Contacts of the helix formed by residues 26 - 49 (chain p) 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 p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22p ASN 3.6 2.4 + - - +
23p ALA 3.1 15.4 + - - +
24p PHE 3.0 1.0 + - - -
25p SER* 1.3 79.4 + - - +
27p PRO* 1.4 67.8 - - - +
28p THR* 2.9 24.2 + - - -
29p VAL* 2.7 36.5 + - + -
30p ALA* 2.8 12.1 + - - -
32q THR* 4.0 19.5 + - + +
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Residues in contact with PRO 27 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27o PRO* 3.5 32.4 - - + +
28o THR* 5.5 1.3 - - + -
31o SER* 3.5 19.5 - - - +
25p SER 3.2 6.4 - - - +
26p ASN* 1.4 91.2 - - - +
28p THR* 1.3 60.8 + - - +
30p ALA* 4.0 2.6 - - + +
31p SER* 2.8 30.3 + - - -
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Residues in contact with THR 28 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27o PRO* 5.7 0.2 - - - -
26p ASN* 2.8 14.0 + - - -
27p PRO* 1.3 75.0 - - - +
29p VAL* 1.3 61.0 + - - +
31p SER* 3.1 5.4 + - - -
32p THR* 2.5 46.4 + - - +
26q ASN* 4.8 4.3 - - - +
28q THR* 3.1 33.5 - - + +
29q VAL* 4.6 0.4 - - + -
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Residues in contact with VAL 29 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23p ALA 3.3 29.2 - - - +
24p PHE* 3.8 10.1 - - - -
26p ASN* 2.7 15.0 + - + +
28p THR* 1.3 69.6 - - - +
30p ALA* 1.3 65.4 + - - +
32p THR* 3.7 0.3 - - - -
33p ILE* 3.1 43.9 + - + +
28q THR 4.3 1.3 - - - +
29q VAL* 3.9 30.1 - - + +
32q THR* 3.8 30.1 - - + +
33q ILE* 4.9 6.7 - - + -
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Residues in contact with ALA 30 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30o ALA* 3.6 28.9 - - + -
34o LEU* 4.6 2.2 - - + -
24p PHE* 3.3 36.5 + - + +
25p SER 4.9 0.9 - - - -
26p ASN 2.8 12.4 + - - +
27p PRO* 4.0 4.3 - - + +
29p VAL* 1.3 78.0 - - - +
31p SER* 1.3 58.2 + - - +
33p ILE* 4.0 0.7 - - - +
34p LEU* 2.9 37.0 + - + +
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Residues in contact with SER 31 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25o SER 3.5 24.0 - - - -
27o PRO* 3.5 24.6 - - - +
27p PRO 2.8 20.4 + - - -
28p THR* 3.1 8.1 + - - -
30p ALA* 1.3 77.2 - - - +
32p THR* 1.3 57.9 + - - +
34p LEU* 4.5 0.7 - - - +
35p SER* 2.6 43.0 + - - -
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Residues in contact with THR 32 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28p THR* 2.5 35.0 + - - +
29p VAL 3.7 3.6 - - - -
31p SER* 1.3 79.1 + - - +
33p ILE* 1.3 63.5 + - - +
35p SER* 3.2 3.4 + - - -
36p ASN* 3.1 35.0 + - - +
23q ALA* 3.6 34.3 - - + +
26q ASN* 4.0 15.0 + - + +
29q VAL* 3.7 15.3 - - + +
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Residues in contact with ILE 33 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907 T 5.7 2.2 - - - +
2508 T 3.7 37.9 - - - +
2518 A 4.7 6.3 - - - +
24p PHE* 4.2 14.8 - - + -
29p VAL* 3.1 34.2 + - + +
30p ALA 4.0 1.8 - - - +
32p THR* 1.3 78.0 - - - +
34p LEU* 1.3 59.2 + - - +
36p ASN* 3.1 3.1 + - - +
37p VAL* 3.0 29.1 + - + +
20q LYS* 4.0 22.9 - - + -
23q ALA* 3.8 21.8 - - + -
29q VAL* 4.9 7.9 - - + -
33q ILE* 5.3 5.6 - - + -
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Residues in contact with LEU 34 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2498 A 4.9 7.0 - - + +
