Contacts of the helix formed by residues 9 - 26 (chain x) 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 x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53w THR* 4.2 5.4 - - - -
8x ARG* 1.3 75.9 - - - +
10x TYR* 1.3 66.4 + - - +
11x SER* 2.7 27.6 + - - -
12x GLN* 2.8 24.0 + - - +
13x ARG* 3.0 20.7 + - - +
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Residues in contact with TYR 10 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46w GLN* 5.2 14.4 + - - +
49w VAL* 4.6 6.3 - - + -
50w PRO* 3.7 41.4 - - + +
53w THR* 3.1 39.7 - - + +
9x SER* 1.3 76.1 - - - +
11x SER* 1.3 76.8 + - - +
13x ARG* 3.5 6.5 - - - +
14x TYR* 2.8 50.8 + + + -
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Residues in contact with SER 11 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9x SER* 2.7 21.9 + - - -
10x TYR* 1.3 102.7 - - - +
12x GLN* 1.3 59.7 + - - +
14x TYR* 3.9 4.1 - - - +
15x ALA* 2.9 29.1 + - - +
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Residues in contact with GLN 12 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3018 A 4.1 3.2 + - - -
7x SER 4.7 1.8 + - - +
8x ARG* 3.6 26.5 - - - +
9x SER* 2.8 40.3 + - - +
10x TYR 3.1 0.2 - - - -
11x SER* 1.3 83.9 + - - +
13x ARG* 1.3 64.7 + - - +
15x ALA* 3.7 5.2 - - - +
16x LYS* 3.1 25.6 + - - +
40y VAL* 5.0 2.2 - - - +
43y GLN* 5.3 7.4 - - + +
44y ASN* 2.9 33.3 + - - +
47y THR* 4.9 15.0 + - - +
48y ASN* 5.5 3.2 - - - +
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Residues in contact with ARG 13 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497 A 3.9 14.8 + - - -
507 T 4.8 5.7 + - - -
3008 T 3.8 30.7 + - + +
3018 A 3.6 57.9 + - - +
45w PHE* 4.5 8.6 - - + -
49w VAL* 3.8 19.2 + - + +
52w PHE* 4.5 4.8 - - - +
53w THR* 2.7 49.3 + - - +
56w ASN* 4.0 11.4 - - - +
8x ARG* 4.3 7.9 - - + -
9x SER 3.0 21.4 + - - +
10x TYR* 3.5 7.0 - - - +
12x GLN* 1.3 77.5 - - - +
14x TYR* 1.3 57.1 + - - +
17x TRP* 3.0 29.2 + - - +
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Residues in contact with TYR 14 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42w GLN* 3.9 9.9 + - - +
45w PHE* 3.5 33.1 - + + -
46w GLN* 3.4 41.4 + - + -
10x TYR* 2.8 34.4 + + + +
11x SER* 3.9 4.0 - - - +
13x ARG* 1.3 75.1 - - - +
15x ALA* 1.3 70.9 + - + +
17x TRP* 3.0 13.8 + + - -
18x GLN* 2.7 60.3 + - + +
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Residues in contact with ALA 15 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11x SER 2.9 18.8 + - - +
12x GLN* 3.3 8.5 + - - +
14x TYR* 1.3 84.5 - - + +
16x LYS* 1.3 61.7 + - - +
18x GLN* 3.3 5.4 + - - +
19x ALA* 3.1 19.6 + - - +
40y VAL* 4.1 21.6 - - + +
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Residues in contact with LYS 16 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407 T 3.7 33.8 + - - +
417 A 2.8 32.3 + - - -
3008 T 3.3 33.7 + - - +
3018 A 3.9 22.4 + - - +
12x GLN 3.1 12.2 + - - +
15x ALA* 1.3 77.6 - - - +
17x TRP* 1.3 67.1 + - - +
19x ALA* 3.1 4.7 + - - +
20x LYS* 3.0 24.9 + - + +
37y VAL* 4.7 8.5 - - + -
40y VAL* 3.9 18.6 - - + +
44y ASN* 5.5 2.9 - - - +
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Residues in contact with TRP 17 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517 A 3.8 34.4 + - + -
2998 A 3.8 27.4 + - + -
3008 T 3.8 19.8 - - - +
41w ALA* 4.1 20.9 - - + -
42w GLN* 4.2 7.2 - - + -
45w PHE* 3.5 55.8 - + + -
13x ARG 3.0 20.2 + - - +
14x TYR* 3.0 15.7 + + - +
16x LYS* 1.3 76.2 - - - +
18x GLN* 1.3 91.7 + - - +
20x LYS* 3.4 1.9 + - - +
21x PHE* 2.9 53.7 + + + +
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Residues in contact with GLN 18 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42w GLN* 3.2 38.7 - - - +
