Contacts of the helix formed by residues 26 - 49 (chain l) 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 l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22l ASN 3.6 2.7 + - - +
23l ALA 3.1 15.6 + - - +
24l PHE 3.0 1.0 + - - -
25l SER* 1.3 78.3 + - - +
27l PRO* 1.4 67.4 - - - +
28l THR* 2.9 24.4 + - - -
29l VAL* 2.7 37.9 + - + -
30l ALA* 2.8 11.7 + - - -
32m THR* 4.0 18.2 + - + +
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Residues in contact with PRO 27 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27k PRO* 3.5 33.9 - - + +
28k THR* 5.5 1.3 - - + -
31k SER* 3.5 18.6 - - - +
25l SER 3.2 6.8 - - - +
26l ASN* 1.4 92.3 - - - +
28l THR* 1.3 60.6 + - - +
30l ALA* 4.0 2.5 - - + +
31l SER* 2.8 30.0 + - - -
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Residues in contact with THR 28 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26l ASN* 2.8 14.5 + - - -
27l PRO* 1.3 75.8 - - - +
29l VAL* 1.3 61.0 + - - +
31l SER* 3.1 5.2 + - - +
32l THR* 2.5 46.6 + - - +
26m ASN* 4.8 4.3 - - - +
28m THR* 3.1 32.8 - - + +
29m VAL* 4.6 0.7 - - + -
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Residues in contact with VAL 29 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23l ALA 3.3 28.5 - - - +
24l PHE* 3.8 10.1 - - - -
26l ASN* 2.7 14.4 + - + +
28l THR* 1.3 70.6 - - - +
30l ALA* 1.3 65.0 + - - +
32l THR* 3.7 0.3 - - - -
33l ILE* 3.1 44.1 + - + +
28m THR 4.3 1.1 - - - +
29m VAL* 3.9 29.4 - - + +
32m THR* 3.8 31.0 - - + +
33m ILE* 4.9 7.2 - - + -
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Residues in contact with ALA 30 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25k SER 4.9 0.2 - - - -
30k ALA* 3.6 28.9 - - + -
34k LEU* 4.6 2.2 - - + -
24l PHE* 3.3 36.5 + - + +
25l SER 4.9 1.3 - - - +
26l ASN 2.8 11.5 + - - +
27l PRO* 4.0 4.5 - - + +
29l VAL* 1.3 78.9 - - - +
31l SER* 1.3 57.4 + - - +
33l ILE* 4.0 0.7 - - - +
34l LEU* 2.9 36.9 + - + +
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Residues in contact with SER 31 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25k SER 3.5 23.8 - - - -
27k PRO* 3.5 25.3 - - - +
27l PRO 2.8 20.6 + - - -
28l THR* 3.1 8.3 + - - -
30l ALA* 1.3 76.8 - - - +
32l THR* 1.3 58.2 + - - +
34l LEU* 4.5 0.7 - - - +
35l SER* 2.6 42.4 + - - -
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Residues in contact with THR 32 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28l THR* 2.5 34.8 + - - +
29l VAL 3.7 4.0 - - - -
31l SER* 1.3 77.6 + - - +
33l ILE* 1.3 64.0 + - - +
35l SER* 3.2 3.4 + - - -
36l ASN* 3.1 35.4 + - - +
23m ALA* 3.6 35.0 - - + +
26m ASN* 4.0 14.6 + - + +
29m VAL* 3.7 14.5 - - + +
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Residues in contact with ILE 33 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147 T 5.7 2.2 - - - +
2268 T 3.7 37.2 - - - +
2278 A 4.7 6.7 - - - +
24l PHE* 4.2 14.6 - - + -
29l VAL* 3.1 34.8 + - + +
30l ALA 4.0 1.6 - - - +
32l THR* 1.3 77.3 - - - +
34l LEU* 1.3 60.0 + - - +
36l ASN* 3.1 3.3 + - - +
37l VAL* 3.0 29.0 + - + +
20m LYS* 4.0 23.6 - - + -
23m ALA* 3.8 22.2 - - + -
29m VAL* 4.9 7.9 - - + -
33m ILE* 5.3 5.4 - - + -
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Residues in contact with LEU 34 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2258 A 4.9 7.4 - - + -
