Contacts of the helix formed by residues 9 - 26 (chain t) 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 t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53s THR* 4.2 4.7 - - - -
8t ARG* 1.3 75.6 - - - +
10t TYR* 1.3 64.0 + - - +
11t SER* 2.7 28.1 + - - -
12t GLN* 2.8 23.8 + - - +
13t ARG* 3.0 21.4 + - - +
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Residues in contact with TYR 10 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46s GLN* 5.2 13.7 + - + +
49s VAL* 4.6 6.3 - - + -
50s PRO* 3.7 40.4 - - + -
53s THR* 3.1 39.7 - - + +
9t SER* 1.3 75.3 - - - +
11t SER* 1.3 76.7 - - - +
13t ARG* 3.5 6.5 - - - +
14t TYR* 2.8 49.7 + + + -
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Residues in contact with SER 11 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9t SER* 2.7 21.7 + - - -
10t TYR* 1.3 102.7 - - - +
12t GLN* 1.3 59.0 + - - +
14t TYR* 3.9 3.9 - - - +
15t ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 12 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2778 A 4.1 3.6 + - - -
7t SER 4.7 1.5 + - - +
8t ARG* 3.6 27.8 - - - +
9t SER* 2.8 39.2 + - - +
10t TYR 3.1 0.2 - - - -
11t SER* 1.3 82.7 + - - +
13t ARG* 1.3 65.3 + - - +
15t ALA* 3.7 5.4 - - - +
16t LYS* 3.1 26.0 + - - +
40u VAL* 5.0 2.1 - - - +
43u GLN* 5.3 7.8 - - + +
44u ASN* 2.9 32.9 + - - +
47u THR* 4.9 15.2 + - - +
48u ASN* 5.5 3.0 - - - +
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Residues in contact with ARG 13 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737 A 3.9 14.8 + - - -
747 T 4.8 5.5 + - - -
2768 T 3.8 30.5 + - + +
2778 A 3.6 58.4 + - - +
45s PHE* 4.5 7.1 - - + -
49s VAL* 3.8 20.5 + - + +
52s PHE* 4.5 4.6 - - - +
53s THR* 2.7 47.9 + - - +
56s ASN* 4.0 11.2 - - - +
8t ARG* 4.3 8.1 - - + -
9t SER 3.0 21.0 + - - +
10t TYR* 3.5 7.4 - - + +
12t GLN* 1.3 76.5 - - - +
14t TYR* 1.3 57.2 + - - +
17t TRP* 3.0 30.6 + - - +
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Residues in contact with TYR 14 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42s GLN* 3.9 11.0 + - - +
45s PHE* 3.5 32.9 - + + -
46s GLN* 3.4 41.4 + - + -
10t TYR* 2.8 35.2 + + + +
11t SER* 3.9 4.3 - - - +
13t ARG* 1.3 74.7 - - - +
15t ALA* 1.3 72.3 + - + +
17t TRP* 3.0 13.9 + + - +
18t GLN* 2.7 60.5 + - + +
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Residues in contact with ALA 15 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11t SER 2.9 20.7 + - - +
12t GLN* 3.3 7.8 + - - +
14t TYR* 1.3 84.9 - - + +
16t LYS* 1.3 62.4 + - - +
18t GLN* 3.3 6.0 + - - +
19t ALA* 3.1 19.1 + - - +
40u VAL* 4.1 22.5 - - + +
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Residues in contact with LYS 16 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647 T 3.7 34.1 + - - +
657 A 2.8 31.9 + - - -
2768 T 3.3 33.3 + - - +
2778 A 3.9 22.6 + - - +
12t GLN 3.1 12.2 + - - +
15t ALA* 1.3 76.1 - - - +
17t TRP* 1.3 66.8 + - - +
19t ALA* 3.1 5.0 + - - +
20t LYS* 2.9 26.0 + - + +
37u VAL* 4.7 7.9 - - + -
40u VAL* 3.9 19.0 - - + +
44u ASN* 5.5 3.1 - - - +
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Residues in contact with TRP 17 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757 A 3.8 33.3 + - + -
2758 A 3.8 25.8 + - + -
2768 T 3.8 19.2 - - - +
41s ALA* 4.1 20.6 - - + -
42s GLN* 4.2 7.0 - - + -
45s PHE* 3.5 55.1 - + + -
13t ARG 3.0 21.1 + - - +
14t TYR* 3.0 15.7 + + - +
16t LYS* 1.3 75.7 - - - +
18t GLN* 1.3 92.3 + - - +
20t LYS* 3.8 1.9 - - - +
21t PHE* 2.9 53.3 + + + +
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Residues in contact with GLN 18 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42s GLN* 3.2 39.6 - - - +
