Contacts of the helix formed by residues 26 - 49 (chain Z) 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 ASN 26 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Z ASN 3.6 2.9 + - - +
23Z ALA 3.1 15.3 + - - +
24Z PHE 3.0 1.4 + - - -
25Z SER* 1.3 78.3 + - - +
27Z PRO* 1.4 67.5 - - - +
28Z THR* 2.9 23.7 + - - -
29Z VAL* 2.7 38.0 + - + -
30Z ALA* 2.8 11.9 + - - -
32a THR* 4.0 19.0 + - + +
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Residues in contact with PRO 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Y PRO* 3.5 32.3 - - + +
28Y THR* 5.5 1.3 - - + -
31Y SER* 3.5 18.2 - - - +
25Z SER 3.2 6.6 - - - +
26Z ASN* 1.4 92.6 - - - +
28Z THR* 1.3 60.7 + - - +
30Z ALA* 4.0 2.2 - - + +
31Z SER* 2.8 29.9 + - - -
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Residues in contact with THR 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Z ASN* 2.8 15.8 + - - -
27Z PRO* 1.3 75.2 - - - +
29Z VAL* 1.3 60.3 + - - +
31Z SER* 3.1 4.7 + - - -
32Z THR* 2.5 47.1 + - - +
26a ASN* 4.8 4.3 - - - +
28a THR* 3.1 33.3 - - + +
29a VAL* 4.6 1.1 - - + -
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Residues in contact with VAL 29 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Z ALA 3.3 28.5 - - - +
24Z PHE* 3.8 10.5 - - + +
26Z ASN* 2.7 14.6 + - + +
28Z THR* 1.3 70.9 - - - +
30Z ALA* 1.3 65.3 + - - +
33Z ILE* 3.1 44.0 + - + +
28a THR 4.3 1.3 - - - +
29a VAL* 3.9 30.1 - - + +
32a THR* 3.8 30.5 - - + +
33a ILE* 4.9 6.7 - - + -
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Residues in contact with ALA 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Y ALA* 3.6 28.9 - - + -
34Y LEU* 4.6 2.5 - - + -
24Z PHE* 3.3 36.0 + - + +
25Z SER 4.9 0.9 - - - -
26Z ASN 2.8 11.5 + - - +
27Z PRO* 4.0 4.5 - - + +
29Z VAL* 1.3 77.3 - - - +
31Z SER* 1.3 58.9 + - - +
33Z ILE* 4.0 0.7 - - - +
34Z LEU* 2.9 36.2 + - + +
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Residues in contact with SER 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y SER 3.5 23.3 + - - -
27Y PRO* 3.5 25.3 - - - +
27Z PRO 2.8 21.0 + - - -
28Z THR* 3.1 8.1 + - - +
30Z ALA* 1.3 77.7 - - - +
32Z THR* 1.3 58.5 + - - +
34Z LEU 4.5 0.2 - - - +
35Z SER* 2.6 43.1 + - - -
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Residues in contact with THR 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Z THR* 2.5 34.6 + - - +
29Z VAL 3.7 3.6 - - - -
31Z SER* 1.3 78.3 + - - +
33Z ILE* 1.3 63.6 + - - +
35Z SER* 3.2 3.4 + - - -
36Z ASN* 3.1 35.7 + - - +
23a ALA* 3.6 34.3 - - + +
26a ASN* 4.0 15.5 + - + +
29a VAL* 3.7 15.6 - - + +
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Residues in contact with ILE 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867 T 5.7 2.2 - - - +
1548 T 3.7 37.7 - - - +
1558 A 4.7 6.1 - - - +
24Z PHE* 4.2 14.6 - - + -
29Z VAL* 3.1 33.9 + - + +
30Z ALA 4.0 2.2 - - - +
32Z THR* 1.3 79.4 - - - +
34Z LEU* 1.3 59.3 + - - +
36Z ASN* 3.1 2.9 + - - +
37Z VAL* 3.0 30.0 + - + +
20a LYS* 4.0 24.5 - - + -
23a ALA* 3.8 21.3 - - + -
29a VAL* 4.9 7.4 - - + -
33a ILE* 5.3 5.8 - - + -
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Residues in contact with LEU 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538 A 4.9 7.9 - - + -