2268 T 4.6 13.9 - - - +
21k PHE* 4.1 20.5 - - + -
24k PHE* 3.5 41.7 - - + +
25k SER* 3.9 25.4 - - - -
24l PHE* 4.0 23.3 - - + -
30l ALA* 2.9 28.6 + - + +
31l SER 4.3 0.4 - - - +
33l ILE* 1.3 77.0 - - - +
35l SER* 1.3 51.7 + - - +
37l VAL* 3.4 8.3 + - + +
38l SER* 2.6 37.0 + - - -
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Residues in contact with SER 35 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25k SER* 4.6 9.1 - - - -
31l SER* 2.6 27.1 + - - -
32l THR* 3.2 6.6 + - - -
34l LEU* 1.3 76.9 - - - +
36l ASN* 1.3 70.1 + - - +
38l SER* 3.4 20.3 + - - -
39l PRO* 4.1 3.1 - - - +
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Residues in contact with ASN 36 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32l THR* 3.1 23.8 + - - +
33l ILE 3.1 5.0 + - - +
35l SER* 1.3 86.4 + - - +
37l VAL* 1.3 57.4 - - - +
38l SER 3.3 0.7 + - - -
39l PRO* 3.6 12.6 - - - +
40l VAL* 4.3 2.1 - - - +
19m ALA* 3.4 30.8 + - + +
22m ASN* 4.0 10.1 + - - +
23m ALA* 3.4 31.0 - - + +
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Residues in contact with VAL 37 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2258 A 4.1 20.0 - - - +
2268 T 3.9 6.7 - - - +
21k PHE* 4.6 9.4 - - + -
33l ILE* 3.0 20.3 + - + +
34l LEU* 3.5 16.8 - - + +
36l ASN* 1.3 76.3 - - - +
38l SER* 1.3 64.7 - - - +
39l PRO* 3.5 1.3 - - - -
40l VAL* 3.3 8.5 + - + +
41l ALA* 2.8 23.7 + - + +
16m LYS* 4.9 9.0 - - + -
19m ALA* 3.7 22.0 - - + -
20m LYS* 3.7 27.4 - - + -
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Residues in contact with SER 38 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21k PHE* 3.6 22.3 - - - -
22k ASN* 5.5 2.3 + - - -
25k SER* 4.6 5.0 + - - -
34l LEU 2.6 21.5 + - - -
35l SER* 3.4 15.0 - - - -
36l ASN 3.3 0.2 - - - -
37l VAL* 1.3 80.9 - - - +
39l PRO* 1.4 72.7 - - - +
41l ALA* 2.9 10.6 + - - +
42l GLN* 3.0 25.5 + - - +
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Residues in contact with PRO 39 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35l SER 4.1 4.0 - - - +
36l ASN 3.6 12.1 - - - +
37l VAL 3.5 2.0 - - - -
38l SER* 1.4 96.5 - - - +
40l VAL* 1.3 68.0 + - + +
42l GLN* 3.4 19.3 + - + +
43l GLN* 3.1 21.3 + - - +
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Residues in contact with VAL 40 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2258 A 4.8 1.6 - - - +
36l ASN 4.3 6.3 - - - +
37l VAL* 3.5 11.2 - - + +
38l SER 3.0 0.4 - - - -
39l PRO* 1.3 79.3 - - + +
41l ALA* 1.3 67.8 + - - +
43l GLN* 3.1 9.7 + - + +
44l ASN* 3.1 33.2 + - - +
12m GLN* 5.2 1.3 - - - +
15m ALA* 4.0 30.3 - - + +
16m LYS* 3.9 32.8 - - + +
19m ALA* 4.3 13.5 - - + -
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Residues in contact with ALA 41 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2248 T 4.2 2.9 - - - +
2258 A 3.7 35.7 - - - -
17k TRP* 4.1 17.5 - - + -
21k PHE* 4.3 11.9 - - + -
37l VAL* 2.8 13.9 + - - +
38l SER 3.3 9.0 - - - +
40l VAL* 1.3 75.6 - - - +
42l GLN* 1.3 57.7 + - - +
44l ASN* 3.1 2.1 + - - +
45l PHE* 2.8 32.1 + - - +
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Residues in contact with GLN 42 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14k TYR* 3.7 11.5 + - - +
