Contacts of the helix formed by residues 39 - 52 (chain Q) 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 THR 39 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38Q LYS* 1.3 74.9 - - - +
40Q ALA* 1.3 63.7 + - - +
41Q GLY* 3.1 10.5 - - - +
42Q GLU* 2.6 38.9 + - + +
43Q ALA* 2.8 22.2 + - - +
107Q GLU 2.9 24.7 - - - +
108Q ALA* 3.7 17.0 + - - -
109Q MET 3.4 5.9 - - - -
110Q THR* 4.5 4.5 + - - +
111Q ILE* 4.6 0.2 - - - -
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Residues in contact with ALA 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q LYS 3.9 0.6 + - - -
39Q THR* 1.3 72.8 - - - +
41Q GLY* 1.3 62.3 + - - +
43Q ALA* 3.1 4.4 + - - +
44Q VAL* 3.0 27.9 + - - +
92Q LEU* 4.3 12.6 - - + +
96Q VAL* 3.6 24.0 - - + -
106Q GLY 3.6 15.5 - - - +
107Q GLU* 3.4 9.4 - - - +
109Q MET 2.9 13.3 + - - +
111Q ILE* 4.4 4.0 - - - +
147Q LEU* 4.1 12.8 - - + -
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Residues in contact with GLY 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q THR* 3.7 4.7 - - - -
40Q ALA* 1.3 74.2 - - - +
42Q GLU* 1.3 63.7 + - - +
44Q VAL* 3.3 9.0 + - - +
45Q ASP* 3.1 30.1 + - - +
107Q GLU* 2.9 30.5 + - - +
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Residues in contact with GLU 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q GLY 4.7 0.7 - - - +
38Q LYS* 3.4 20.2 - - + +
39Q THR* 2.6 50.4 + - + +
41Q GLY* 1.3 74.7 - - - +
43Q ALA* 1.3 57.3 + - - +
45Q ASP* 3.2 9.6 + - - +
46Q TYR* 2.8 31.0 + - - +
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Residues in contact with ALA 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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35Q ILE* 4.3 13.2 - - + -
38Q LYS* 4.4 7.5 - - + +
39Q THR 2.8 11.2 + - - +
40Q ALA 3.3 9.2 - - - +
42Q GLU* 1.3 76.5 - - - +
44Q VAL* 1.3 63.0 + - - +
46Q TYR* 3.1 8.2 + - - +
47Q LEU* 2.9 28.7 + - - +
92Q LEU* 3.8 16.4 - - + -
111Q ILE* 3.7 24.7 - - + -
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Residues in contact with VAL 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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40Q ALA* 3.0 18.2 + - + +
41Q GLY* 3.6 9.4 - - - +
42Q GLU 3.3 0.2 - - - -
43Q ALA* 1.3 75.6 - - - +
45Q ASP* 1.3 64.3 + - - +
47Q LEU 3.4 0.2 + - - -
48Q GLU* 2.9 48.0 + - - +
89Q LEU* 3.8 23.4 - - + +
92Q LEU* 4.3 22.0 - - + -
93Q GLU* 5.8 0.4 - - - +
96Q VAL* 5.7 3.6 - - + -
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Residues in contact with ASP 45 (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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41Q GLY 3.1 16.1 + - - +
42Q GLU* 3.6 8.8 - - - +
44Q VAL* 1.3 78.8 - - - +
46Q TYR* 1.3 63.4 + - - +
48Q GLU* 3.3 17.1 + - - +
49Q ALA* 3.1 22.7 + - - +
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Residues in contact with TYR 46 (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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31Q ILE* 5.7 0.9 - - + -
34Q GLU* 3.2 36.0 + - + +
35Q ILE* 3.8 11.4 - - + -
38Q LYS* 3.2 27.1 - - - +
42Q GLU 2.8 14.5 + - - +
43Q ALA* 3.1 8.7 + - - +
45Q ASP* 1.3 75.2 - - - +
47Q LEU* 1.3 79.9 + - + +
49Q ALA* 3.0 17.6 + - - +
50Q VAL* 3.0 30.1 + - + +
55Q GLN* 3.3 34.1 - - + -
56Q PRO 3.0 20.5 + - - -
57Q VAL* 3.4 15.4 - - + +
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Residues in contact with LEU 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q ILE* 3.9 20.4 - - + -
35Q ILE* 4.4 8.1 - - + -
43Q ALA 2.9 22.4 + - - +
46Q TYR* 1.3 92.1 - - + +
48Q GLU* 1.3 57.8 + - - +
50Q VAL* 3.3 5.8 + - + +
51Q ILE* 2.9 35.5 + - - +
57Q VAL* 5.4 0.2 - - + -
85Q SER* 3.7 28.9 - - - +
88Q PHE* 3.6 30.3 - - + -
89Q LEU* 3.9 18.2 - - + -
92Q LEU* 4.0 16.8 - - + -
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Residues in contact with GLU 48 (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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44Q VAL* 2.9 37.1 + - - +
45Q ASP* 3.7 19.6 - - - +
46Q TYR 3.2 0.2 - - - -
47Q LEU* 1.3 78.7 - - - +
49Q ALA* 1.3 56.6 + - - +
51Q ILE* 3.5 9.7 + - - +
52Q GLU* 2.9 28.8 + - - +
89Q LEU* 4.2 16.9 - - + +
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Residues in contact with ALA 49 (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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45Q ASP 3.1 12.3 + - - +
46Q TYR* 3.0 11.3 + - - +
48Q GLU* 1.3 76.3 - - - +
50Q VAL* 1.3 59.8 + - - +
52Q GLU* 3.3 6.9 + - - -
53Q GLY 2.8 22.9 + - - -
54Q ASP* 2.8 22.2 + - + +
55Q GLN* 3.5 22.9 - - + +
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Residues in contact with VAL 50 (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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46Q TYR* 3.0 31.1 + - + +
47Q LEU* 3.4 11.7 - - + +
49Q ALA* 1.3 77.8 - - - +
51Q ILE* 1.3 64.8 + - - +
53Q GLY* 2.9 15.2 + - - -
55Q GLN* 3.2 22.0 - - + +
57Q VAL* 3.8 25.4 - - + -
80Q TYR* 3.6 39.1 - - - +
81Q PRO* 4.1 1.3 - - + +
85Q SER* 3.7 17.5 - - - +
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Residues in contact with ILE 51 (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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47Q LEU 2.9 21.3 + - - +
48Q GLU* 3.7 7.0 - - - +
50Q VAL* 1.3 76.3 - - - +
52Q GLU* 1.3 61.8 + - - +
53Q GLY* 3.4 0.7 + - - -
82Q GLU* 4.2 25.0 - - + +
85Q SER* 3.9 18.4 - - - -
86Q LYS* 3.6 38.1 - - + -
89Q LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q GLU 2.9 18.9 + - - +
49Q ALA* 3.6 4.0 - - - +
50Q VAL 3.1 0.2 - - - -
51Q ILE* 1.3 78.9 - - - +
53Q GLY* 1.3 59.1 + - - +
54Q ASP* 3.0 31.0 - - - +
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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