Contacts of the helix formed by residues 37 - 46 (chain D) in PDB entry 1JJ2
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 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D MET* 2.9 28.0 - - + +
27D ILE* 3.3 32.3 - - + -
35D ALA 2.6 6.7 + - - +
36D ASN* 1.3 79.7 - - - +
38D GLU* 1.3 64.9 + - - +
40D ILE* 2.8 32.7 - - + +
71D ALA* 6.4 0.7 - - + -
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Residues in contact with GLU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D MET* 4.8 0.4 - - - -
35D ALA 2.9 18.3 + - - +
37D ALA* 1.3 75.4 - - - +
39D ASP* 1.3 57.8 + - - +
41D LEU* 2.6 32.1 + - - +
42D GLY 2.8 10.9 + - - -
48D MET* 5.9 1.2 - - - +
49D PRO* 3.6 36.6 - - + +
51D ARG* 2.6 53.1 + - - -
71D ALA* 3.8 23.5 - - + +
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Residues in contact with ASP 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASN* 2.5 30.3 - - - +
38D GLU* 1.3 78.0 - - - +
40D ILE* 1.3 63.6 + - + +
42D GLY* 3.2 9.9 + - - -
43D GLU* 3.3 24.7 + - - +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D MET* 3.4 28.9 - - + -
36D ASN 5.5 1.6 - - - +
37D ALA* 2.8 28.4 + - + +
39D ASP* 1.3 77.2 - - + +
41D LEU* 1.3 61.4 + - + +
43D GLU* 3.3 13.4 + - - +
44D ILE* 2.8 32.9 + - - +
128D LEU* 5.3 5.6 - - + -
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 3.5 42.0 - - + +
25D MET* 3.2 37.9 - - + +
38D GLU* 2.6 19.0 + - - +
40D ILE* 1.3 77.5 - - - +
42D GLY* 1.3 51.3 + - - +
44D ILE* 2.9 22.5 - - + +
45D THR* 2.5 28.4 + - - -
49D PRO* 4.4 2.7 - - + -
71D ALA* 3.9 39.0 - - + +
73D VAL* 4.2 12.6 - - + -
128D LEU* 4.6 9.0 - - + -
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Residues in contact with GLY 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLU 2.8 11.6 + - - -
39D ASP* 3.2 4.5 + - - -
40D ILE 3.2 0.4 - - - -
41D LEU* 1.3 77.9 - - - +
43D GLU* 1.3 55.6 + - - +
45D THR* 3.9 3.6 - - - -
46D GLY* 2.7 34.0 + - - -
47D GLN 4.1 13.7 - - - -
48D MET* 5.5 0.2 - - - -
49D PRO* 4.3 7.7 - - - +
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 3.4 18.7 - - - +
40D ILE* 3.3 16.9 + - - +
41D LEU 3.2 0.4 - - - -
42D GLY* 1.3 75.1 - - - +
44D ILE* 1.3 63.9 + - - +
45D THR 3.2 3.0 + - - -
46D GLY* 4.3 3.0 + - - -
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 5.8 0.2 - - + -
40D ILE* 2.8 18.1 + - + +
41D LEU* 2.9 39.0 - - + +
43D GLU* 1.3 77.5 - - - +
45D THR* 1.3 65.9 + - + +
83D PHE* 3.2 38.6 - - + -
128D LEU* 4.2 27.1 - - + -
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Residues in contact with THR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 3.3 34.1 - - + -
41D LEU 2.5 22.4 + - - +
43D GLU 4.4 1.8 - - - -
44D ILE* 1.3 86.8 - - + +
46D GLY* 1.3 64.7 + - - +
47D GLN 3.6 13.7 + - - -
73D VAL* 3.8 5.4 - - + +
75D LEU* 3.6 36.1 - - + +
79D MET* 4.8 12.3 - - - +
83D PHE* 3.9 12.1 - - + +
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Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLY 2.7 23.0 + - - -
43D GLU 4.3 2.2 + - - -
45D THR* 1.3 75.0 + - - +
47D GLN* 1.3 61.5 + - - +
79D MET* 3.8 13.9 - - - +
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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