Contacts of the helix formed by residues 29 - 41 (chain B) in PDB entry 1JRX
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 LEU 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.0 21.8 - - + -
26B ASN* 2.8 21.0 + - - +
28B SER* 1.4 80.8 - - - +
30B THR* 1.4 67.0 + - - +
32B GLU* 3.2 31.0 - - + +
33B ASN* 2.9 29.6 + - - +
69B THR* 3.4 28.3 - - + +
275B ASN* 5.4 0.9 - - - +
298B TYR* 3.6 40.4 - - + +
801B HEM 4.1 16.2 - - + +
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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
----------------------------------------------------------
25B SER* 3.2 1.0 + - - -
26B ASN* 3.0 27.6 + - - -
28B SER* 3.2 14.9 - - - -
29B LEU* 1.4 78.3 - - - +
31B TYR* 1.3 65.1 + - - +
33B ASN* 3.8 4.0 - - - +
34B THR* 2.9 31.8 + - - +
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Residues in contact with TYR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP 4.6 3.8 + - - -
17B CYS 3.7 7.0 - - - -
18B HIS 3.5 28.1 + - - -
19B THR* 3.5 25.8 - - + -
20B PRO* 4.8 6.7 - - + +
25B SER* 3.0 25.7 + - - +
30B THR* 1.3 79.0 - - - +
32B GLU* 1.3 68.4 + - - +
34B THR* 2.9 19.1 + - + -
35B GLN* 3.0 51.0 + - + +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B CYS* 3.6 23.4 - - + +
18B HIS* 4.6 7.2 + - + +
19B THR* 4.2 4.7 - - - +
23B GLU 3.7 5.2 - - - +
24B LEU* 3.3 21.2 - - + +
25B SER* 2.6 48.6 + - - -
29B LEU* 3.2 27.6 - - + +
31B TYR* 1.3 74.4 - - - +
33B ASN* 1.3 64.0 + - - +
35B GLN* 3.0 13.3 + - - +
36B CYS* 3.1 16.4 + - - -
69B THR* 5.5 0.4 - - - -
801B HEM 4.1 24.9 - - + -
802B HEM 4.6 2.1 - - + +
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER 3.3 12.7 + - - -
29B LEU* 2.9 30.1 + - - +
30B THR* 3.9 4.0 - - - +
32B GLU* 1.3 79.1 - - - +
34B THR* 1.3 62.0 + - - +
36B CYS* 3.1 6.9 + - - +
37B VAL* 3.0 26.8 + - + +
67B ALA* 3.5 19.0 - - + +
68B CYS* 3.0 15.7 + - - +
69B THR* 2.8 51.2 + - - +
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 2.9 21.6 + - - +
31B TYR* 2.9 13.6 + - + -
33B ASN* 1.3 74.5 - - - +
35B GLN* 1.3 69.7 + - - +
37B VAL* 3.2 8.6 + - + +
38B SER* 2.7 29.2 + - - -
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 3.4 26.2 + - - +
17B CYS* 3.6 13.5 - - + +
31B TYR* 3.0 62.5 + - + +
32B GLU 3.0 6.7 + - - +
34B THR* 1.3 87.4 - - - +
36B CYS* 1.4 67.4 + - - +
38B SER* 2.6 33.2 + - - -
39B CYS 3.3 2.8 + - - -
802B HEM 3.5 10.2 - - + +
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Residues in contact with CYS 36 (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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32B GLU 3.1 17.3 + - - -
33B ASN* 3.1 17.8 + - - +
35B GLN* 1.4 75.7 - - - +
37B VAL* 1.3 60.3 + - - +
39B CYS 3.3 0.2 + - - -
40B HIS* 2.8 34.0 + - - +
68B CYS* 3.7 21.5 - - - -
802B HEM 2.5 70.4 - - + +
803B HEM 4.1 4.3 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.0 17.6 + - + +
34B THR* 3.7 9.9 - - + +
36B CYS* 1.3 73.0 - - - +
38B SER* 1.3 64.3 + - - +
41B GLY* 2.6 55.5 + - - +
42B THR* 3.8 18.6 - - + +
43B LEU 5.0 0.2 - - - +
68B CYS* 4.2 3.6 - - - -
803B HEM 3.8 20.0 - - + -
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Residues in contact with SER 38 (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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34B THR* 2.7 19.9 + - - -
35B GLN* 2.6 33.9 + - - -
37B VAL* 1.3 74.2 - - - +
39B CYS* 1.3 69.3 + - - +
41B GLY* 4.5 0.7 + - - -
802B HEM 4.7 0.9 - - - +
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Residues in contact with CYS 39 (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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36B CYS 3.3 3.8 + - - +
37B VAL 3.2 0.2 - - - -
38B SER* 1.3 92.1 + - - +
40B HIS* 1.3 66.7 + - - +
41B GLY 3.5 0.2 - - - -
802B HEM 2.7 70.3 - - + +
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Residues in contact with HIS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B CYS 2.8 20.8 + - - +
39B CYS* 1.3 74.3 + - - +
41B GLY* 1.3 60.7 + - - +
45B GLU* 4.4 3.1 - - - +
46B VAL* 3.7 17.3 + - + +
802B HEM 2.0 100.8 + + + -
803B HEM 3.4 44.8 - - + +
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 2.6 40.9 + - - +
38B SER 4.5 0.8 + - - -
39B CYS 3.5 1.2 - - - -
40B HIS* 1.3 76.3 - - - +
42B THR* 1.3 70.6 + - - +
45B GLU* 3.1 16.2 - - - -
46B VAL* 3.7 5.9 - - - +
803B HEM 3.8 1.7 - - - +
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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