Contacts of the helix formed by residues 24 - 36 (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 SER 24 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13700 G 2.8 41.8 + - - -
20520 U 4.9 10.4 + - - -
23Q MET* 1.3 74.7 - - - +
25Q PHE* 1.3 59.4 + - - +
26Q LYS 3.2 1.4 + - - -
27Q HIS* 2.8 46.5 + - - +
28Q SER* 3.0 25.5 + - - -
83Q LYS* 5.6 0.4 - - - +
84Q ALA* 4.6 1.7 - - - +
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Residues in contact with PHE 25 (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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5230 C 3.3 27.1 - - - -
5240 A 3.7 10.3 - - - -
13700 G 4.3 3.4 + - - -
23Q MET 3.2 4.2 + - - -
24Q SER* 1.3 71.9 - - - +
26Q LYS* 1.3 64.9 + - + +
28Q SER* 3.2 2.3 + - - -
29Q LYS* 3.0 55.4 + - + +
116Q ALA* 3.5 22.9 - - + -
117Q HIS* 3.5 5.8 - - - -
118Q LYS* 3.3 42.8 - - + -
139Q PRO* 4.4 8.5 - - + +
141Q VAL* 3.7 24.2 - - + -
8506Q CL 4.0 23.6 - - + -
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Residues in contact with LYS 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13670 A 5.2 9.5 + - - -
13680 U 4.4 3.2 + - - -
13690 A 2.9 27.7 + - - +
13700 G 2.8 52.9 + - + +
24Q SER* 3.2 7.0 + - - +
25Q PHE* 1.3 77.0 - - - +
27Q HIS* 1.3 66.0 + - + +
28Q SER 3.3 0.3 + - - -
29Q LYS* 3.4 8.8 + - - +
30Q ALA* 3.4 21.0 + - - +
62Q HIS* 3.4 56.6 - - + +
8506Q CL 4.1 23.6 - - + -
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Residues in contact with HIS 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13700 G 3.8 24.9 + + - -
20500 G 6.0 0.4 - - - -
20510 G 3.6 28.3 + - - -
20520 U 5.1 7.4 + - - -
20530 G 5.7 1.3 - - - -
24Q SER* 2.8 34.6 + - - +
26Q LYS* 1.3 77.3 - - + +
28Q SER* 1.3 57.7 + - - +
30Q ALA* 3.5 6.5 + - - +
31Q ILE* 3.1 35.3 + - - +
59Q PHE* 3.7 28.6 - + - -
79Q ARG* 5.6 4.0 + - - -
81Q PRO* 3.7 27.9 - - + +
83Q LYS* 6.2 0.2 - - - +
84Q ALA* 4.0 10.2 + - + +
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Residues in contact with SER 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q MET* 3.2 29.0 - - - +
24Q SER 3.0 15.0 + - - -
25Q PHE* 3.4 12.6 - - - -
26Q LYS 3.1 0.6 - - - -
27Q HIS* 1.3 76.2 - - - +
29Q LYS* 1.3 65.2 + - - +
32Q ALA* 2.9 26.5 + - - +
84Q ALA* 4.1 2.8 - - - +
88Q PHE* 3.7 18.8 - - - -
116Q ALA* 3.6 21.5 - - - +
141Q VAL* 4.2 2.3 - - - +
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Residues in contact with LYS 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5230 C 3.5 8.3 + - - -
5240 A 3.0 43.6 + - - +
5250 G 4.7 8.1 + - - +
13670 A 5.4 3.6 + - - -
25Q PHE* 3.0 52.3 + - + +
26Q LYS* 3.9 4.7 - - - +
27Q HIS 3.4 0.2 - - - -
28Q SER* 1.3 75.6 - - - +
30Q ALA* 1.3 58.8 + - - +
32Q ALA* 3.8 4.4 - - - +
33Q ARG* 2.9 45.3 + - - +
61Q GLN* 4.5 5.1 + - - +
62Q HIS* 3.1 39.2 + - + +
116Q ALA* 4.4 4.7 - - + +
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Residues in contact with ALA 30 (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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26Q LYS 3.4 10.3 + - - +
27Q HIS 3.7 8.3 - - - +
28Q SER 3.2 0.2 - - - -
