Contacts of the helix formed by residues 16 - 31 (chain B) in PDB entry 2HXO
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 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B PRO 3.3 7.8 + - - -
15B LEU* 1.3 73.9 - - - +
17B ARG* 1.3 63.5 + - - +
18B GLU* 3.8 10.8 + - - +
19B ARG* 3.3 25.2 + - - +
20B ILE* 3.0 29.3 + - - +
55B HIS* 5.4 4.9 - - - -
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Residues in contact with ARG 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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16B SER* 1.3 72.7 - - - +
18B GLU* 1.3 88.0 + - - +
20B ILE* 3.0 8.0 + - - +
21B VAL* 3.0 36.6 + - + +
55B HIS 5.8 1.6 + - - -
65B ALA* 4.0 24.1 - - - +
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Residues in contact with GLU 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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16B SER* 3.6 8.7 + - - +
17B ARG* 1.3 96.3 + - - +
19B ARG* 1.3 53.7 + - - +
21B VAL* 3.9 4.9 - - - +
22B GLY* 2.6 34.3 + - - -
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Residues in contact with ARG 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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14B PRO* 3.7 29.0 + - - +
15B LEU* 3.9 15.7 - - - +
16B SER* 3.3 23.6 + - - +
17B ARG 3.1 0.6 - - - -
18B GLU* 1.3 76.2 - - - +
20B ILE* 1.3 68.4 + - + +
22B GLY* 3.7 0.8 - - - -
23B ALA* 2.9 26.3 + - - +
44B ARG 5.7 0.8 + - - -
45B LEU* 3.4 43.0 + - + +
46B ALA* 5.2 4.4 + - - +
47B THR* 4.0 3.4 + - - -
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Residues in contact with ILE 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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15B LEU* 4.1 17.3 - - + -
16B SER 3.0 18.2 - - - +
17B ARG* 3.0 8.0 + - - +
19B ARG* 1.3 77.6 - - - +
21B VAL* 1.3 66.3 + - + +
23B ALA* 3.2 3.8 + - - +
24B ALA* 3.1 19.4 + - - +
41B LEU* 3.9 7.7 - - + +
45B LEU* 3.3 30.3 - - + -
52B ILE* 4.8 2.7 - - + -
55B HIS* 4.2 19.1 - - + +
56B ILE* 3.1 36.1 - - + -
62B LEU* 3.8 19.3 - - + -
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Residues in contact with VAL 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 ARG* 3.0 32.1 + - + +
18B GLU* 3.9 5.4 - - - +
20B ILE* 1.3 76.2 - - + +
22B GLY* 1.3 67.4 + - - +
24B ALA* 3.1 7.4 + - - +
25B VAL* 3.0 25.0 + - + +
62B LEU* 4.8 6.7 - - + -
65B ALA* 3.7 39.3 - - + +
66B ALA* 3.7 13.2 - - - +
69B ALA* 3.7 19.1 - - + -
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Residues in contact with GLY 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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18B GLU 2.6 23.3 + - - -
19B ARG* 3.7 1.1 - - - -
21B VAL* 1.3 73.1 - - - +
23B ALA* 1.3 60.3 + - - +
25B VAL* 3.3 9.5 + - - +
26B GLU* 3.1 35.3 + - - +
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Residues in contact with ALA 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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19B ARG 2.9 17.3 + - - +
20B ILE 3.4 5.4 - - - +
21B VAL 3.1 0.2 - - - -
22B GLY* 1.3 77.4 - - - +
24B ALA* 1.3 61.6 + - - +
26B GLU* 3.3 12.2 + - - +
27B LEU* 3.0 29.2 + - + +
41B LEU* 3.7 17.0 - - + -
44B ARG* 4.9 14.8 - - + +
45B LEU* 4.1 15.0 - - + +
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Residues in contact with ALA 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 ILE 3.1 7.2 + - - +
21B VAL* 3.1 8.8 + - - +
23B ALA* 1.3 78.8 - - - +
25B VAL* 1.3 51.6 + - - +
27B LEU* 3.3 3.0 + - - +
28B LEU* 2.7 45.3 + - + +
36B LEU* 3.8 28.9 - - + -
41B LEU* 4.2 2.4 - - + +
62B LEU* 3.9 27.6 - - + -
66B ALA* 4.7 4.9 - - + -
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Residues in contact with VAL 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 VAL* 3.0 27.3 + - + +
22B GLY* 3.5 10.3 - - - +
24B ALA* 1.3 76.7 - - - +
26B GLU* 1.3 58.8 + - + +
28B LEU* 3.0 9.7 + - - +
29B ASP* 2.8 44.5 + - - +
66B ALA* 4.0 19.3 - - + -
69B ALA* 5.4 1.1 - - + -
70B VAL* 4.1 20.0 - - + -
104B HIS* 3.8 18.6 - - + +
106B TRP* 4.3 3.4 - - + -
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Residues in contact with GLU 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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22B GLY* 3.1 25.8 + - - +
23B ALA* 3.6 11.6 + - - +
25B VAL* 1.3 77.1 - - + +
27B LEU* 1.3 62.4 + - - +
29B ASP* 3.3 9.1 + - - +
30B THR* 3.1 29.8 + - + +
44B ARG* 4.2 22.2 + - - +
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Residues in contact with LEU 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 ALA 3.0 22.2 + - - +
24B ALA* 3.5 6.3 - - - +
26B GLU* 1.3 74.5 - - - +
28B LEU* 1.3 60.3 + - - +
30B THR* 3.1 3.5 + - - -
31B VAL* 2.7 51.9 + - + +
32B GLY 3.1 0.8 + - - -
35B GLY 4.8 0.4 - - - +
36B LEU* 3.9 22.7 - - + -
40B ALA* 4.0 19.5 - - + +
41B LEU* 3.8 32.3 - - - +
44B ARG* 3.2 44.0 - - + +
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Residues in contact with LEU 28 (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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24B ALA* 2.7 30.8 + - + +
25B VAL 3.5 4.3 - - - +
27B LEU* 1.3 73.1 - - - +
29B ASP* 1.3 62.2 + - - +
32B GLY* 3.2 35.7 + - - +
33B GLU* 3.7 18.4 - - + +
36B LEU* 4.0 12.6 - - + -
63B LEU* 3.8 24.7 - - + -
66B ALA* 3.8 27.6 - - + -
105B PRO* 5.5 0.9 - - - +
106B TRP* 3.3 50.6 - - + +
110B GLN* 6.2 0.4 - - + +
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Residues in contact with ASP 29 (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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25B VAL* 2.8 22.6 + - - +
26B GLU* 3.5 8.4 - - - +
28B LEU* 1.3 79.6 - - - +
30B THR* 1.3 63.1 + - + +
103B ALA 4.5 5.2 - - - -
104B HIS* 2.7 45.1 + - - +
105B PRO* 4.6 9.4 - - + +
106B TRP* 2.7 22.5 + - - +
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Residues in contact with THR 30 (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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26B GLU 3.1 17.2 + - - +
27B LEU* 3.3 4.5 + - - -
29B ASP* 1.3 84.2 - - + +
31B VAL* 1.3 73.3 + - - +
32B GLY 3.6 0.4 - - - -
44B ARG* 3.5 28.3 + - - +
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Residues in contact with VAL 31 (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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27B LEU* 2.7 40.6 + - + +
30B THR* 1.3 85.2 + - - +
32B GLY* 1.3 57.8 + - - +
34B ARG* 4.7 2.1 + - - +
35B GLY* 3.3 46.0 + - - +
44B ARG* 5.0 6.7 - - - +
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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