Contacts of the helix formed by residues 9 - 28 (chain Q) in PDB entry 6P19
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 9 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7Q ASN 5.3 2.5 - - - +
8Q LEU* 1.3 84.1 - - - +
10Q LYS* 1.3 60.3 + - - +
11Q GLU* 2.7 27.5 + - - +
12Q GLN* 2.4 28.9 + - - +
13Q HIS* 3.1 19.4 + - - +
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Residues in contact with LYS 10 (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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8Q LEU 4.1 11.9 - - - +
9Q THR* 1.3 72.8 - - - +
11Q GLU* 1.3 62.1 + - - +
13Q HIS* 3.1 38.5 + - + +
14Q GLU* 2.9 29.7 + - - +
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Residues in contact with GLU 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q THR* 2.7 35.4 + - - +
10Q LYS* 1.3 71.9 + - - +
12Q GLN* 1.3 74.3 + - + +
14Q GLU* 2.9 30.5 - - + +
15Q TRP* 2.9 19.8 + - - +
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Residues in contact with GLN 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q LEU* 3.4 28.8 - - + +
9Q THR* 2.4 34.7 + - - +
10Q LYS 3.3 0.2 - - - -
11Q GLU* 1.3 90.0 - - + +
13Q HIS* 1.3 57.2 + - - +
15Q TRP* 3.3 4.0 + - - +
16Q LEU* 2.9 31.9 + - - +
142Q TYR* 3.3 40.0 + - + +
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Residues in contact with HIS 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q LEU* 3.6 14.8 - - + +
9Q THR 3.1 15.1 + - - +
10Q LYS* 3.1 42.7 + - + +
12Q GLN* 1.3 77.6 - - - +
14Q GLU* 1.3 57.5 + - - +
16Q LEU* 3.2 19.7 - - + +
17Q ASN* 2.9 52.4 + - - -
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Residues in contact with GLU 14 (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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10Q LYS 2.9 20.8 + - - +
11Q GLU* 2.9 30.3 - - - +
13Q HIS* 1.3 75.0 + - - +
15Q TRP* 1.3 65.7 + - - +
17Q ASN* 3.5 11.8 - - + +
18Q GLY* 2.9 25.5 + - - -
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Residues in contact with TRP 15 (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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11Q GLU 2.9 18.8 + - - +
12Q GLN* 3.5 6.3 - - - +
13Q HIS 3.2 0.2 - - - -
14Q GLU* 1.3 84.6 - - - +
16Q LEU* 1.3 58.7 + - - +
18Q GLY* 3.4 1.4 + - - -
19Q TRP* 2.9 72.9 + + - +
142Q TYR* 3.2 41.1 - + - +
145Q LEU* 4.7 22.4 - - + -
146Q ASP* 4.0 12.3 - - - -
149Q PHE* 4.5 27.1 - + + -
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Residues in contact with LEU 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q LEU* 3.7 19.7 - - + -
12Q GLN 2.9 18.8 + - - +
13Q HIS* 3.2 30.3 - - + +
15Q TRP* 1.3 76.9 - - + +
17Q ASN* 1.3 79.7 + - - +
19Q TRP* 4.3 5.8 - - - -
20Q LEU* 2.9 40.3 + - + +
88Q TYR* 5.1 0.7 - - - +
138Q LEU* 3.7 42.8 - - + +
142Q TYR* 3.6 28.3 - - + -
145Q LEU* 6.1 4.3 - - + -
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Residues in contact with ASN 17 (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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13Q HIS* 2.9 46.6 + - - +
14Q GLU* 3.5 10.4 - - - +
15Q TRP 3.3 0.2 - - - -
16Q LEU* 1.3 93.1 - - - +
18Q GLY* 1.3 57.2 + - - +
21Q GLU* 2.9 33.4 + - - +
87Q TYR* 5.4 5.1 + - - -
88Q TYR* 4.1 15.8 + - - -
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Residues in contact with GLY 18 (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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14Q GLU 2.9 16.1 + - - -
15Q TRP 3.9 1.1 - - - -
17Q ASN* 1.3 76.3 - - - +
19Q TRP* 1.3 58.4 + - - +
21Q GLU* 3.4 7.0 + - - +
22Q LEU* 2.9 29.8 + - - +
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Residues in contact with TRP 19 (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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15Q TRP* 2.9 70.2 + + + +
16Q LEU* 4.0 6.1 - - - +
18Q GLY* 1.3 77.3 - - - +
20Q LEU* 1.3 62.7 + - + +
22Q LEU* 3.3 23.5 + - + +
23Q TRP* 2.9 27.1 + - - +
62Q ASP* 4.5 28.5 - - + -
66Q ILE* 4.5 28.5 - - + -
145Q LEU* 5.5 10.5 - - + -
149Q PHE* 3.5 35.2 - + - -
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Residues in contact with LEU 20 (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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16Q LEU* 2.9 22.0 + - + +
19Q TRP* 1.3 76.1 - - + +