14x TYR* 2.7 58.3 + - + +
15x ALA* 3.5 7.0 - - - +
17x TRP* 1.3 83.4 - - - +
19x ALA* 1.3 62.6 + - - +
21x PHE* 3.2 6.1 + - - -
22x ASN* 2.9 63.0 + - - +
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Residues in contact with ALA 19 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15x ALA 3.1 9.4 + - - +
16x LYS* 3.1 10.2 + - - +
18x GLN* 1.3 79.7 - - - +
20x LYS* 1.3 59.1 + - - +
22x ASN* 3.5 10.2 + - - +
23x ALA* 3.0 26.7 + - - +
36y ASN* 3.4 35.5 - - - +
37y VAL* 3.7 16.8 - - + -
40y VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 20 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417 A 2.8 32.0 + - - +
427 T 3.1 24.7 + - - -
2998 A 3.4 44.4 + - - +
3008 T 3.2 21.7 + - - +
16x LYS* 3.0 21.3 + - + +
17x TRP 3.9 3.4 - - - +
19x ALA* 1.3 74.7 - - - +
21x PHE* 1.3 67.0 + - - +
23x ALA* 3.3 4.1 + - + +
24x PHE* 3.0 24.1 + - - +
33y ILE* 3.9 19.5 - - + -
37y VAL* 3.6 17.0 - - + -
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Residues in contact with PHE 21 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517 A 5.7 2.5 - + - -
527 T 4.5 23.3 - - - -
2988 T 6.0 1.8 - - - -
2998 A 5.2 2.6 - - - -
34w LEU* 3.9 29.8 - - + -
37w VAL* 4.5 4.9 - - + -
38w SER* 3.5 37.5 - - - -
41w ALA* 4.5 9.2 - - + -
42w GLN* 5.8 0.4 - - + -
17x TRP* 2.9 50.4 + + + +
18x GLN* 3.6 11.9 - - - +
20x LYS* 1.3 77.0 - - - +
22x ASN* 1.3 71.6 + - - +
24x PHE* 3.3 11.6 + + - +
25x SER* 3.0 23.6 + - - -
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Residues in contact with ASN 22 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38w SER* 5.5 2.3 + - - -
42w GLN* 4.6 3.5 + - - -
18x GLN* 2.9 51.3 + - - +
19x ALA* 3.5 8.9 - - - +
21x PHE* 1.3 80.5 - - - +
23x ALA* 1.3 62.5 + - - +
25x SER* 2.6 26.3 + - - -
26x ASN* 3.6 4.3 + - - +
36y ASN* 4.0 11.2 - - - +
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Residues in contact with ALA 23 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19x ALA 3.0 14.4 + - - +
20x LYS* 3.5 9.2 - - + +
21x PHE 3.2 0.4 - - - -
22x ASN* 1.3 79.2 - - - +
24x PHE* 1.3 62.4 + - - +
26x ASN* 3.1 21.8 + - - +
29x VAL* 3.3 11.2 - - + +
32y THR* 3.6 14.6 - - + -
33y ILE* 3.8 27.8 - - + -
36y ASN* 3.5 16.1 - - - +
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Residues in contact with PHE 24 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537 A 6.0 0.2 - - - -
2988 T 3.7 51.6 - - + +
2998 A 5.4 2.9 - - - +
24w PHE* 4.4 9.4 - + - -
34w LEU* 3.5 31.6 - - + -
20x LYS 3.0 17.0 + - - +
21x PHE* 3.7 11.0 - + + +
23x ALA* 1.3 77.1 - - - +
25x SER* 1.3 62.2 + - - +
26x ASN 3.0 1.8 + - - -
29x VAL* 3.8 6.1 - - + -
30x ALA* 3.3 44.8 + - - +
33x ILE* 4.2 18.8 - - + -
34x LEU* 4.0 25.4 - - + -
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Residues in contact with SER 25 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31w SER* 3.4 22.2 - - - +
34w LEU* 3.8 37.9 - - - -
35w SER* 4.5 6.8 - - - -
38w SER* 4.7 6.9 + - - -
21x PHE* 3.0 14.3 + - - -
22x ASN* 2.6 23.7 + - - -
24x PHE* 1.3 75.9 - - - +
26x ASN* 1.3 60.8 + - - +
27x PRO* 3.2 4.9 - - - +
30x ALA* 4.9 0.6 - - - +
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Residues in contact with ASN 26 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22x ASN 4.5 2.5 - - - +
23x ALA 3.1 15.3 + - - +
24x PHE 3.0 1.2 + - - -
25x SER* 1.3 78.3 + - - +
27x PRO* 1.4 67.4 - - - +
28x THR* 2.9 24.5 + - - -
29x VAL* 2.7 36.9 + - + -
30x ALA* 2.8 11.3 + - - -
32y THR* 4.0 18.2 + - + +
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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
------------------------------------------------------------
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