Contacts of the helix formed by residues 9 - 26 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ARG* 1.3 74.7 - - - +
10S TYR* 1.3 61.0 + - - +
11S SER* 3.6 9.6 + - - -
12S GLN* 2.8 36.0 + - - +
13S ARG* 2.8 27.3 + - - +
53T THR* 4.3 3.1 - - - -
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Residues in contact with TYR 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S SER* 1.3 74.4 - - - +
11S SER* 1.3 72.5 + - - +
13S ARG* 3.0 5.1 + - + -
14S TYR* 2.9 47.6 + + + +
45T PHE* 4.1 1.1 - + - -
46T GLN* 3.3 36.1 + - - +
49T VAL* 3.8 17.0 - - + -
50T PRO* 3.5 48.0 - - + -
53T THR* 3.5 32.0 - - + +
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Residues in contact with SER 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S SER* 3.2 9.5 + - - -
10S TYR* 1.3 87.6 - - - +
12S GLN* 1.3 60.6 + - - +
14S TYR* 4.1 2.9 - - - +
15S ALA* 3.0 31.1 + - - +
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Residues in contact with GLN 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2367 T 4.5 3.4 + - - -
40R VAL* 5.2 1.9 - - - +
43R GLN* 5.3 8.8 - - + +
44R ASN* 2.9 34.0 + - - +
47R THR* 4.6 19.7 + - - +
48R ASN* 5.2 1.6 - - - +
7S SER 4.2 5.2 + - - +
8S ARG* 3.6 28.4 - - - +
9S SER* 2.8 38.9 + - - +
11S SER* 1.3 77.7 - - - +
13S ARG* 1.3 65.2 + - - +
15S ALA* 3.7 5.6 - - - +
16S LYS* 3.2 25.1 + - - +
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Residues in contact with ARG 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2357 A 3.4 52.9 + - + +
2367 T 3.6 40.4 + - - -
1148 T 4.1 7.3 + - - -
1158 A 5.3 5.5 + - - -
8S ARG* 4.1 6.3 - - + +
9S SER 2.8 21.7 + - - +
10S TYR* 3.0 9.8 + - + +
12S GLN* 1.3 72.3 - - - +
14S TYR* 1.3 63.9 + - - +
17S TRP* 3.1 23.5 + - - +
45T PHE* 4.6 7.8 - - + -
49T VAL* 3.7 21.0 + - - +
52T PHE* 4.6 4.8 - - - +
53T THR* 2.8 44.4 + - - +
56T ASN* 4.3 11.4 - - - +
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Residues in contact with TYR 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S TYR* 2.9 37.0 + + + +
11S SER* 4.1 3.6 - - - +
13S ARG* 1.3 77.6 - - - +
15S ALA* 1.3 68.7 + - - +
17S TRP* 3.1 15.8 + + - -
18S GLN* 2.7 58.2 + - + +
42T GLN* 3.7 8.9 + - - +
45T PHE* 3.4 35.4 - + + -
46T GLN* 2.9 37.4 + - + -
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Residues in contact with ALA 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R VAL* 4.0 22.2 - - + +
11S SER 3.0 21.0 + - - +
12S GLN* 3.4 7.8 + - - +
14S TYR* 1.3 82.0 - - - +
16S LYS* 1.3 63.4 + - - +
18S GLN* 3.3 6.9 + - - +
19S ALA* 3.2 19.2 + - - +
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Residues in contact with LYS 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2357 A 3.3 42.5 + - - +
2367 T 4.3 14.7 + - - +
1058 A 3.8 37.4 + - - +
1068 T 2.8 35.2 + - - +
37R VAL* 4.9 7.9 - - + -
40R VAL* 3.9 18.6 - - + -
44R ASN* 5.0 2.5 - - - +
8S ARG* 6.0 0.4 - - - +
12S GLN 3.2 12.8 + - - +
15S ALA* 1.3 76.4 - - - +
17S TRP* 1.3 66.9 + - - +
19S ALA* 3.1 4.7 + - - +
20S LYS* 3.0 25.1 + - + +
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Residues in contact with TRP 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2347 T 3.6 19.6 + - + +
2357 A 3.5 27.9 - - - +
1158 A 5.0 0.2 - + - -
1168 T 2.9 36.3 + - + -
13S ARG 3.1 18.9 + - - +
14S TYR* 3.1 22.5 + + - +
16S LYS* 1.3 76.8 - - - +
18S GLN* 1.3 94.6 + - - +
20S LYS* 3.4 1.8 + - - +
21S PHE* 2.9 51.3 + + + +
41T ALA* 4.1 21.5 - - + -
42T GLN* 4.3 5.4 - - + -
45T PHE* 3.5 44.5 - + + -
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Residues in contact with GLN 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14S TYR* 2.7 50.8 + - + +
