Contacts of the helix formed by residues 9 - 27 (chain B) in PDB entry 2Q33
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 GLY 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B DAS 2.9 18.6 + - - -
8B DIL 1.3 80.8 + - - +
10B DPR 1.3 76.5 + - - +
11B DPN 3.2 3.6 - - - -
12B DTH 3.0 14.3 + - - -
13B DGN 3.0 13.7 + - - +
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Residues in contact with DPR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY* 1.3 83.5 - - - +
11B DPN 1.3 63.8 + - - +
13B DGN 3.8 9.9 - - - +
14B DSG 3.0 23.2 + - - +
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Residues in contact with DPN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A DTY 3.7 26.5 - + - -
75A DGL 4.2 4.3 - - - -
82A DAR 3.3 29.6 + - - -
6B DIL 5.7 4.0 - - + -
9B GLY 3.2 1.2 - - - -
10B DPR 1.3 77.4 + - - +
12B DTH 1.3 68.8 + - - +
14B DSG 3.1 10.2 + - + +
15B DLE 3.1 43.3 + - + +
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Residues in contact with DTH 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A DLE 4.3 4.0 - - + +
6B DIL 4.6 7.1 - - - +
7B DAS 2.9 20.6 + - - -
8B DIL 3.6 16.5 - - + -
9B GLY 3.0 10.2 + - - -
11B DPN 1.3 78.9 + - - +
13B DGN 1.3 66.9 + - - +
15B DLE 3.0 21.2 + - + +
16B GLY 3.1 9.2 + - - -
37B DVA 3.5 28.8 - - + +
41B DCY 3.7 26.0 - - + -
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Residues in contact with DGN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B DIL 3.2 25.3 + - - +
9B GLY 3.0 18.3 + - - +
10B DPR 3.3 10.1 + - - +
12B DTH 1.3 75.6 + - - +
14B DSG 1.3 62.9 + - - +
16B GLY 3.1 2.4 + - - -
17B DLY 3.0 20.1 + - - +
34B DPN 3.5 16.8 - - + -
36B DLY 3.5 14.3 - - - +
37B DVA 2.9 50.9 + - - +
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Residues in contact with DSG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A DAR 3.7 17.9 + - - +
10B DPR 3.0 13.6 + - - +
11B DPN 3.3 13.5 - - + +
12B DTH 3.1 0.2 - - - -
13B DGN 1.3 78.9 + - - +
15B DLE 1.3 56.7 + - - +
17B DLY 3.3 12.4 + - - +
18B DPN 3.0 27.4 + - - +
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Residues in contact with DLE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A DTY 3.7 44.9 - - + -
60A DLE 3.8 17.3 - - + -
73A DIL 3.2 26.3 - - + +
82A DAR 3.6 34.5 - - - +
6B DIL 5.7 0.4 - - + -
11B DPN 3.1 37.1 + - + +
12B DTH 3.0 16.4 + - + +
14B DSG 1.3 76.7 + - - +
16B GLY* 1.3 57.2 + - - +
18B DPN 3.3 4.9 + - + +
19B DAL 3.0 23.0 + - - -
41B DCY 5.3 0.9 - - - -
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Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A DLE 3.7 9.8 - - - +
62A DVA 4.3 3.7 - - - +
12B DTH 3.1 10.5 + - - -
13B DGN 3.1 4.6 + - - -
15B DLE 1.3 74.5 + - - +
17B DLY 1.3 62.8 + - - +
19B DAL 3.3 5.1 + - - +
20B DVA 3.0 28.2 + - - +
34B DPN 3.6 9.4 - - - -
37B DVA 3.5 20.2 - - - -
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Residues in contact with DLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B DGN 3.0 12.3 + - - +
14B DSG 3.3 17.0 + - - +
16B GLY* 1.3 72.3 + - - +
18B DPN 1.3 67.3 + - - +
20B DVA 3.3 19.5 + - - +
21B DAS 2.9 42.8 + - - +
34B DPN 3.6 32.2 + - + +
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Residues in contact with DPN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A DIL 3.9 26.9 - - + -
82A DAR 3.6 56.1 - - + +