21Q GLU* 1.3 59.5 + - - +
23Q TRP* 3.7 25.4 - - + +
24Q GLY* 2.9 23.6 + - - -
66Q ILE* 5.4 6.1 - - + -
70Q VAL* 5.5 9.2 - - + -
88Q TYR* 3.5 49.1 - - + +
138Q LEU* 3.7 34.1 - - + -
141Q ILE* 5.5 6.7 - - + -
145Q LEU* 5.3 11.7 - - + -
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Residues in contact with GLU 21 (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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17Q ASN 2.9 23.4 + - - +
18Q GLY* 3.6 7.2 - - - +
19Q TRP 3.2 0.2 - - - -
20Q LEU* 1.3 76.2 - - - +
22Q LEU* 1.3 62.4 + - - +
24Q GLY* 3.4 1.0 + - - -
25Q ALA* 2.9 26.0 + - - +
55Q ARG* 3.3 42.3 - - - +
56Q PRO* 4.4 9.5 - - - +
88Q TYR* 3.9 16.8 - - + +
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Residues in contact with LEU 22 (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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18Q GLY 2.9 18.3 + - - +
19Q TRP* 3.6 25.1 - - + +
21Q GLU* 1.3 80.5 + - - +
23Q TRP* 1.3 59.9 + - + +
25Q ALA 3.4 0.5 + - - -
26Q TRP* 2.9 27.9 + - - +
56Q PRO* 3.3 37.6 - - + +
57Q MET* 3.4 19.5 - - - +
58Q CYS* 3.7 31.0 - - + -
62Q ASP* 5.4 0.2 - - - +
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Residues in contact with TRP 23 (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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393D THR* 5.8 4.0 - - + -
19Q TRP 2.9 17.8 + - - +
20Q LEU* 3.7 28.7 - - + +
21Q GLU 3.2 0.2 - - - -
22Q LEU* 1.3 78.3 - - - +
24Q GLY* 1.3 67.1 + - - +
26Q TRP* 3.1 24.1 + + - +
27Q VAL* 2.9 44.3 + - + +
58Q CYS* 5.4 0.4 - - - -
63Q GLY* 4.8 0.2 - - - -
66Q ILE* 3.6 31.6 - - + +
67Q SER* 3.2 22.1 + - - -
70Q VAL* 3.8 35.2 - - + -
81Q PHE* 4.7 5.8 - + - -
84Q LEU* 3.6 32.5 - - + -
85Q LEU* 4.6 15.0 - - + -
88Q TYR* 5.1 6.7 - + + -
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Residues in contact with GLY 24 (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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20Q LEU 2.9 16.8 + - - -
21Q GLU 3.9 0.4 - - - -
23Q TRP* 1.3 75.5 - - - +
25Q ALA* 1.3 60.1 + - - +
27Q VAL* 3.5 12.4 - - - +
28Q TYR* 2.9 31.7 + - - +
88Q TYR* 3.6 31.8 - - - +
89Q ALA* 4.1 0.7 - - - -
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Residues in contact with ALA 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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21Q GLU* 2.9 19.2 + - - +
22Q LEU 3.7 0.2 - - - +
24Q GLY* 1.3 74.1 - - - +
26Q TRP* 1.3 63.7 + - - +
28Q TYR* 3.7 11.1 + - - +
29Q SER* 3.8 6.4 + - - -
55Q ARG* 3.8 28.9 - - + +
56Q PRO 3.5 20.4 - - - +
57Q MET* 3.5 14.6 - - + +
88Q TYR 4.3 1.0 + - - -
56R A 4.4 14.7 + - + +
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Residues in contact with TRP 26 (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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393D THR* 6.0 0.4 - - + -
395D LYS* 3.5 45.7 - - + +
396D ALA* 4.9 9.6 - - + -
399D LYS* 4.7 5.6 - - + -
22Q LEU 2.9 14.1 + - - +
23Q TRP* 3.1 24.9 + + - +
25Q ALA* 1.3 78.0 - - - +
27Q VAL* 1.3 71.6 + - + +
28Q TYR 3.3 1.0 + - - -
29Q SER* 3.4 14.7 + - - -
57Q MET* 3.8 23.5 - - + +
58Q CYS* 3.5 21.5 - - - -
60Q ASP* 2.5 44.9 + - + -
63Q GLY* 3.4 21.5 - - - -
64Q MET* 4.0 9.6 - - + -
67Q SER* 3.3 24.9 - - - -
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Residues in contact with VAL 27 (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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393D THR* 4.2 32.9 + - + +
395D LYS* 4.3 10.6 + - + +
23Q TRP* 2.9 42.0 + - + +
24Q GLY* 3.5 18.6 - - - +
26Q TRP* 1.3 89.4 - - + +
28Q TYR* 1.3 59.7 + - - +
29Q SER 3.4 0.4 + - - -
30Q GLY* 4.1 7.9 + - - -
31Q ARG* 5.1 2.1 + - - +
85Q LEU* 4.8 16.6 - - + -
89Q ALA* 4.7 11.4 - - + +
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Residues in contact with TYR 28 (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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24Q GLY 2.9 18.6 + - - +
25Q ALA* 4.1 7.2 - - - +
26Q TRP 3.2 0.8 - - - -
27Q VAL* 1.3 76.5 - - - +
29Q SER* 1.3 50.2 + - - +
30Q GLY 3.2 9.6 + - - -
31Q ARG* 2.5 77.1 + - + -
89Q ALA* 3.1 44.0 - - + +
90Q HIS* 4.3 20.8 - - + -
55R G 4.8 4.6 - - - -
56R A 3.2 51.7 + + + -
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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