Contacts of the helix formed by residues 26 - 49 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ASN 3.6 2.9 + - - +
23H ALA 3.1 16.0 + - - +
24H PHE 3.0 1.2 + - - -
25H SER* 1.3 77.7 + - - +
27H PRO* 1.4 67.8 - - - +
28H THR* 2.9 23.6 + - - -
29H VAL* 2.7 37.5 + - + -
30H ALA* 2.8 11.7 + - - -
32I THR* 4.0 18.8 + - + +
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Residues in contact with PRO 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PRO* 3.5 32.8 - - + +
28G THR* 5.5 1.6 - - + -
31G SER* 3.5 18.2 - - - +
25H SER 3.2 6.8 - - - +
26H ASN* 1.4 91.9 - - - +
28H THR* 1.3 61.6 + - - +
30H ALA* 4.0 2.2 - - + +
31H SER* 2.8 29.9 + - - -
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Residues in contact with THR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ASN* 2.8 15.0 + - - -
27H PRO* 1.3 75.4 - - - +
29H VAL* 1.3 59.8 + - - +
31H SER* 3.1 4.5 + - - -
32H THR* 2.5 47.2 + - - +
26I ASN* 4.8 4.3 - - - +
28I THR* 3.1 33.7 - - + +
29I VAL* 4.6 0.9 - - + -
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Residues in contact with VAL 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H ALA 3.3 28.7 - - - +
24H PHE* 3.8 10.1 - - - +
26H ASN* 2.7 14.6 + - + +
28H THR* 1.3 70.2 - - - +
30H ALA* 1.3 65.3 + - - +
33H ILE* 3.1 43.6 + - + +
28I THR 4.3 1.1 - - - +
29I VAL* 3.9 30.5 - - + +
32I THR* 3.8 30.5 - - + +
33I ILE* 4.9 6.3 - - + -
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Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ALA* 3.6 29.2 - - + -
34G LEU* 4.6 2.5 - - + -
24H PHE* 3.3 36.2 + - + +
25H SER 4.9 0.7 - - - -
26H ASN 2.8 11.9 + - - +
27H PRO* 4.0 4.0 - - + +
29H VAL* 1.3 77.9 - - - +
31H SER* 1.3 59.1 + - - +
33H ILE* 4.0 0.7 - - - +
34H LEU* 2.9 36.6 + - + +
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Residues in contact with SER 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G SER 3.5 24.0 + - - -
27G PRO* 3.5 24.9 - - - +
27H PRO 2.8 20.6 + - - -
28H THR* 3.1 8.5 + - - +
30H ALA* 1.3 76.6 - - - +
32H THR* 1.3 58.6 + - - +
34H LEU* 4.5 0.4 - - - +
35H SER* 2.6 42.8 + - - -
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Residues in contact with THR 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR* 2.5 34.8 + - - +
29H VAL 3.7 3.1 - - - -
30H ALA 3.3 0.2 - - - -
31H SER* 1.3 78.4 + - - +
33H ILE* 1.3 62.1 + - - +
35H SER* 3.2 3.0 + - - -
36H ASN* 3.1 35.7 + - - +
23I ALA* 3.6 34.3 - - + +
26I ASN* 4.0 16.0 + - + +
29I VAL* 3.7 15.4 - - + +
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Residues in contact with ILE 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2947 T 5.7 2.5 - - - +
468 T 3.7 37.2 - - - +
478 A 4.7 6.5 - - - +
24H PHE* 4.2 14.8 - - + -
29H VAL* 3.1 33.2 + - + +
30H ALA 4.0 2.2 - - - +
32H THR* 1.3 78.3 - - - +
34H LEU* 1.3 58.9 + - - +
36H ASN* 3.1 3.3 + - - +
37H VAL* 3.0 29.5 + - + +
20I LYS* 4.0 23.8 - - + -
23I ALA* 3.8 21.5 - - + -
29I VAL* 4.9 7.9 - - + -
33I ILE* 5.3 5.8 - - + -
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458 A 4.9 7.2 - - + -