1548 T 4.6 13.5 - - - +
21Y PHE* 4.1 21.4 - - + -
24Y PHE* 3.4 41.1 - - + +
25Y SER* 3.9 25.4 - - - -
30Y ALA* 4.5 0.2 - - + -
24Z PHE* 4.0 23.1 - - + -
30Z ALA* 2.9 29.0 + - + +
31Z SER 4.3 0.4 - - - +
33Z ILE* 1.3 77.2 - - - +
35Z SER* 1.3 52.8 + - - +
37Z VAL* 3.4 8.4 + - + +
38Z SER* 2.6 36.5 + - - -
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Residues in contact with SER 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y SER* 4.6 8.4 - - - -
31Z SER* 2.6 27.5 + - - -
32Z THR* 3.2 6.1 + - - -
34Z LEU* 1.3 77.3 - - - +
36Z ASN* 1.3 70.5 + - - +
38Z SER* 3.4 19.9 + - - -
39Z PRO* 4.1 3.8 - - - +
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Residues in contact with ASN 36 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Z THR* 3.1 23.7 + - - +
33Z ILE 3.1 6.0 + - - +
35Z SER* 1.3 86.7 + - - +
37Z VAL* 1.3 57.8 + - - +
38Z SER 3.3 0.8 + - - -
39Z PRO* 3.6 12.6 - - - +
40Z VAL* 4.3 2.1 - - - +
19a ALA* 3.4 30.5 + - + +
22a ASN* 4.0 10.8 - - - +
23a ALA* 3.4 31.1 - - + +
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Residues in contact with VAL 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538 A 4.1 19.7 - - - +
1548 T 3.9 5.8 - - - +
21Y PHE* 4.6 9.2 - - + -
33Z ILE* 3.0 19.9 + - + +
34Z LEU* 3.5 16.8 - - + +
36Z ASN* 1.3 76.0 - - - +
38Z SER* 1.3 66.3 + - - +
39Z PRO* 3.5 1.3 - - - -
40Z VAL* 3.3 9.4 + - + +
41Z ALA* 2.8 23.5 + - + +
16a LYS* 4.9 8.5 - - + -
19a ALA* 3.7 22.2 - - + -
20a LYS* 3.7 27.6 - - + -
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Residues in contact with SER 38 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Y PHE* 3.6 21.3 - - - -
22Y ASN* 5.5 2.7 + - - -
25Y SER* 4.6 5.0 + - - -
34Z LEU 2.6 21.6 + - - -
35Z SER* 3.4 14.9 - - - -
37Z VAL* 1.3 81.4 - - - +
39Z PRO* 1.4 72.4 - - - +
41Z ALA* 2.9 11.3 + - - +
42Z GLN* 3.0 24.7 + - - +
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Residues in contact with PRO 39 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z SER 4.1 4.0 - - - +
36Z ASN 3.6 12.3 - - - +
37Z VAL 3.5 1.6 - - - -
38Z SER* 1.4 98.0 - - - +
40Z VAL* 1.3 68.1 + - + +
42Z GLN* 3.4 19.1 + - - +
43Z GLN* 3.1 21.3 + - - +
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Residues in contact with VAL 40 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538 A 4.8 1.6 - - - +
36Z ASN 4.3 13.7 - - - +
37Z VAL* 3.5 11.7 - - + +
38Z SER 3.0 0.6 + - - -
39Z PRO* 1.3 78.4 - - + +
41Z ALA* 1.3 66.2 + - - +
43Z GLN* 3.1 9.2 + - + +
44Z ASN* 3.1 33.1 + - - +
12a GLN* 5.2 1.6 - - - +
15a ALA* 4.0 30.1 - - + +
16a LYS* 3.9 33.2 - - + +
19a ALA* 4.3 6.5 - - + -
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Residues in contact with ALA 41 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1528 T 4.2 3.0 - - - +
1538 A 3.7 35.2 - - - -
17Y TRP* 4.1 16.9 - - + -
21Y PHE* 4.3 11.7 - - + -
37Z VAL 2.8 12.9 + - - +
38Z SER 3.3 8.7 - - - +
40Z VAL* 1.3 77.2 - - - +
42Z GLN* 1.3 56.6 + - - +
44Z ASN* 3.1 2.6 + - - +
45Z PHE* 2.8 31.7 + - - +