83A DLY 3.9 15.5 - - - -
84A DLE 4.1 2.5 - - + -
14B DSG 3.0 14.6 + - - +
15B DLE 3.4 11.2 - - - +
17B DLY 1.3 78.6 + - - +
19B DAL 1.3 63.5 + - - +
21B DAS 3.3 8.6 + - + +
22B DGL 3.0 57.2 + - + +
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Residues in contact with DAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A DVA 4.8 2.7 - - + -
71A DAL 3.9 16.4 - - + -
73A DIL 3.7 15.9 - - + -
84A DLE 3.9 23.9 - - + +
87A DPN 3.9 7.1 - - + -
15B DLE 3.0 14.0 + - - +
16B GLY* 3.5 11.7 - - - +
17B DLY 3.2 0.2 - - - -
18B DPN 1.3 78.3 + - - +
20B DVA 1.3 57.1 + - - +
22B DGL 3.4 2.4 + - - +
23B DGL 2.9 29.6 + - - +
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Residues in contact with DVA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A DVA 3.9 15.0 - - + -
64A DAL 4.0 12.8 - - + -
87A DPN 4.4 6.5 - - + -
16B GLY 3.0 14.5 + - - +
17B DLY 3.3 19.0 + - - +
19B DAL 1.3 75.3 + - - +
21B DAS 1.3 58.4 + - - +
23B DGL 3.2 6.4 + - - +
24B DSG 2.9 45.7 + - - +
32B DLE 4.0 15.7 - - + +
34B DPN 3.8 34.1 - - + +
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Residues in contact with DAS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B DLY 2.9 52.3 + - - +
18B DPN 3.6 8.9 - - + +
20B DVA 1.3 79.4 + - - +
22B DGL 1.3 65.6 + - + +
24B DSG 3.4 18.1 + - - +
25B DLY 3.5 21.2 + - - +
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Residues in contact with DGL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A DLE 3.7 27.4 + - + +
18B DPN 3.0 54.9 + - + +
19B DAL 3.8 0.7 - - - +
21B DAS 1.3 75.1 + - - +
23B DGL 1.3 66.1 + - - +
25B DLY 2.8 55.2 + - - +
26B DIL 3.5 12.4 + - + +
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Residues in contact with DGL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A DLE 3.8 3.1 - - + +
87A DPN 3.2 54.9 - - + +
19B DAL 2.9 19.0 + - - +
20B DVA 3.6 4.9 - - - +
22B DGL 1.3 78.1 + - - +
24B DSG 1.3 55.8 + - - +
26B DIL 2.9 21.4 + - - +
27B GLY* 2.8 25.1 + - - -
28B DGN 3.4 31.7 + - - +
29B DTY 3.5 11.0 - - + +
30B GLY 5.2 1.1 - - - +
32B DLE 4.0 13.5 - - + -
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Residues in contact with DSG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B DVA 2.9 26.3 + - - +
21B DAS 3.7 12.8 + - - +
22B DGL 3.2 0.2 - - - -
23B DGL 1.3 77.5 + - - +
25B DLY 1.3 59.9 + - - +
26B DIL 3.6 0.2 + - - -
27B GLY* 3.6 10.5 + - - -
30B GLY 3.5 11.2 - - - +
31B DAR 3.7 10.3 - - + +
32B DLE 2.8 51.8 + - - +
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Residues in contact with DLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B DAS 3.5 17.9 - - - +
22B DGL 2.8 42.9 + - - +
23B DGL 3.1 0.4 - - - -
24B DSG 1.3 77.8 + - + +
26B DIL 1.3 63.7 + - + +
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Residues in contact with DIL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A DLE 4.3 12.3 - - + -
22B DGL 3.6 13.2 - - - +
23B DGL 2.9 25.3 + - - +
25B DLY 1.3 83.0 + - + +
27B GLY* 1.3 60.0 + - - +
28B DGN 3.2 23.0 + - + +
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B DGL 2.8 11.9 + - - -
24B DSG 3.6 9.1 + - - -
25B DLY 3.5 1.8 - - - -
26B DIL 1.3 76.9 + - - -
28B DGN 1.3 64.5 + - - +
29B DTY 3.2 2.9 - - - -
30B GLY* 3.0 24.9 + - - -
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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