14t TYR* 2.7 57.0 + - + +
15t ALA* 3.5 6.3 - - - +
17t TRP* 1.3 82.8 - - - +
19t ALA* 1.3 62.3 + - - +
21t PHE* 3.2 6.7 + - - +
22t ASN* 2.9 62.7 + - - +
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Residues in contact with ALA 19 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15t ALA 3.1 9.4 + - - +
16t LYS* 3.1 11.3 + - - +
18t GLN* 1.3 80.1 - - - +
20t LYS* 1.3 58.6 + - - +
22t ASN* 3.5 9.5 + - - +
23t ALA* 3.0 26.5 + - - +
36u ASN* 3.4 34.7 - - - +
37u VAL* 3.7 16.6 - - + -
40u VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 20 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657 A 2.8 31.1 + - - +
667 T 3.1 24.9 + - - -
2758 A 3.4 43.5 + - - +
2768 T 3.2 21.2 + - - +
16t LYS* 2.9 21.3 + - + +
17t TRP 3.9 3.4 - - - +
19t ALA* 1.3 74.1 - - - +
21t PHE* 1.3 66.4 + - - +
23t ALA* 3.3 4.1 + - + +
24t PHE* 3.0 24.6 + - - +
33u ILE* 3.9 19.5 - - + -
37u VAL* 3.6 17.0 - - + -
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Residues in contact with PHE 21 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757 A 5.7 2.9 - + - -
767 T 4.5 23.3 - - - -
2748 T 6.0 1.8 - - - -
2758 A 5.2 2.6 - - - -
34s LEU* 3.9 30.5 - - + -
37s VAL* 4.5 5.2 - - + -
38s SER* 3.5 37.5 - - - -
41s ALA* 4.5 9.2 - - + -
42s GLN* 5.8 0.2 - - + -
17t TRP* 2.9 49.9 + + + +
18t GLN* 3.2 12.1 + - - +
20t LYS* 1.3 77.8 - - - +
22t ASN* 1.3 72.3 + - - +
24t PHE* 3.3 12.1 + + - +
25t SER* 3.0 22.2 + - - -
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Residues in contact with ASN 22 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38s SER* 5.5 2.3 + - - -
42s GLN* 4.6 3.3 + - - -
18t GLN* 2.9 52.9 + - - +
19t ALA* 3.5 8.9 - - - +
21t PHE* 1.3 80.7 - - - +
23t ALA* 1.3 63.1 + - - +
25t SER* 2.6 25.5 + - - -
26t ASN* 3.6 3.8 + - - +
36u ASN* 4.0 11.7 - - - +
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Residues in contact with ALA 23 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19t ALA 3.0 14.0 + - - +
20t LYS* 3.5 9.6 - - + +
21t PHE 3.2 0.2 - - - -
22t ASN* 1.3 79.4 - - - +
24t PHE* 1.3 63.1 + - - +
26t ASN* 3.1 21.8 + - - +
29t VAL* 3.3 11.4 - - + +
32u THR* 3.6 14.1 - - + -
33u ILE* 3.8 27.4 - - + -
36u ASN* 3.5 17.4 - - - +
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Residues in contact with PHE 24 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777 A 6.0 0.4 - - - -
2748 T 3.7 50.3 - - + +
2758 A 5.4 3.1 - - - -
24s PHE* 4.4 9.0 - + - -
34s LEU* 3.5 30.7 - - + -
20t LYS 3.0 16.3 + - - +
21t PHE* 3.7 11.2 - + - +
23t ALA* 1.3 76.5 - - - +
25t SER* 1.3 61.7 + - - +
26t ASN 3.0 1.6 + - - -
29t VAL* 3.8 6.1 - - + -
30t ALA* 3.3 46.2 + - - +
33t ILE* 4.2 19.5 - - + -
34t LEU* 4.0 25.1 - - + -
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Residues in contact with SER 25 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31s SER* 3.4 21.7 - - - +
34s LEU* 3.8 37.5 - - - -
35s SER* 4.5 7.0 - - - -
38s SER* 4.7 6.8 + - - -
21t PHE* 3.0 15.4 + - - -
22t ASN* 2.6 23.9 + - - -
24t PHE* 1.3 75.7 - - - +
26t ASN* 1.3 61.8 + - - +
27t PRO* 3.2 4.2 - - - +
30t ALA* 4.9 0.7 - - - -
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Residues in contact with ASN 26 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22t ASN 4.5 2.0 - - - +
23t ALA 3.1 16.3 + - - +
24t PHE 3.0 1.6 + - - -
25t SER* 1.3 78.5 + - - +
27t PRO* 1.4 68.4 - - - +
28t THR* 2.9 24.5 + - - -
29t VAL* 2.7 36.8 + - + -
30t ALA* 2.8 11.0 + - - -
32u THR* 4.0 18.4 + - + +
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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