2508 T 4.6 14.1 - - - +
21o PHE* 4.1 21.2 - - + -
24o PHE* 3.4 40.8 - - + +
25o SER* 3.9 26.7 - - - -
24p PHE* 4.0 22.7 - - + -
30p ALA* 2.9 28.6 + - + +
31p SER 4.3 0.2 - - - +
33p ILE* 1.3 76.9 - - - +
35p SER* 1.3 51.6 + - - +
37p VAL* 3.4 8.7 + - + +
38p SER* 2.6 37.1 + - - -
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Residues in contact with SER 35 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25o SER* 4.6 9.1 - - - -
31p SER* 2.6 26.5 + - - -
32p THR* 3.2 6.1 + - - -
34p LEU* 1.3 78.2 - - - +
36p ASN* 1.3 69.9 + - - +
38p SER* 3.3 20.3 + - - -
39p PRO* 4.1 3.3 - - - +
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Residues in contact with ASN 36 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32p THR* 3.1 24.4 + - - +
33p ILE 3.1 4.8 + - - +
35p SER* 1.3 85.6 + - - +
37p VAL* 1.3 57.8 + - - +
38p SER 3.3 1.1 + - - -
39p PRO* 3.6 12.5 - - - +
40p VAL* 4.3 2.1 - - - +
19q ALA* 3.4 30.0 + - + +
22q ASN* 4.0 9.9 - - - +
23q ALA* 3.4 31.1 - - + +
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Residues in contact with VAL 37 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2498 A 4.1 20.2 - - - +
2508 T 3.9 6.3 - - - +
21o PHE* 4.6 8.7 - - + -
33p ILE* 3.0 20.9 + - + +
34p LEU* 3.5 16.8 - - + +
36p ASN* 1.3 76.0 - - - +
38p SER* 1.3 65.4 + - - +
39p PRO* 3.5 1.3 - - - -
40p VAL* 3.9 8.1 - - + -
41p ALA* 2.8 24.5 + - + +
16q LYS* 4.9 8.5 - - + -
19q ALA* 3.7 22.4 - - + -
20q LYS* 3.7 26.7 - - + -
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Residues in contact with SER 38 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21o PHE* 3.6 21.8 - - - -
22o ASN* 5.5 2.3 + - - -
25o SER* 4.6 5.2 + - - -
34p LEU 2.6 21.2 + - - -
35p SER* 3.3 16.5 - - - -
36p ASN 3.3 0.2 - - - -
37p VAL* 1.3 81.0 - - - +
39p PRO* 1.4 71.4 - - - +
41p ALA* 2.9 10.9 + - - +
42p GLN* 3.0 25.2 + - - +
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Residues in contact with PRO 39 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35p SER 4.1 4.0 - - - +
36p ASN 3.6 11.9 - - - +
37p VAL 3.5 2.0 - - - -
38p SER* 1.4 98.5 - - - +
40p VAL* 1.3 67.1 + - + +
42p GLN* 3.4 19.6 + - - +
43p GLN* 3.1 20.8 + - - +
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Residues in contact with VAL 40 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2498 A 4.8 1.6 - - - +
36p ASN 4.3 5.6 - - - +
37p VAL* 3.5 11.7 - - + +
38p SER 3.0 0.4 - - - -
39p PRO* 1.3 78.3 - - + +
41p ALA* 1.3 67.2 + - - +
43p GLN* 3.1 9.6 + - - +
44p ASN* 3.1 33.1 + - - +
12q GLN* 5.2 1.6 - - - +
15q ALA* 4.0 29.6 - - + +
16q LYS* 3.9 34.3 - - + +
19q ALA* 4.3 13.9 - - + -
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Residues in contact with ALA 41 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2488 T 4.2 3.3 - - - +
2498 A 3.7 35.2 + - - -
17o TRP* 4.1 17.8 - - + -
21o PHE* 4.3 12.6 - - + -
37p VAL 2.8 13.8 + - - +
38p SER 3.3 9.0 - - - +
40p VAL* 1.3 74.9 - - - +
42p GLN* 1.3 56.0 + - - +
44p ASN* 3.1 2.3 + - - +
45p PHE* 2.8 31.4 + - - +
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Residues in contact with GLN 42 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14o TYR* 3.7 11.8 + - - +
