Contacts of the helix formed by residues 15 - 31 (chain B) in PDB entry 2BXE
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 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B PHE* 2.7 23.5 + - - -
12B LYS 3.7 4.6 + - - -
13B ASP 3.6 1.4 - - - -
14B LEU* 1.3 74.3 - - - +
16B GLU* 1.3 69.0 + - - -
17B GLU 3.2 3.8 + - - -
19B PHE* 2.9 23.5 + - - +
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Residues in contact with GLU 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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11B PHE* 3.9 31.3 - - + -
15B GLY* 1.3 70.2 - - - +
17B GLU* 1.3 68.9 + - + +
19B PHE* 3.6 2.8 - - - +
20B LYS* 2.9 41.9 + - + +
47B THR* 4.6 2.9 - - + +
51B LYS* 2.9 36.0 + - - -
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Residues in contact with GLU 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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15B GLY 3.2 1.2 + - - -
16B GLU* 1.3 76.5 - - + +
18B ASN* 1.3 73.7 + - - +
20B LYS* 2.8 20.8 + - + +
21B ALA* 3.0 12.5 + - - +
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Residues in contact with ASN 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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14B LEU* 3.5 35.3 + - + +
15B GLY 3.6 1.2 + - - -
17B GLU* 1.3 82.3 - - - +
19B PHE* 1.3 55.9 + - - +
21B ALA* 3.3 4.2 + - - +
22B LEU* 2.8 37.4 + - + +
155B LEU* 3.8 27.4 - - + +
283B LEU* 5.4 10.9 - - - +
284B LEU* 5.0 15.8 - - - +
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Residues in contact with PHE 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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7B VAL* 4.2 16.6 - - + -
10B ARG* 4.2 6.1 - - + -
11B PHE* 3.7 42.0 - + + -
14B LEU* 4.2 9.8 - - + +
15B GLY 2.9 23.4 + - - +
16B GLU* 3.6 5.2 - - - +
17B GLU 2.9 0.2 + - - -
18B ASN* 1.3 77.1 - - - +
20B LYS* 1.3 67.2 + - - +
22B LEU* 4.0 4.1 - - - +
23B VAL* 3.0 48.3 + - + +
46B VAL* 4.5 11.0 - - + -
47B THR* 4.2 23.3 - - + -
50B ALA* 4.0 22.7 - - + -
70B PHE* 5.4 2.0 - + - -
251B LEU* 4.2 23.6 - - + -
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Residues in contact with LYS 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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16B GLU* 2.9 32.8 + - + +
17B GLU* 2.8 15.3 + - - +
19B PHE* 1.3 75.4 - - - +
21B ALA* 1.3 61.1 + - - +
23B VAL 3.4 1.0 + - - -
24B LEU* 3.1 23.4 + - - +
43B VAL* 3.6 18.3 - - + +
44B ASN* 2.6 32.2 + - - +
47B THR* 3.8 30.7 - - + +
136B LYS* 3.9 24.2 - - - +
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Residues in contact with ALA 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 GLU 3.0 10.9 + - - +
18B ASN* 3.5 9.2 - - - +
20B LYS* 1.3 76.4 - - - +
22B LEU* 1.3 63.5 + - - +
24B LEU* 3.0 15.5 + - - +
25B ILE* 3.1 19.6 + - - +
139B LEU* 3.9 17.5 - - + -
155B LEU* 3.3 28.5 - - + -
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Residues in contact with LEU 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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14B LEU* 4.3 14.6 - - + -
18B ASN 2.8 22.7 + - - +
19B PHE 4.1 0.4 - - - +
21B ALA* 1.3 74.0 - - - +
23B VAL* 1.3 63.0 + - - +
25B ILE* 3.5 8.7 + - + +
26B ALA* 3.1 23.4 + - - +
151B ALA* 3.8 32.1 - - + -
152B PRO* 4.5 0.4 - - + -
155B LEU* 4.0 25.6 - - + -
250B LEU* 4.1 12.3 - - + +
251B LEU* 3.6 28.3 - - + -
254B ALA* 3.3 33.7 - - + -
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Residues in contact with VAL 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 PHE* 3.0 45.3 + - + +
20B LYS 3.8 3.6 - - - +
21B ALA 3.2 0.4 - - - -
22B LEU* 1.3 74.7 - - - +
24B LEU* 1.3 62.7 + - - +
26B ALA* 3.5 3.9 + - - -
27B PHE* 2.7 58.3 + - + -
43B VAL* 4.2 17.9 - - + -
46B VAL* 4.5 11.4 - - + -
