Contacts of the helix formed by residues 9 - 26 (chain D) in PDB entry 3J9X
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 9 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C THR* 4.2 5.2 - - - -
8D ARG* 1.3 75.2 - - - +
10D TYR* 1.3 64.9 + - - +
11D SER* 2.7 28.2 + - - -
12D GLN* 2.8 24.1 + - - +
13D ARG* 3.0 21.0 + - - +
47h THR* 5.8 6.5 - - - -
50h PRO* 6.4 2.0 - - - -
51h LYS* 6.4 2.2 - - - -
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Residues in contact with TYR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 5.3 0.4 - + - -
46C GLN* 5.2 12.3 + - - +
49C VAL* 4.6 6.1 - - + -
50C PRO* 3.7 35.0 - - + -
53C THR* 3.1 40.4 - - + +
9D SER* 1.3 75.3 - - - +
11D SER* 1.3 76.4 + - - +
13D ARG* 3.5 6.1 - - - +
14D TYR* 2.8 49.6 + + + -
10g TYR* 2.8 47.7 + + - -
11g SER* 5.0 3.5 + - - -
14g TYR* 5.5 1.9 - - - -
50h PRO* 4.1 16.8 - - + -
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Residues in contact with SER 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER* 2.7 21.2 + - - -
10D TYR* 1.3 100.4 - - - +
12D GLN* 1.3 59.9 + - - +
14D TYR* 3.9 4.3 - - - +
15D ALA* 2.9 29.5 + - - +
10g TYR* 5.5 0.2 - - - -
43h GLN* 5.2 6.5 + - - -
46h GLN* 4.3 37.7 + - - +
47h THR* 5.0 3.8 + - - -
50h PRO* 5.7 0.4 - - - -
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Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 A 4.1 3.1 + - - -
7D SER 4.7 1.5 + - - +
8D ARG* 3.6 26.9 - - - +
9D SER* 2.8 38.9 + - - +
10D TYR 3.1 0.4 - - - -
11D SER* 1.3 83.6 + - - +
13D ARG* 1.3 64.5 + - - +
15D ALA* 3.7 5.6 - - - +
16D LYS* 3.1 26.3 + - - +
40E VAL* 5.0 2.6 - - + +
43E GLN* 5.3 8.1 - - + +
44E ASN* 2.9 32.0 + - - +
47E THR* 4.9 15.9 + - - +
48E ASN* 5.5 3.4 - - - +
43h GLN* 6.2 1.8 - - - +
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3257 A 3.9 15.0 + - - -
3267 T 4.8 5.7 + - - -
248 T 3.8 30.3 + - + +
258 A 3.6 58.5 + - - +
45C PHE* 4.5 7.3 - - + -
49C VAL* 3.8 19.9 + - + +
52C PHE* 4.5 4.8 - - - +
53C THR* 2.7 48.2 + - - +
56C ASN* 4.0 11.2 - - - +
8D ARG* 4.3 7.4 - - + -
9D SER 3.0 20.9 + - - +
10D TYR* 3.2 7.6 + - + +
12D GLN* 1.3 77.5 - - - +
14D TYR* 1.3 56.3 + - - +
17D TRP* 3.0 30.2 + - - +
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Residues in contact with TYR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLN* 3.9 10.3 + - - +
45C PHE* 3.5 34.0 - + + -
46C GLN* 3.4 41.0 + - + -
10D TYR* 2.8 35.4 + + + +
11D SER* 3.9 4.3 - - - +
13D ARG* 1.3 74.7 - - - +
15D ALA* 1.3 71.5 + - - +
17D TRP* 3.0 14.7 + + - +
18D GLN* 2.7 60.2 + - + +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER 2.9 21.1 + - - +
12D GLN* 3.3 7.8 + - - +
14D TYR* 1.3 84.3 - - + +
16D LYS* 1.3 62.4 + - - +
18D GLN* 3.3 5.4 + - - +
19D ALA* 3.1 19.6 + - - +
40E VAL* 4.1 21.7 - - + +
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Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3167 T 3.7 33.8 + - - +
3177 A 2.8 32.3 + - - -
248 T 3.3 32.6 + - - +
258 A 3.9 22.2 + - - +
12D GLN 3.1 12.8 + - - +
15D ALA* 1.3 77.0 - - - +
17D TRP* 1.3 67.9 + - - +
19D ALA* 3.1 5.1 + - - +
20D LYS* 3.0 26.1 + - + +
37E VAL* 4.7 8.3 - - + -
40E VAL* 3.9 18.1 - - + +
44E ASN* 5.5 3.4 - - - +
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Residues in contact with TRP 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3277 A 3.8 33.5 + - + -
238 A 3.8 27.6 + - + -
248 T 3.8 18.8 - - - +
41C ALA* 4.1 21.1 - - + -
42C GLN* 4.2 7.2 - - + -