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Residues in contact with GLN 42 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Y TYR* 3.7 11.7 + - - +
17Y TRP* 4.3 11.7 - - + -
18Y GLN* 3.2 39.3 - - - +
21Y PHE* 5.8 0.9 - - + -
22Y ASN* 4.7 2.4 + - - -
38Z SER* 3.0 20.1 + - - +
39Z PRO* 3.5 28.7 - - - +
41Z ALA* 1.3 77.3 - - - +
43Z GLN* 1.3 57.6 + - - +
45Z PHE* 3.7 0.7 - - - +
46Z GLN* 2.9 43.9 + - - +
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Residues in contact with GLN 43 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z PRO 3.1 9.6 + - - +
40Z VAL* 3.1 11.7 + - - +
42Z GLN* 1.3 81.0 - - - +
44Z ASN* 1.3 60.0 + - - +
46Z GLN* 3.4 13.5 + - - +
47Z THR* 2.6 60.7 + - - +
12a GLN* 5.3 9.0 - - + +
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Residues in contact with ASN 44 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1887 T 5.5 0.2 + - - -
1528 T 3.5 28.7 - - - +
1538 A 3.0 21.6 + - - -
40Z VAL* 3.1 23.1 + - - +
41Z ALA 3.1 3.3 + - - +
43Z GLN* 1.3 75.6 - - - +
45Z PHE* 1.3 65.3 + - - +
47Z THR* 3.4 4.8 + - - -
48Z ASN* 3.1 23.1 + - - +
8a ARG* 3.6 25.2 - - - +
12a GLN* 2.9 34.1 + - - +
16a LYS* 5.0 4.2 - - - +
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Residues in contact with PHE 45 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1997 A 5.2 5.4 - - - -
1518 A 4.6 10.3 - + - -
1528 T 3.6 23.7 - - - -
10Y TYR* 4.1 2.2 - + - -
13Y ARG* 4.5 6.5 - - + -
14Y TYR* 3.4 42.8 - + + -
17Y TRP* 3.5 59.9 - + + -
41Z ALA 2.8 17.0 + - - +
42Z GLN 3.7 3.6 - - - +
44Z ASN* 1.3 77.2 - - - +
46Z GLN* 1.3 63.5 + - - +
49Z VAL* 3.0 64.4 + - + +
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Residues in contact with GLN 46 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y TYR* 3.3 21.1 + - - +
14Y TYR* 2.9 39.5 + - + -
42Z GLN* 2.9 34.1 + - - +
43Z GLN* 3.7 16.2 + - - +
45Z PHE* 1.3 77.1 - - - +
47Z THR* 1.3 61.9 + - - +
50Z PRO* 3.1 21.7 - - - +
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Residues in contact with THR 47 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Z GLN* 2.6 42.7 + - - +
44Z ASN* 3.7 6.5 - - - -
45Z PHE 3.2 0.2 - - - -
46Z GLN* 1.3 81.3 - - - +
48Z ASN* 1.3 73.5 + - - +
50Z PRO* 3.7 6.2 - - - +
51Z LYS* 3.4 22.6 - - - +
12a GLN* 4.6 14.0 + - - +
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Residues in contact with ASN 48 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518 A 3.8 20.6 + - - +
1528 T 3.1 20.8 + - - -
44Z ASN 3.1 10.7 + - - +
47Z THR* 1.3 86.2 - - - +
49Z VAL* 1.3 62.1 + - - +
50Z PRO* 3.4 2.0 - - - -
51Z LYS* 3.0 33.4 + - + +
52Z PHE* 3.1 27.2 - - + -
88Z ASN* 4.9 4.8 + - - +
7a SER 3.9 15.0 + - - +
8a ARG* 3.4 14.3 - - - +
12a GLN* 5.2 2.2 - - - +
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Residues in contact with VAL 49 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518 A 3.9 27.1 - - + +
10Y TYR* 3.8 10.1 - - + -
13Y ARG* 3.7 27.6 - - + +
45Z PHE* 3.0 63.6 + - + +
48Z ASN* 1.3 71.7 - - - +
50Z PRO* 1.4 64.5 - - + +
51Z LYS 3.0 3.6 - - - -
52Z PHE* 2.8 26.8 + - - +
53Z THR 3.2 6.8 + - - -
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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