468 T 4.6 14.1 - - - +
21G PHE* 4.1 21.8 - - + -
24G PHE* 3.5 42.0 - - + +
25G SER* 3.9 25.4 - - - -
30G ALA* 4.5 0.2 - - + -
24H PHE* 4.0 22.7 - - + -
30H ALA* 2.9 28.1 + - + +
31H SER 4.3 0.4 - - - +
33H ILE* 1.3 77.8 - - - +
35H SER* 1.3 52.8 + - - +
37H VAL* 3.4 9.1 + - + +
38H SER* 2.6 36.5 + - - -
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Residues in contact with SER 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G SER* 4.6 8.4 - - - -
31H SER* 2.6 27.6 + - - -
32H THR* 3.2 6.4 + - - -
34H LEU* 1.3 78.0 - - - +
36H ASN* 1.3 68.8 + - - +
38H SER* 3.4 20.3 + - - -
39H PRO* 4.1 3.8 - - - +
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Residues in contact with ASN 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H THR* 3.1 23.5 + - - +
33H ILE 3.1 6.3 + - - +
35H SER* 1.3 86.6 + - - +
37H VAL* 1.3 58.0 + - - +
38H SER 3.3 1.0 + - - -
39H PRO* 3.6 12.5 - - - +
40H VAL* 4.3 1.9 - - - +
19I ALA* 3.4 30.1 + - + +
22I ASN* 4.0 10.3 - - - +
23I ALA* 3.4 30.7 - - + +
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Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458 A 4.1 20.6 - - - +
468 T 3.9 6.7 - - - +
21G PHE* 4.6 9.2 - - + -
33H ILE* 3.0 20.3 + - + +
34H LEU* 3.5 16.6 - - + +
36H ASN* 1.3 76.0 - - - +
38H SER* 1.3 66.0 + - - +
39H PRO* 3.5 1.6 - - - -
40H VAL* 3.3 9.8 + - + +
41H ALA* 2.8 23.3 + - + +
16I LYS* 4.9 7.9 - - + -
19I ALA* 3.7 21.8 - - + -
20I LYS* 3.7 27.1 - - + -
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Residues in contact with SER 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G PHE* 3.6 21.3 - - - -
22G ASN* 5.5 2.5 + - - -
25G SER* 4.6 4.9 + - - -
34H LEU 2.6 21.6 + - - -
35H SER* 3.4 15.5 - - - -
37H VAL* 1.3 81.4 - - - +
39H PRO* 1.4 73.0 - - - +
41H ALA* 2.9 11.3 + - - +
42H GLN* 3.0 25.1 + - - +
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Residues in contact with PRO 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H SER 4.1 4.0 - - - +
36H ASN 3.6 12.8 - - - +
37H VAL 3.5 1.3 - - - -
38H SER* 1.4 98.5 - - - +
40H VAL* 1.3 68.8 + - + +
42H GLN* 3.4 19.3 + - - +
43H GLN* 3.1 21.0 + - - +
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Residues in contact with VAL 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458 A 4.8 1.6 - - - +
36H ASN 4.3 13.5 - - - +
37H VAL* 3.5 11.4 - - + +
38H SER 3.0 0.8 + - - -
39H PRO* 1.3 77.9 - - + +
41H ALA* 1.3 67.2 + - - +
43H GLN* 3.1 9.6 + - + +
44H ASN* 3.1 33.2 + - - +
12I GLN* 5.2 1.6 - - - +
15I ALA* 4.0 30.1 - - + +
16I LYS* 3.9 33.7 - - + +
19I ALA* 4.3 6.7 - - + -
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Residues in contact with ALA 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448 T 4.2 2.5 - - - +
458 A 3.7 35.2 - - - -
17G TRP* 4.1 17.3 - - + -
21G PHE* 4.3 11.2 - - + -
37H VAL 2.8 12.8 + - - +
38H SER 3.3 9.0 - - - +
40H VAL* 1.3 76.5 - - - +
42H GLN* 1.3 57.7 + - - +
44H ASN* 3.1 2.5 + - - +
45H PHE* 2.8 31.9 + - - +