17o TRP* 4.3 10.3 - - + -
18o GLN* 3.2 41.3 - - - +
21o PHE* 5.8 0.7 - - + -
22o ASN* 4.7 1.8 + - - -
38p SER* 3.0 20.5 + - - +
39p PRO* 3.5 29.1 - - + +
40p VAL 3.1 0.2 - - - -
41p ALA* 1.3 76.9 - - - +
43p GLN* 1.3 56.3 + - - +
45p PHE* 3.4 1.0 + - - +
46p GLN* 2.9 44.0 + - - +
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Residues in contact with GLN 43 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L SER* 5.2 5.5 + - - -
12L GLN* 6.2 2.4 - - - +
43M GLN* 3.1 38.8 - - - +
39p PRO 3.1 9.4 + - - +
40p VAL* 3.1 11.8 + - + +
42p GLN* 1.3 80.5 - - - +
44p ASN* 1.3 62.4 + - - +
46p GLN* 3.7 14.1 + - - +
47p THR* 2.6 60.5 + - - +
12q GLN* 5.3 8.3 - - + +
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Residues in contact with ASN 44 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927 T 5.5 0.2 + - - -
2488 T 3.5 28.8 - - - +
2498 A 3.0 22.0 + - - -
40p VAL* 3.1 22.5 + - - +
41p ALA 3.1 3.3 + - - +
43p GLN* 1.3 75.9 - - - +
45p PHE* 1.3 65.6 + - - +
47p THR* 3.4 4.6 + - - -
48p ASN* 3.1 23.2 + - - +
8q ARG* 3.6 25.2 - - - +
12q GLN* 2.9 33.6 + - - +
16q LYS* 5.0 4.4 - - - +
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Residues in contact with PHE 45 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037 A 5.2 5.6 - - - -
2478 A 4.6 10.3 - + - -
2488 T 3.6 23.2 - - - -
10o TYR* 4.1 2.0 - + - -
13o ARG* 4.5 5.8 - - + -
14o TYR* 3.4 43.1 - + + -
17o TRP* 3.5 59.2 - + + -
41p ALA 2.8 16.4 + - - +
42p GLN 3.7 2.9 - - - +
44p ASN* 1.3 76.5 - - - +
46p GLN* 1.3 65.2 + - - +
49p VAL* 3.0 64.8 + - + +
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Residues in contact with GLN 46 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L SER* 4.3 25.9 - - - +
10o TYR* 3.3 20.9 + - - +
14o TYR* 2.9 39.8 + - + -
42p GLN* 2.9 33.3 + - - +
43p GLN* 3.7 15.2 + - - +
45p PHE* 1.3 77.7 - - - +
47p THR* 1.3 62.8 - - - +
50p PRO* 3.1 21.7 - - - +
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Residues in contact with THR 47 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L SER* 6.0 1.6 - - - -
11L SER* 5.0 5.1 + - - -
43p GLN* 2.6 43.6 + - - +
44p ASN* 3.7 6.7 - - - -
46p GLN* 1.3 80.8 - - - +
48p ASN* 1.3 75.0 + - - +
50p PRO* 3.7 6.2 - - - +
51p LYS* 3.4 23.2 - - - +
12q GLN* 4.6 14.0 + - - +
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Residues in contact with ASN 48 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2478 A 3.8 20.2 - - - +
2488 T 3.1 20.8 + - - -
44p ASN 3.1 10.9 + - - +
47p THR* 1.3 87.5 - - - +
49p VAL* 1.3 62.7 + - - +
50p PRO* 3.4 1.3 - - - -
51p LYS* 3.0 33.6 + - + +
52p PHE* 3.1 28.1 - - + -
88p ASN* 4.9 4.3 + - - -
7q SER 3.9 13.2 + - - +
8q ARG* 3.4 15.0 - - - +
12q GLN* 5.2 2.2 - - - +
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Residues in contact with VAL 49 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2478 A 3.9 28.0 - - + +
10o TYR* 3.8 10.8 - - + -
13o ARG* 3.7 26.2 - - - +
45p PHE* 3.0 64.9 + - + +
48p ASN* 1.3 71.7 - - - +
50p PRO* 1.4 61.9 - - + +
51p LYS 3.0 4.3 - - - -
52p PHE* 2.8 30.1 + - + +
53p THR 3.2 7.3 + - - -
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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