12.0 - - - +
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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