15S ALA* 3.5 10.1 - - - +
17S TRP* 1.3 87.1 - - - +
19S ALA* 1.3 63.7 + - - +
21S PHE* 3.2 6.7 + - - +
22S ASN* 2.9 62.6 + - - +
42T GLN* 3.2 37.7 - - - +
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Residues in contact with ALA 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R ASN* 3.4 35.2 - - - +
37R VAL* 3.7 17.3 - - + -
40R VAL* 4.3 7.0 - - + -
15S ALA 3.2 9.4 + - - +
16S LYS 3.1 9.5 + - - +
18S GLN* 1.3 80.8 - - - +
20S LYS* 1.3 59.1 + - - +
22S ASN* 3.5 9.4 + - - +
23S ALA* 3.1 26.0 + - - +
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Residues in contact with LYS 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2347 T 3.5 40.9 + - + +
2357 A 3.1 30.6 + - - +
1068 T 2.8 31.6 + - - +
1078 A 3.2 27.9 + - - -
33R ILE* 4.0 21.3 - - + -
37R VAL* 3.7 15.7 - - + -
16S LYS* 3.0 16.8 + - + +
17S TRP 3.9 2.9 - - - +
19S ALA* 1.3 72.6 - - - +
21S PHE* 1.3 66.5 + - - +
23S ALA* 3.3 3.5 + - - +
24S PHE* 3.0 24.3 + - - +
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Residues in contact with PHE 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2337 A 6.1 4.0 - + - -
2347 T 5.6 2.8 - - - +
1168 T 5.8 0.4 - - - -
1178 A 4.5 23.8 - - - -
17S TRP* 2.9 45.7 + + + +
18S GLN* 3.6 10.1 - - - +
20S LYS* 1.3 77.2 - - - +
22S ASN* 1.3 74.1 + - - +
24S PHE* 3.3 12.7 + + - +
25S SER* 3.1 22.5 + - - -
34T LEU* 4.1 30.7 - - + -
37T VAL* 4.6 4.9 - - + -
38T SER* 3.6 37.0 - - - -
41T ALA* 4.3 11.9 - - + -
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Residues in contact with ASN 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R ASN* 4.0 12.2 - - - +
18S GLN* 2.9 52.7 + - - +
19S ALA* 3.6 7.7 - - - +
21S PHE* 1.3 80.5 - - - +
23S ALA* 1.3 63.1 + - - +
25S SER* 2.6 25.3 + - - -
26S ASN* 3.6 3.5 + - - +
38T SER* 5.5 2.3 + - - -
42T GLN* 4.7 2.9 + - - -
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Residues in contact with ALA 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R THR* 3.6 15.9 - - + +
33R ILE* 3.8 28.0 - - + -
36R ASN* 3.4 17.2 - - + +
19S ALA 3.1 11.2 + - - +
20S LYS* 3.5 11.9 - - - +
22S ASN* 1.3 78.4 - - - +
24S PHE* 1.3 63.6 + - - +
26S ASN* 3.1 22.3 + - - +
29S VAL* 3.5 9.6 - - - +
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Residues in contact with PHE 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2337 A 3.7 51.8 - - + -
2347 T 4.6 8.3 - - - +
20S LYS 3.0 16.3 + - - +
21S PHE* 3.3 12.1 + + - +
23S ALA* 1.3 75.7 - - - +
25S SER* 1.3 62.9 + - - +
26S ASN 3.0 1.7 + - - -
29S VAL* 4.0 6.1 - - - -
30S ALA* 3.3 45.4 + - + +
33S ILE* 4.3 14.1 - - + -
34S LEU* 4.0 22.2 - - + -
24T PHE* 4.4 8.7 - + - -
34T LEU* 3.5 30.7 - - + -
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Residues in contact with SER 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S PHE* 3.1 15.7 + - - -
22S ASN* 2.6 23.3 + - - -
24S PHE* 1.3 75.9 - - - +
26S ASN* 1.3 61.8 + - - +
27S PRO* 3.2 4.3 - - - +
30S ALA* 5.0 0.6 - - - +
31T SER* 3.5 21.8 - - - +
34T LEU* 3.9 35.2 - - - -
35T SER* 4.6 6.4 - - - -
38T SER* 4.6 8.2 + - - -
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Residues in contact with ASN 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R THR* 4.9 2.8 - - - +
32R THR* 4.0 19.4 + - + +
22S ASN 3.6 2.2 + - - +
23S ALA 3.1 16.2 + - - +
24S PHE 3.0 0.8 + - - -
25S SER* 1.3 78.5 + - - +
27S PRO* 1.4 66.4 - - - +
28S THR* 2.7 33.7 + - - +
29S VAL* 2.7 33.6 + - + -
30S ALA* 2.9 12.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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