Contacts of the helix formed by residues 34 - 47 (chain Q) in PDB entry 2ZJQ
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 THR 34 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q LYS 5.2 1.3 - - - -
33Q ALA* 1.3 86.7 - - - +
35Q LYS* 1.3 55.6 + - - +
36Q THR* 3.2 8.9 + - - -
37Q GLU* 2.5 38.1 + - - +
38Q ILE* 2.7 21.1 + - - +
55Q THR* 5.9 0.2 - - - -
76Q LYS* 4.5 4.2 - - - +
1614X C 4.0 7.2 - - - +
1615X C 3.0 30.3 - - - -
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Residues in contact with LYS 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q THR* 1.3 70.4 - - - +
36Q THR* 1.3 59.9 + - + +
38Q ILE* 2.7 24.3 - - - +
39Q LYS* 2.7 19.8 + - + +
53Q ILE* 3.2 51.1 + - + +
55Q THR* 4.0 21.4 - - - +
1355X A 3.8 28.1 + - - -
1356X G 4.4 3.4 + - - +
1613X G 5.9 1.1 - - - +
1614X C 3.0 40.9 + - - +
1615X C 2.4 36.9 + - - +
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Residues in contact with THR 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q THR* 3.2 11.8 + - - -
35Q LYS* 1.3 74.4 - - + +
37Q GLU* 1.3 78.9 + - - +
39Q LYS* 2.8 10.9 + - - +
40Q ASP* 2.7 20.8 + - - +
1613X G 4.3 22.4 - - - +
1614X C 3.9 26.9 + - - -
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Residues in contact with GLU 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q ILE* 5.0 15.8 - - + +
33Q ALA* 4.2 3.0 - - - +
34Q THR* 2.5 48.4 + - - +
36Q THR* 1.3 90.2 + - - +
38Q ILE* 1.3 51.5 + - - +
40Q ASP* 2.7 37.4 + - - +
41Q ALA* 2.8 12.4 + - - +
137X A 6.2 4.0 - - - -
138X G 5.9 2.7 - - - +
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Residues in contact with ILE 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q ILE* 5.0 7.2 - - + +
27Q PHE* 6.1 3.6 - - + -
29Q VAL* 3.1 41.1 - - + -
33Q ALA* 3.1 14.1 + - + +
34Q THR 2.7 19.2 + - - +
35Q LYS* 2.7 33.9 - - + +
37Q GLU* 1.3 72.7 - - - +
39Q LYS* 1.3 65.3 + - - +
40Q ASP 3.1 0.5 + - - -
41Q ALA* 3.7 7.9 - - + +
42Q ILE* 2.7 29.4 + - + +
53Q ILE* 4.3 13.7 - - + -
55Q THR* 4.9 4.3 - - - +
76Q LYS* 6.2 0.4 - - - -
78Q ALA* 3.4 20.4 - - + -
80Q VAL* 5.6 2.0 - - + -
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Residues in contact with LYS 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q LYS* 2.7 24.0 + - + +
36Q THR* 2.8 6.5 + - - +
38Q ILE* 1.3 74.1 - - - +
40Q ASP* 1.3 67.1 + - - +
42Q ILE* 2.8 17.6 - - - +
43Q GLN* 3.3 23.5 - - - +
50Q VAL* 2.8 53.5 + - + -
51Q ILE 4.2 9.9 + - - -
53Q ILE* 4.6 18.5 - - + +
80Q VAL* 5.3 3.1 - - - -
1612X U 4.5 12.5 + - - -
1613X G 3.0 38.2 + - - +
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Residues in contact with ASP 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q SER 5.1 1.4 - - - +
3Q HIS* 3.4 29.9 + - - -
36Q THR 2.7 9.4 + - - +
37Q GLU* 2.7 15.4 + - - +
39Q LYS* 1.3 82.1 - - - +
41Q ALA* 1.3 81.6 + - - +
43Q GLN* 2.9 23.3 + - - +
44Q GLN* 3.5 8.0 + - - +