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Residues in contact with GLN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G TYR* 3.7 12.4 + - - +
17G TRP* 4.3 11.4 - - + -
18G GLN* 3.2 39.5 - - - +
21G PHE* 5.8 0.9 - - + -
22G ASN* 4.7 2.8 + - - -
38H SER* 3.0 20.3 + - - +
39H PRO* 3.5 28.9 - - - +
40H VAL 3.1 0.2 - - - -
41H ALA* 1.3 76.3 - - - +
43H GLN* 1.3 57.6 + - - +
45H PHE* 3.7 0.7 - - - +
46H GLN* 2.9 43.5 + - - +
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Residues in contact with GLN 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H PRO 3.1 9.6 + - - +
40H VAL* 3.1 11.9 + - - +
42H GLN* 1.3 80.8 - - - +
44H ASN* 1.3 60.5 + - - +
46H GLN* 3.4 13.8 + - - +
47H THR* 2.6 59.9 + - - +
12I GLN* 5.3 9.0 - - + +
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Residues in contact with ASN 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2967 T 5.5 0.2 + - - -
448 T 3.5 29.2 - - - +
458 A 3.0 21.2 + - - -
40H VAL* 3.1 23.3 + - - +
41H ALA 3.1 2.9 + - - +
43H GLN* 1.3 75.5 - - - +
45H PHE* 1.3 65.4 + - - +
47H THR* 3.4 5.1 + - - -
48H ASN* 3.1 22.7 + - - +
8I ARG* 3.6 25.2 - - - +
12I GLN* 2.9 33.9 + - - +
16I LYS* 5.0 4.2 - - - +
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Residues in contact with PHE 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3077 A 5.2 5.6 - - - -
438 A 4.6 10.3 - + - -
448 T 3.6 24.1 - - - -
10G TYR* 4.1 2.0 - + - -
13G ARG* 4.5 6.3 - - + -
14G TYR* 3.4 43.1 - + + -
17G TRP* 3.5 59.0 - + + -
41H ALA 2.8 17.0 + - - +
42H GLN 3.7 3.4 - - - +
44H ASN* 1.3 75.9 - - - +
46H GLN* 1.3 63.5 + - - +
49H VAL* 3.0 65.2 + - + +
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Residues in contact with GLN 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G TYR* 3.3 21.1 + - - +
14G TYR* 2.9 38.7 + - + -
42H GLN* 2.9 34.3 + - - +
43H GLN* 3.7 15.8 + - - +
45H PHE* 1.3 77.7 - - - +
47H THR* 1.3 63.3 + - - +
50H PRO* 3.1 21.7 - - - +
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Residues in contact with THR 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLN* 2.6 42.3 + - - +
44H ASN* 3.7 6.2 - - - -
45H PHE 3.2 0.2 - - - -
46H GLN* 1.3 81.1 - - - +
48H ASN* 1.3 73.6 + - - +
50H PRO* 3.7 6.6 - - - +
51H LYS* 3.4 23.7 - - - +
12I GLN* 4.6 13.4 + - - +
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Residues in contact with ASN 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438 A 3.8 20.2 - - - +
448 T 3.1 20.6 + - - -
44H ASN 3.1 10.2 + - - +
47H THR* 1.3 86.2 - - - +
49H VAL* 1.3 62.1 + - - +
50H PRO* 3.4 2.0 - - - -
51H LYS* 3.0 34.0 + - + +
52H PHE* 3.1 27.3 - - + -
88H ASN* 4.9 4.8 + - - -
7I SER 3.9 15.0 + - - +
8I ARG* 3.4 14.3 - - - +
12I GLN* 5.2 2.4 - - - +
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Residues in contact with VAL 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438 A 3.9 26.7 - - + +
10G TYR* 3.8 10.3 - - + -
13G ARG* 3.7 27.6 - - + +
45H PHE* 3.0 64.1 + - + +
48H ASN* 1.3 71.7 - - - +
50H PRO* 1.3 61.7 - - + +
51H LYS 3.0 4.0 - - - -
52H PHE* 2.8 30.8 + - - +
53H 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