45C PHE* 3.5 56.0 - + + -
13D ARG 3.0 20.7 + - - +
14D TYR* 3.4 15.0 - + - +
16D LYS* 1.3 76.3 - - - +
18D GLN* 1.3 93.6 + - - +
20D LYS* 3.4 2.3 + - - +
21D PHE* 2.8 52.8 + + + +
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Residues in contact with GLN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN* 3.2 40.0 - - - +
14D TYR* 2.7 57.3 + - + +
15D ALA* 3.5 7.0 - - - +
17D TRP* 1.3 83.0 - - - +
19D ALA* 1.3 62.7 + - - +
21D PHE* 3.2 5.7 + - - -
22D ASN* 2.9 62.1 + - - +
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA 3.1 9.4 + - - +
16D LYS* 3.1 10.8 + - - +
18D GLN* 1.3 78.9 - - - +
20D LYS* 1.3 59.6 + - - +
22D ASN* 3.5 9.7 + - - +
23D ALA* 3.0 26.3 + - - +
36E ASN* 3.4 33.5 - - - +
37E VAL* 3.7 17.3 - - + -
40E VAL* 4.5 4.3 - - + -
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3177 A 2.8 31.1 + - - +
3187 T 3.1 24.7 + - - -
238 A 3.4 42.6 + - - +
248 T 3.2 21.5 + - - +
16D LYS* 3.0 21.0 + - + +
17D TRP 3.9 3.6 - - - +
19D ALA* 1.3 75.0 - - - +
21D PHE* 1.3 65.8 + - - +
23D ALA* 3.3 4.4 + - + +
24D PHE* 3.0 24.6 + - - +
33E ILE* 3.9 18.6 - - + -
37E VAL* 3.6 17.3 - - + -
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Residues in contact with PHE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3277 A 5.7 2.7 - + - -
3287 T 4.5 23.6 - - - -
228 T 6.0 1.8 - - - -
238 A 5.2 2.4 - - - -
34C LEU* 3.9 31.2 - - + -
37C VAL* 4.5 4.9 - - + -
38C SER* 3.5 37.9 - - - -
41C ALA* 4.5 9.2 - - + -
42C GLN* 5.8 0.2 - - + -
17D TRP* 2.8 48.8 + + + +
18D GLN* 3.6 12.3 - - - +
20D LYS* 1.3 77.2 - - - +
22D ASN* 1.3 73.6 + - - +
24D PHE* 3.3 12.2 + + - +
25D SER* 3.0 23.0 + - - -
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C SER* 5.5 2.3 + - - -
42C GLN* 4.6 2.6 + - - -
18D GLN* 2.9 51.4 + - - +
19D ALA* 3.5 8.7 - - - +
21D PHE* 1.3 81.2 - - - +
23D ALA* 1.3 62.3 + - - +
25D SER* 2.6 25.7 + - - -
26D ASN* 3.6 4.2 + - - +
36E ASN* 4.0 11.9 - - - +
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA 3.0 14.7 + - - +
20D LYS* 3.5 8.7 - - + +
21D PHE 3.2 0.2 - - - -
22D ASN* 1.3 78.7 - - - +
24D PHE* 1.3 63.3 + - - +
26D ASN* 3.1 22.0 + - - +
29D VAL* 3.3 11.2 - - + +
32E THR* 3.6 14.4 - - + -
33E ILE* 3.8 27.8 - - + -
36E ASN* 3.5 15.7 - - - +
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Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3297 A 6.0 0.2 - - - -
228 T 3.7 51.4 - - + +
238 A 5.4 2.7 - - - -
24C PHE* 4.4 8.7 - + - -
34C LEU* 3.5 30.7 - - + -
20D LYS 3.0 17.0 + - - +
21D PHE* 3.3 11.4 + + - +
23D ALA* 1.3 76.7 - - - +
25D SER* 1.3 61.9 + - - +
26D ASN 3.0 1.4 + - - -
29D VAL* 3.8 5.8 - - - -
30D ALA* 3.3 45.2 + - - +
33D ILE* 4.2 19.3 - - + -
34D LEU* 4.0 25.1 - - + -
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER* 3.4 22.5 - - - +
34C LEU* 3.8 36.6 - - - -
35C SER* 4.5 6.7 - - - -
38C SER* 4.7 7.1 + - - -
21D PHE* 3.0 15.4 + - - -
22D ASN* 2.6 23.5 + - - -
24D PHE* 1.3 75.1 - - - +
26D ASN* 1.3 61.5 + - - +
27D PRO* 3.2 4.3 - - - +
30D ALA* 4.9 0.7 - - - -
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Residues in contact with ASN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ASN 4.5 2.7 - - - +
23D ALA 3.1 15.4 + - - +
24D PHE 3.0 1.4 + - - -
25D SER* 1.3 78.6 + - - +
27D PRO* 1.4 66.8 - - - +
28D THR* 2.9 23.9 + - - -
29D VAL* 2.7 37.2 + - + -
30D ALA* 2.8 11.9 + - - -
32E THR* 4.0 19.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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