136X A 6.1 0.9 - - - -
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Residues in contact with ALA 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q HIS* 3.7 26.7 + - - +
5Q ASP* 4.6 1.6 - - - +
6Q ILE* 4.5 17.0 - - + -
7Q LEU* 5.6 2.7 - - + +
37Q GLU 2.8 8.2 + - - +
38Q ILE* 3.7 12.1 - - + +
40Q ASP* 1.3 85.5 + - - +
42Q ILE* 1.3 69.9 + - - +
44Q GLN* 3.0 12.5 + - - +
45Q ALA* 3.1 13.0 + - - +
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Residues in contact with ILE 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q LEU* 6.4 0.9 - - - +
25Q TYR* 6.3 0.2 - - + -
27Q PHE* 3.4 35.7 - - + -
38Q ILE* 2.7 30.0 + - + +
39Q LYS* 2.8 23.1 - - - +
41Q ALA* 1.3 73.3 - - - +
43Q GLN* 1.3 70.8 + - - +
45Q ALA* 2.5 19.8 + - - -
46Q PHE* 3.0 37.4 + - + -
48Q VAL* 5.1 5.2 - - + -
50Q VAL* 4.3 16.4 - - + -
80Q VAL* 4.7 12.1 - - + -
82Q LEU* 5.4 2.9 - - + -
88Q ILE* 5.3 6.3 - - + -
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Residues in contact with GLN 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Q LYS* 3.3 37.0 + - - +
40Q ASP* 2.9 16.1 + - - +
42Q ILE* 1.3 83.9 - - - +
44Q GLN* 1.3 60.9 + - + +
46Q PHE 2.8 2.1 + - - -
47Q GLY* 2.5 36.7 + - - -
48Q VAL* 2.8 24.8 - - - +
49Q ARG* 2.9 28.5 - - - +
50Q VAL* 3.7 18.0 - - + +
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Residues in contact with GLN 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q HIS* 3.1 51.5 + - + +
4Q TYR* 3.6 15.5 + - - -
40Q ASP* 3.5 8.5 + - - +
41Q ALA 3.0 3.8 + - - +
43Q GLN* 1.3 84.1 + - + +
45Q ALA* 1.3 57.3 + - - +
46Q PHE 3.4 0.2 - - - -
47Q GLY* 4.2 8.2 - - - +
48Q VAL 5.6 1.2 + - - +
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Residues in contact with ALA 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q HIS 5.0 1.1 - - - +
4Q TYR* 3.3 40.9 + - + +
41Q ALA 3.1 8.6 + - - +
42Q ILE* 2.5 16.5 + - - +
44Q GLN* 1.3 74.4 - - - +
46Q PHE* 1.3 85.4 + - + +
47Q GLY 3.7 0.2 - - - -
89Q GLU* 5.3 2.3 - - - +
23V LYS* 5.6 1.9 + - - -
26V MET* 5.0 5.1 - - + +
27V GLU* 5.6 0.2 - - - +
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Residues in contact with PHE 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q LEU* 5.8 3.4 - - + -
27Q PHE* 4.5 9.2 - + - -
42Q ILE* 3.0 35.6 + - + +
43Q GLN 2.8 2.1 + - - +
45Q ALA* 1.3 101.3 - - + +
47Q GLY* 1.3 67.4 + - - +
48Q VAL* 4.2 6.3 - - + +
88Q ILE* 3.8 37.9 - - + -
89Q GLU* 3.2 42.1 + - + +
91Q LEU* 5.1 0.7 - - + -
26V MET* 3.5 28.7 - - + -
27V GLU* 4.5 2.2 - - - -
30V PHE* 3.9 20.4 - + - -
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Residues in contact with GLY 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Q GLN 2.5 15.3 + - - -
44Q GLN* 4.2 8.3 - - - -
45Q ALA 3.7 1.4 - - - +
46Q PHE* 1.3 80.9 - - - +
48Q VAL* 1.3 60.7 + - - +
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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