Contacts of the helix formed by residues 21 - 32 (chain B) in PDB entry 1EJD
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 ALA 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B GLY* 1.3 70.2 - - - -
22B LYS* 1.3 55.9 + - - +
23B ASN* 4.2 2.7 - - + +
24B ALA* 3.1 8.0 + - + +
25B ALA* 2.8 36.2 + - - +
190B GLU* 4.4 11.9 - - + +
228B VAL* 3.7 1.8 - - - +
229B LEU* 3.0 33.0 + - + +
230B PRO 4.0 0.7 - - - +
231B ASP* 3.6 26.7 - - - +
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Residues in contact with LYS 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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20B GLY 3.4 5.1 + - - -
21B ALA* 1.3 71.6 - - - +
23B ASN* 1.3 72.4 + - - +
25B ALA* 3.8 2.2 - - - +
26B LEU* 2.9 57.4 + - + +
45B PRO* 4.1 8.3 - - - -
47B LEU* 3.9 23.6 - - + -
49B ASP* 3.1 25.7 + - + +
50B ILE* 4.4 11.4 - - + -
231B ASP* 4.7 4.9 + - - +
370B LEU* 6.0 1.4 - - - +
397B ARG* 3.3 30.9 + - - +
398B GLY* 4.3 11.4 - - - +
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Residues in contact with ASN 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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21B ALA* 3.1 2.9 - - + +
22B LYS* 1.3 101.9 + - - +
24B ALA* 1.3 55.5 + - - +
26B LEU* 4.2 8.6 - - - +
27B PRO* 3.2 20.8 - - - +
95B TRP* 4.9 9.0 - - + -
163B VAL* 5.8 3.0 - - + +
190B GLU* 3.5 25.4 - - + +
2422B PO4 3.4 26.0 + - - -
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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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21B ALA 3.1 7.1 + - - +
23B ASN* 1.3 76.6 - - - +
25B ALA* 1.3 68.2 + - - +
26B LEU 3.3 1.6 - - - -
27B PRO* 3.3 6.3 - - - +
28B ILE* 3.2 31.2 + - - +
190B GLU* 3.9 17.2 - - + +
193B ASP* 3.8 13.7 - - + +
228B VAL* 3.9 2.9 - - + -
229B LEU* 3.3 34.8 - - + -
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Residues in contact with ALA 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 2.8 16.7 + - - +
22B LYS 3.8 3.8 - - - +
24B ALA* 1.3 78.6 - - - +
26B LEU* 1.3 56.3 + - - +
28B ILE* 3.3 2.2 + - - +
29B LEU* 2.9 35.8 + - - +
44B VAL* 4.2 10.5 - - + -
45B PRO* 4.1 15.9 - - + -
50B ILE* 3.9 19.5 - - + -
228B VAL* 3.8 19.6 - - + +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 2.9 41.8 + - + +
23B ASN* 4.2 9.0 - - - +
25B ALA* 1.3 75.8 - - - +
27B PRO* 1.3 71.9 - - + +
28B ILE 3.2 0.2 + - - -
29B LEU* 3.2 4.2 + - + +
30B PHE* 3.1 32.9 + - + -
49B ASP* 3.7 25.4 - - + +
50B ILE* 3.9 17.7 - - + -
53B THR* 3.1 30.1 - - + +
90B MET* 4.5 2.7 - - - -
92B ALA* 4.2 16.2 - - + -
95B TRP* 3.9 11.0 - - + -
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Residues in contact with PRO 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 ASN 3.2 28.3 - - - +
24B ALA 3.3 12.3 - - - +
26B LEU* 1.3 94.1 - - + +
28B ILE* 1.3 55.2 + - - -
30B PHE* 3.5 3.9 + - + +
31B ALA* 2.9 29.0 + - - +
95B TRP* 3.6 23.6 - - + -
167B VAL* 3.7 32.9 - - + +
190B GLU* 5.0 1.1 - - + +
194B THR* 3.4 23.0 - - + +
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Residues in contact with ILE 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* 3.2 22.6 + - + +
25B ALA* 3.7 3.1 - - - +
26B LEU 3.1 0.6 - - - -
27B PRO* 1.3 74.3 - - - +
29B LEU* 1.3 65.0 + - - +
31B ALA* 3.2 6.9 + - - +
32B ALA* 2.9 20.6 + - - +
41B ILE* 3.7 38.4 - - + -
193B ASP* 3.6 36.8 - - - +
194B THR* 4.1 13.2 - - - +
197B PHE* 3.6 27.5 - - + -
226B TYR* 4.1 12.6 - - + -
228B VAL* 4.2 9.0 - - + -
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Residues in contact with LEU 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 ALA* 2.9 24.5 + - + +
26B LEU* 3.8 4.9 - - - +
28B ILE* 1.3 75.8 - - - +
30B PHE* 1.3 62.5 + - - +
32B ALA* 3.3 18.8 - - - +
33B LEU* 4.1 1.6 + - - +
41B ILE* 4.3 15.3 - - + -
44B VAL* 4.5 5.4 - - + -
50B ILE* 4.0 35.7 - - + +
53B THR* 3.9 24.9 - - + -
54B MET* 5.5 2.5 - - + -
57B LEU* 3.9 18.0 - - + +
70B VAL* 3.9 25.1 - - + -
72B ILE* 3.6 22.7 - - + -
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Residues in contact with PHE 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 LEU* 3.1 28.2 + - + +
27B PRO 4.0 2.9 - - - +
29B LEU* 1.3 73.5 - - - +
31B ALA* 1.3 64.1 + - - +
32B ALA 3.1 1.8 - - - -
33B LEU* 3.0 26.0 + - + +
53B THR* 3.8 33.9 - - + -
56B LEU* 4.0 24.2 - - + -
57B LEU* 4.3 10.1 - - + -
90B MET* 3.9 14.4 - - + -
92B ALA* 3.5 22.7 - - + -
93B SER* 4.0 1.3 - - - -
95B TRP* 3.6 34.5 - + + +
96B ALA* 3.7 32.5 - - + -
99B PRO* 3.6 9.2 - - + +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PRO 2.9 19.3 + - - +
28B ILE* 3.2 5.8 + - - +
30B PHE* 1.3 75.8 - - - +
32B ALA* 1.3 56.8 + - - +
33B LEU 3.0 0.2 - - - -
34B LEU* 2.9 31.8 + - + +
35B ALA 4.2 0.5 + - - -
99B PRO* 4.4 10.5 - - - +
171B SER* 4.4 10.5 - - - +
194B THR* 4.9 2.9 - - + -
197B PHE* 3.8 20.2 - - + -
198B LEU* 4.0 19.7 - - + -
201B LEU* 4.6 2.1 - - - +
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Residues in contact with ALA 32 (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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28B ILE 2.9 11.5 + - - +
29B LEU* 3.3 14.8 - - - +
30B PHE 3.1 0.6 - - - -
31B ALA* 1.3 72.8 - - - +
33B LEU* 1.3 59.4 + - - +
34B LEU 3.0 5.6 - - - -
35B ALA* 3.1 21.5 + - - +
39B VAL* 4.0 17.0 - - + -
41B ILE* 5.2 1.6 - - + -
72B ILE* 3.7 27.5 - - + +
74B ALA* 4.0 10.4 - - - +
197B PHE* 4.2 12.8 - - + -
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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