70B PHE* 3.9 18.8 - - + -
251B LEU* 4.2 11.2 - - + -
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Residues in contact with LEU 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 LYS 3.1 13.1 + - - +
21B ALA* 3.0 9.8 + - - +
23B VAL* 1.3 77.6 - - - +
25B ILE* 1.3 52.8 + - - +
27B PHE* 3.1 5.6 + - - +
28B ALA* 2.8 34.4 + - + +
36B PHE* 4.8 1.1 - - + -
39B HIS* 4.3 18.4 - - + -
40B VAL* 4.4 12.1 - - + +
43B VAL* 3.5 28.7 - - + +
136B LYS* 3.3 45.3 - - + +
139B LEU* 4.3 17.3 - - + -
140B TYR* 4.3 14.1 - - + +
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Residues in contact with ILE 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 ALA 3.1 16.2 + - - +
22B LEU* 3.7 13.5 - - + +
24B LEU* 1.3 74.3 - - - +
26B ALA* 1.3 65.2 + - - +
28B ALA* 3.2 1.4 + - - +
29B GLN* 3.0 46.9 + - - +
139B LEU* 4.3 21.3 - - + -
143B ALA* 3.8 21.1 - - + -
149B PHE 5.5 0.4 - - - +
151B ALA* 4.7 11.7 - - + +
154B LEU* 3.9 32.5 - - + -
155B LEU* 4.2 22.0 - - + -
250B LEU* 4.0 7.9 - - + -
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Residues in contact with ALA 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 LEU 3.1 14.5 + - - +
23B VAL* 3.7 8.3 - - - +
24B LEU 3.2 0.2 - - - -
25B ILE* 1.3 75.9 - - - +
27B PHE* 1.3 69.9 + - + +
29B GLN* 3.2 5.6 + - - +
30B TYR* 3.1 33.9 + - + +
70B PHE* 5.2 8.1 - - + -
248B GLY 4.9 5.2 - - - +
250B LEU* 3.4 28.7 - - + +
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Residues in contact with PHE 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 VAL* 2.7 36.3 - - + +
24B LEU* 3.1 8.7 + - - +
26B ALA* 1.3 75.3 - - + +
28B ALA* 1.3 66.3 + - - +
29B GLN 3.0 1.6 - - - -
30B TYR* 3.1 4.3 + + - +
31B LEU* 3.0 28.4 + - - +
39B HIS* 5.1 16.4 - - + -
42B LEU* 4.0 30.1 - - + -
43B VAL* 5.1 3.6 - - + -
46B VAL* 4.3 13.7 - - + -
70B PHE* 3.3 45.3 - + + -
73B LYS* 4.3 7.9 - - + -
74B LEU* 3.1 38.3 - - + +
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Residues in contact with ALA 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 LEU* 2.8 21.2 + - + +
25B ILE* 3.2 1.5 + - - +
27B PHE* 1.3 72.4 - - - +
29B GLN* 1.3 60.8 + - - +
31B LEU 4.9 2.9 - - - -
32B GLN* 3.5 9.6 - - - -
39B HIS* 5.7 2.4 - - - +
140B TYR* 4.0 35.2 - - + +
143B ALA* 3.4 26.5 - - + -
144B ARG* 3.1 26.1 - - + +
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Residues in contact with GLN 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 ILE* 3.0 28.6 + - - +
26B ALA* 3.7 4.4 - - - +
27B PHE 3.0 0.4 - - - -
28B ALA* 1.3 79.6 - - - +
30B TYR* 1.3 64.0 + - + +
31B LEU 3.4 0.4 - - - -
32B GLN* 3.9 14.0 - - - +
106B LYS* 3.8 28.9 + - - +
143B ALA* 3.0 21.6 + - + +
146B HIS 2.9 25.7 + - - -
147B PRO* 3.3 25.6 - - + +
148B TYR 3.6 1.6 - - - +
149B PHE* 3.7 19.0 + - - +
250B LEU* 3.7 23.7 - - - +
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Residues in contact with TYR 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 ALA* 3.1 23.9 + - + +
27B PHE* 3.1 4.4 + + - +
29B GLN* 1.3 85.0 - - + +
31B LEU* 1.3 59.6 + - - +
32B GLN* 3.8 0.8 + - - -
67B HIS* 4.6 5.8 - - - -
70B PHE* 5.8 7.0 - - + -
74B LEU* 3.6 32.8 - - + -
99B ASN* 3.0 31.4 + - - -
102B PHE* 4.2 41.2 - + + +
103B LEU* 3.4 29.6 - - + +
105B HIS* 6.0 2.3 - - - +
106B LYS* 4.2 12.9 - - - -
247B HIS 4.0 6.2 + - - -
248B GLY* 4.0 16.2 + - - -
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Residues in contact with LEU 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 PHE 3.0 15.9 + - - +
28B ALA* 4.0 2.8 - - - +
30B TYR* 1.3 80.8 - - + +
32B GLN* 1.3 62.7 + - - +
33B GLN 3.2 4.8 + - - -
34B CYS* 3.4 33.5 + - + +
74B LEU* 4.9 13.9 - - + -
102B PHE* 6.4 1.6 - - + -
140B TYR* 5.5 2.6 - - - -
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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