Contacts of the helix formed by residues 39 - 49 (chain W) in PDB entry 2JA7
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 ASP 39 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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995N ARG* 5.5 4.0 + - - -
997N GLU* 5.7 0.9 - - - +
998N ASP* 4.2 6.4 - - - +
35O ARG* 3.5 18.9 + - - -
40O GLU* 4.4 0.2 - - - +
165O LYS* 3.4 26.9 + - - -
38W GLU* 1.3 84.7 + - - +
40W HIS* 1.3 73.9 + - + +
41W THR* 3.6 17.5 + - - +
42W LEU* 3.1 4.2 + - - -
43W GLY 2.8 18.9 + - - -
63W VAL* 5.1 7.0 - - + -
69W ALA* 5.5 3.4 - - + -
70W ARG 5.1 1.1 - - - +
71W PHE* 3.2 17.4 - - - -
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Residues in contact with HIS 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998N ASP* 3.9 11.9 - - - -
1076N HIS* 3.1 65.3 + + + +
35O ARG* 3.1 15.9 - - - +
39W ASP* 1.3 79.7 - - + +
41W THR* 1.3 66.3 + - - +
43W GLY 2.8 12.1 + - - +
44W ASN* 2.9 17.2 + - - +
61W TYR* 2.5 37.7 + + - +
63W VAL* 3.7 37.5 - - + +
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Residues in contact with THR 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997N GLU* 5.3 1.9 - - - +
32O SER* 3.8 23.9 + - - +
35O ARG* 2.5 51.2 + - - +
36O VAL* 3.8 24.6 + - + -
40O GLU* 3.5 22.6 + - - +
165O LYS* 5.9 0.2 - - - -
251O LEU* 4.7 5.2 - - + +
254O LYS* 3.7 10.8 - - + +
39W ASP* 3.6 13.3 + - - -
40W HIS* 1.3 74.4 - - - +
42W LEU* 1.3 60.4 + - + +
45W LEU* 3.9 6.6 - - - +
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Residues in contact with LEU 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251O LEU* 5.0 2.7 - - + +
254O LYS* 3.5 39.7 - - + +
255O VAL* 3.8 20.4 - - + +
258O ILE* 4.0 19.1 - - + -
35W PHE* 4.0 14.6 - - + -
38W GLU* 3.8 22.4 - - - +
39W ASP* 3.1 4.9 + - - +
40W HIS 2.9 0.2 + - - -
41W THR* 1.3 83.0 - - + +
43W GLY* 1.3 62.3 + - - +
45W LEU* 4.2 7.2 - - + -
46W ILE* 2.8 65.5 + - + +
71W PHE* 4.3 3.4 - - + -
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Residues in contact with GLY 43 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39W ASP 2.8 9.3 + - - -
40W HIS 2.8 2.0 + - - -
42W LEU* 1.3 78.1 - - - +
44W ASN* 1.3 65.2 + - - -
46W ILE* 3.3 4.3 + - - +
47W ARG* 3.0 22.7 + - - +
61W TYR* 3.2 21.4 - - - +
71W PHE* 3.2 26.8 - - - -
73W LEU* 5.6 1.0 - - - +
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Residues in contact with ASN 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548M ASN* 5.7 0.2 + - - -
1076N HIS 3.9 6.3 + - - +
1077N THR* 3.1 51.5 + - - +
28O ALA* 4.2 19.1 + - - +
31O ASN* 5.2 0.4 - - - +
32O SER* 5.2 3.7 + - - +
40W HIS 2.9 17.8 + - - +
43W GLY* 1.3 70.3 - - - -
45W LEU* 1.3 52.5 + - - +
47W ARG* 2.8 30.5 + - - +
48W ALA* 2.7 33.7 + - - +
61W TYR* 3.1 24.0 + - - +
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Residues in contact with LEU 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ALA* 4.6 6.1 - - + -
29O MET* 3.8 34.5 - - + +
32O SER* 3.6 27.3 + - - +
251O LEU* 3.8 32.8 - - + -
255O VAL* 4.4 4.7 - - + -
40W HIS 4.3 0.6 + - - -
41W THR 3.9 9.4 - - - +
42W LEU* 4.0 6.2 - - - +
44W ASN* 1.3 74.5 - - - +
46W ILE* 1.3 58.9 + - + +
47W ARG 2.8 8.9 + - - -
48W ALA* 3.4 0.8 + - + +
49W GLU* 3.1 32.6 + - + +
94W ILE* 3.4 33.6 - - + +
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Residues in contact with ILE 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255O VAL* 5.3 5.2 - - + -
258O ILE* 4.3 11.7 - - + -
35W PHE* 3.8 17.3 - - + -
42W LEU* 2.8 53.6 + - + +
43W GLY* 3.3 5.6 + - - +
45W LEU* 1.3 75.9 - - + +
47W ARG* 1.3 57.1 + - - +
49W GLU* 5.0 0.9 - - - -
50W LEU* 3.0 26.4 + - + +
71W PHE* 5.1 0.4 - - + -
73W LEU* 4.1 11.3 - - + +
87W LEU* 3.3 31.6 - - + -
90W ALA* 5.3 3.5 - - + +
91W CYS* 4.3 12.3 - - - -
94W ILE* 4.1 14.4 - - + -
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Residues in contact with ARG 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544M ASP* 3.3 29.5 + - - +
545M GLN* 5.3 0.2 - - - +
548M ASN* 3.1 28.8 - - - +
43W GLY 3.0 11.9 + - - +
44W ASN* 2.8 40.6 + - - +
46W ILE* 1.3 80.3 - - - +
48W ALA* 1.3 81.7 + - - +
50W LEU* 3.3 5.3 + - - +
51W LEU* 3.2 21.4 + - - +
59W ALA* 3.0 30.6 + - - +
60W ALA* 3.8 22.0 - - - +
61W TYR* 4.0 11.2 - - + +
73W LEU* 4.3 6.7 - - + -
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Residues in contact with ALA 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O ASP* 5.1 12.1 - - + +
28O ALA* 3.8 24.9 - - + -
44W ASN* 2.7 17.2 + - - +
45W LEU* 4.2 2.0 - - + +
47W ARG* 1.3 83.6 - - - +
49W GLU* 1.3 55.8 + - + +
51W LEU* 2.7 35.4 + - - +
52W ASN* 3.7 8.4 + - - +
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Residues in contact with GLU 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O ASP* 3.8 15.7 + - - +
29O MET* 6.5 0.4 - - - -
45W LEU* 3.1 18.7 + - + +
46W ILE* 5.0 0.9 - - - -
48W ALA* 1.3 78.8 - - - +
50W LEU* 1.3 59.6 + - - +
51W LEU 3.0 0.9 + - - -
52W ASN* 3.3 36.1 + - - +
53W ASP* 4.2 2.9 + - - +
90W ALA* 3.8 14.5 - - + +
93W SER* 3.0 23.8 + - - -
94W ILE* 3.3 30.5 - - + -
97W LYS* 3.0 31.6 - - + +
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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