Contacts of the helix formed by residues 22 - 37 (chain u) in PDB entry 5JPQ
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 22 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158d ARG* 6.2 1.4 - - - +
162d GLY* 6.2 2.2 - - - +
163d VAL 4.5 19.5 - - - +
164d PRO* 5.1 6.3 - - - -
165d ILE* 5.4 3.8 - - - -
21u SER* 1.3 70.9 - - - +
23u ARG* 1.3 61.5 + - - +
25u ASP* 4.4 5.4 - - - +
26u ALA* 2.8 30.7 + - - +
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Residues in contact with ARG 23 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21u SER* 4.0 8.0 - - - -
22u SER* 1.3 78.0 - - - +
24u LEU* 1.3 62.6 + - - +
26u ALA* 3.0 7.6 - - - +
27u GLU* 2.9 23.2 + - - +
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Residues in contact with LEU 24 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46d PHE* 3.7 17.5 + - + +
21u SER* 3.0 30.4 + - - +
23u ARG* 1.3 79.0 - - - +
25u ASP* 1.3 54.9 - - - +
26u ALA 3.0 0.2 - - - -
27u GLU* 2.7 30.1 + - - +
28u LEU 2.9 8.1 + - - -
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Residues in contact with ASP 25 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46d PHE* 3.5 24.2 - - + +
48d HIS* 4.3 23.0 - - + +
161d PRO* 6.0 0.9 - - + -
162d GLY* 5.0 11.4 - - - +
21u SER 2.5 19.7 + - - +
22u SER* 4.5 3.8 - - - +
24u LEU* 1.3 69.8 - - - +
26u ALA* 1.3 58.8 + - - +
28u LEU* 2.9 18.0 - - - +
29u LYS* 2.9 10.4 + - - +
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Residues in contact with ALA 26 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22u SER 2.8 23.3 + - - +
23u ARG* 3.0 8.1 - - - +
25u ASP* 1.3 73.2 - - - +
27u GLU* 1.3 54.9 + - - +
28u LEU 2.5 5.8 + - - -
29u LYS* 2.3 35.9 + - - +
30u LEU* 2.9 12.4 + - - +
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Residues in contact with GLU 27 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23u ARG 2.9 11.5 + - - +
24u LEU* 2.7 17.2 + - - +
26u ALA* 1.3 68.9 - - - +
28u LEU* 1.3 60.2 + - - +
30u LEU* 4.4 9.3 - - - +
31u ALA* 4.0 12.5 + - - +
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Residues in contact with LEU 28 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46d PHE 3.2 27.6 - - - +
47d GLU 4.6 4.0 - - - +
48d HIS 4.8 9.9 - - - +
24u LEU 2.9 3.2 + - - -
25u ASP* 2.9 17.7 - - - +
26u ALA 2.5 6.2 + - - -
27u GLU* 1.3 73.2 - - - +
29u LYS* 1.3 62.4 + - - +
31u ALA* 2.7 20.9 + - - +
32u GLY 2.9 8.5 + - - -
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Residues in contact with LYS 29 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48d HIS 5.8 0.4 + - - -
50d GLU* 5.6 11.2 - - + -
25u ASP 2.9 8.5 + - - +
26u ALA* 2.3 23.0 + - - +
28u LEU* 1.3 72.9 - - - +
30u LEU* 1.3 53.7 + - - +
32u GLY* 2.7 22.5 + - - +
33u GLU* 2.9 13.9 + - - +
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Residues in contact with LEU 30 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26u ALA 2.9 10.8 + - - +
27u GLU* 4.7 8.3 - - - +
28u LEU 2.9 0.2 + - - -
29u LYS* 1.3 75.4 - - - +
31u ALA* 1.3 58.5 + - - +
33u GLU* 3.1 10.7 + - - +
34u PHE* 2.8 25.0 + - - +
44u ARG* 5.2 14.4 - - + +
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Residues in contact with ALA 31 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27u GLU 4.0 11.1 + - - +
28u LEU* 2.7 14.2 + - - +
30u LEU* 1.3 73.5 - - - +
32u GLY* 1.3 62.4 + - - +
34u PHE* 2.9 28.2 + - + +
35u GLY 4.2 0.3 + - - -
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Residues in contact with GLY 32 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28u LEU 2.9 7.7 + - - -
29u LYS* 2.7 12.3 + - - -
31u ALA* 1.3 75.6 - - - +
33u GLU* 1.3 61.1 + - - -
34u PHE 2.9 4.7 + - - -
35u GLY 3.4 1.4 + - - -
36u LEU* 3.0 21.6 + - - +
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Residues in contact with GLU 33 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29u LYS 2.9 10.6 + - - +
30u LEU* 3.5 10.8 - - - +
32u GLY* 1.3 74.8 - - - +
34u PHE* 1.3 53.3 + - - +
35u GLY 2.7 12.5 + - - -
36u LEU* 3.4 13.5 - - + -
37u LYS* 3.0 22.9 + - + +
39u LYS* 5.1 0.9 + - - +
44u ARG* 5.4 10.5 - - + -
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Residues in contact with PHE 34 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30u LEU 2.8 6.9 + - - +
31u ALA* 2.9 32.3 - - + +
32u GLY 2.9 1.0 - - - -
33u GLU* 1.3 73.3 - - - +
35u GLY* 1.3 54.4 + - - +
38u ASN 3.4 5.2 - - - +
39u LYS* 3.2 35.0 - - - +
40u LYS* 6.0 2.0 - - - -
41u GLU 6.3 0.4 - - - +
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Residues in contact with GLY 35 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31u ALA 4.2 1.2 + - - -
32u GLY 3.4 3.0 + - - -
33u GLU 2.7 0.6 + - - -
34u PHE* 1.3 75.9 - - - +
36u LEU* 1.3 62.2 + - - +
37u LYS 2.8 24.9 - - - +
38u ASN* 3.8 2.9 - - - -
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Residues in contact with LEU 36 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32u GLY 3.0 19.8 + - - +
33u GLU* 3.4 14.4 - - + -
35u GLY* 1.3 78.2 - - - +
37u LYS* 1.3 57.5 + - + +
105u LEU* 6.2 0.4 - - - -
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Residues in contact with LYS 37 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33u GLU* 3.0 11.6 + - + +
35u GLY 2.8 13.0 - - - +
36u LEU* 1.3 76.6 - - - +
38u ASN* 1.3 68.0 + - - +
39u LYS* 4.7 4.3 - - + +
105u LEU* 4.5 29.4 - - + +
106u GLU* 5.9 0.2 - - - -
110u GLN* 4.8 8.1 - - + +
111u THR* 5.3 10.0 - - - -
122u VAL* 4.3 8.8 - - - +
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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