29Q LYS* 1.3 81.0 - - - +
31Q ILE* 1.3 60.8 + - - +
33Q ARG* 3.5 17.4 - - - +
34Q GLU* 3.1 23.9 + - - +
57Q VAL* 3.8 12.8 - - + +
58Q PRO 3.8 21.2 - - - +
59Q PHE* 3.9 16.8 - - + -
60Q LYS 5.6 0.2 - - - +
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Residues in contact with ILE 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q HIS 3.1 13.9 + - - +
28Q SER 3.8 3.6 - - - +
29Q LYS 3.3 0.2 - - - -
30Q ALA* 1.3 73.5 - - - +
32Q ALA* 1.3 67.9 + - - +
34Q GLU* 3.1 4.6 + - - +
35Q ILE* 3.0 25.9 + - + +
46Q TYR* 5.8 0.4 - - + -
47Q LEU* 3.9 19.3 - - + -
57Q VAL* 4.4 21.8 - - + -
81Q PRO* 4.1 9.4 - - + +
84Q ALA* 3.4 34.8 - - + -
85Q SER* 3.5 25.4 - - - +
88Q PHE* 3.7 28.9 - - + -
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Residues in contact with ALA 32 (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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5250 G 6.2 2.5 - - - -
28Q SER 2.9 17.9 + - - +
29Q LYS* 3.8 4.3 - - - +
31Q ILE* 1.3 78.6 - - - +
33Q ARG* 1.3 65.8 + - - +
34Q GLU 3.1 0.2 + - - -
35Q ILE* 3.2 1.7 + - - +
36Q LYS* 3.1 20.4 + - - +
88Q PHE* 4.1 12.5 - - + -
114Q VAL* 3.4 44.2 - - + +
115Q ALA* 4.3 8.5 - - - -
116Q ALA 4.6 2.7 - - - +
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Residues in contact with ARG 33 (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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120 U 4.8 8.4 + - - -
130 G 5.8 0.4 + - - -
5250 G 3.4 30.1 + - - +
29Q LYS* 2.9 29.1 + - - +
30Q ALA* 3.5 33.3 - - - +
32Q ALA* 1.3 78.6 - - - +
34Q GLU* 1.3 62.8 + - + +
36Q LYS* 4.0 13.3 + - - +
58Q PRO 5.3 2.0 + - - -
60Q LYS* 4.4 30.9 - - - +
61Q GLN* 4.0 35.5 - - - +
62Q HIS* 6.2 1.0 - - - -
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Residues in contact with GLU 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ALA 3.1 17.7 + - - +
31Q ILE* 3.1 5.8 + - - +
33Q ARG* 1.3 80.7 - - - +
35Q ILE* 1.3 59.3 + - - +
36Q LYS 3.7 4.0 + - - +
38Q LYS* 3.8 17.6 + - - +
46Q TYR* 3.2 43.4 + - + +
56Q PRO 5.1 0.5 - - - +
57Q VAL* 4.9 1.1 - - + -
58Q PRO* 3.7 32.2 - - + +
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Residues in contact with ILE 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q ILE* 3.0 17.5 + - + +
32Q ALA* 3.7 5.8 - - - +
34Q GLU* 1.3 72.9 - - - +
36Q LYS* 1.3 71.1 + - - +
38Q LYS* 3.0 28.5 + - + +
43Q ALA* 4.3 11.9 - - + -
46Q TYR* 3.8 30.3 - - + -
47Q LEU* 4.4 11.4 - - + -
88Q PHE* 4.0 26.5 - - + -
92Q LEU* 4.5 16.8 - - + -
111Q ILE* 3.5 26.5 - - + +
114Q VAL* 4.4 13.2 - - + -
145Q LEU* 5.8 1.3 - - + -
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Residues in contact with LYS 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5250 G 3.8 6.6 + - - +
5260 U 2.8 42.0 + - - +
32Q ALA 3.1 10.9 + - - +
33Q ARG* 4.2 9.9 - - - +
34Q GLU 3.5 6.7 - - - +
35Q ILE* 1.3 80.0 - - - +
37Q GLY* 1.3 63.6 + - - +
38Q LYS* 3.2 3.5 + - - +
111Q ILE* 4.0 11.2 - - - +
112Q LYS 3.5 21.4 + - - +
113Q HIS* 4.9 6.4 - - + +
114Q VAL* 3.6 29.2 - - + +
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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