17k TRP* 4.3 11.2 - - + -
18k GLN* 3.2 40.2 - - - +
21k PHE* 5.8 0.7 - - + -
22k ASN* 4.7 2.2 + - - -
38l SER* 3.0 20.0 + - - +
39l PRO* 3.5 28.9 - - + +
40l VAL 3.1 0.2 - - - -
41l ALA* 1.3 76.9 - - - +
43l GLN* 1.3 56.7 + - - +
45l PHE* 3.4 1.0 + - - +
46l GLN* 2.9 43.0 + - - +
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Residues in contact with GLN 43 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H SER* 5.2 5.3 + - - -
12H GLN* 6.2 2.0 - - - +
43I GLN* 3.1 39.6 - - - +
39l PRO 3.1 9.0 + - - +
40l VAL* 3.1 11.9 + - - +
42l GLN* 1.3 79.4 - - - +
44l ASN* 1.3 61.1 + - - +
46l GLN* 3.7 14.6 + - - +
47l THR* 2.6 60.1 + - - +
12m GLN* 5.3 8.5 - - + +
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Residues in contact with ASN 44 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167 T 5.5 0.2 + - - -
2248 T 3.5 29.6 - - - +
2258 A 3.0 21.2 + - - -
40l VAL* 3.1 23.1 + - - +
41l ALA 3.1 3.1 + - - +
43l GLN* 1.3 75.3 - - - +
45l PHE* 1.3 66.0 + - - +
47l THR* 3.4 4.6 + - - -
48l ASN* 3.1 23.2 + - - +
8m ARG* 3.6 23.4 - - - +
12m GLN* 2.9 33.7 + - - +
16m LYS* 5.0 4.8 - - - +
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Residues in contact with PHE 45 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277 A 5.2 5.2 - - - -
2238 A 4.6 11.2 - + - -
2248 T 3.6 23.5 - - - -
10k TYR* 4.1 1.6 - + - -
13k ARG* 4.5 6.7 - - + -
14k TYR* 3.4 43.3 - + + -
17k TRP* 3.5 59.0 - + + -
41l ALA 2.8 15.9 + - - +
42l GLN 3.7 3.4 - - - +
44l ASN* 1.3 77.2 - - - +
46l GLN* 1.3 64.0 + - - +
49l VAL* 3.0 64.7 + - + +
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Residues in contact with GLN 46 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H SER* 4.3 25.7 - - - +
10k TYR* 3.3 21.7 + - - +
14k TYR* 2.9 39.8 + - + -
42l GLN* 2.9 32.6 + - - +
43l GLN* 3.7 15.3 + - - +
45l PHE* 1.3 77.0 - - - +
47l THR* 1.3 61.9 + - - +
50l PRO* 3.1 21.8 - - - +
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Residues in contact with THR 47 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H SER* 5.8 5.0 - - - -
11H SER* 5.0 4.9 - - - -
43l GLN* 2.6 42.6 + - - +
44l ASN* 3.7 6.7 - - - -
45l PHE 3.2 0.2 - - - -
46l GLN* 1.3 80.1 - - - +
48l ASN* 1.3 74.5 + - - +
50l PRO* 3.7 6.2 - - - +
51l LYS* 3.4 23.2 - - - +
12m GLN* 4.6 14.9 + - - +
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Residues in contact with ASN 48 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2238 A 3.8 20.0 - - - +
2248 T 3.1 20.4 + - - -
44l ASN 3.1 11.0 + - - +
47l THR* 1.3 85.8 - - - +
49l VAL* 1.3 62.8 + - - +
50l PRO* 3.4 1.6 - - - -
51l LYS* 3.0 33.2 + - + +
52l PHE* 3.1 27.4 - - + -
88l ASN* 4.9 5.0 + - - +
7m SER 3.9 15.2 + - - +
8m ARG* 3.4 14.6 - - - +
12m GLN* 5.2 2.0 - - - +
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Residues in contact with VAL 49 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2238 A 3.9 28.7 - - + +
10k TYR* 3.8 10.3 - - + -
13k ARG* 3.7 27.6 - - - +
45l PHE* 3.0 62.3 + - + +
48l ASN* 1.3 72.1 - - - +
50l PRO* 1.4 60.6 - - + +
51l LYS 3.0 4.3 - - - -
52l PHE* 2.8 30.4 + - + +
53l THR 3.2 6.9 + - - -
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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