Contacts of the helix formed by residues 9 - 26 (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 SER 9 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G THR* 4.2 5.2 - - - -
8H ARG* 1.3 75.5 - - - +
10H TYR* 1.3 64.4 + - - +
11H SER* 2.7 27.8 + - - -
12H GLN* 2.8 24.6 + - - +
13H ARG* 3.0 21.0 + - - +
47l THR* 5.8 6.5 - - - -
50l PRO* 6.4 2.5 - - - -
51l LYS* 6.4 2.0 - - - -
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Residues in contact with TYR 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G PHE* 5.1 0.4 - + - -
46G GLN* 5.2 12.2 + - + +
49G VAL* 4.6 6.1 - - + -
50G PRO* 3.7 35.0 - - + -
53G THR* 3.1 38.8 - - + +
9H SER* 1.3 76.0 - - - +
11H SER* 1.3 77.4 + - - +
13H ARG* 3.4 7.0 - - - +
14H TYR* 2.8 49.1 + + + -
10k TYR* 2.8 47.5 + + - -
11k SER* 5.0 3.5 + - - -
14k TYR* 5.5 1.9 - - - -
50l PRO* 4.1 16.8 - - + -
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Residues in contact with SER 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H SER* 2.7 21.9 + - - -
10H TYR* 1.3 100.2 - - - +
12H GLN* 1.3 58.9 + - - +
14H TYR* 3.9 3.7 - - - +
15H ALA* 2.9 29.5 + - - +
43l GLN* 5.2 5.7 + - - -
46l GLN* 4.3 38.7 + - - +
47l THR* 5.0 4.0 + - - -
50l PRO* 5.7 0.9 - - - -
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Residues in contact with GLN 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498 A 4.1 3.5 + - - -
7H SER 4.7 1.9 + - - +
8H ARG* 3.6 27.6 - - - +
9H SER* 2.8 38.8 + - - +
11H SER* 1.3 82.7 + - - +
13H ARG* 1.3 66.2 + - - +
15H ALA* 3.7 5.6 - - - +
16H LYS* 3.1 25.6 + - - +
40I VAL* 5.0 2.2 - - - +
43I GLN* 5.3 8.1 - - + +
44I ASN* 2.9 32.3 + - - +
47I THR* 4.9 15.6 + - - +
48I ASN* 5.5 3.2 - - - +
43l GLN* 6.2 1.8 - - - +
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Residues in contact with ARG 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3017 A 3.9 15.4 + - - -
3027 T 4.8 5.3 + - - -
488 T 3.8 31.1 + - + +
498 A 3.6 56.4 + - - +
45G PHE* 4.5 8.8 - - + -
49G VAL* 3.8 19.9 + - + +
52G PHE* 4.5 4.6 - - - +
53G THR* 2.7 48.6 + - - +
56G ASN* 4.0 11.2 - - - +
8H ARG* 4.3 8.3 - - + -
9H SER 3.0 20.4 + - - +
10H TYR* 3.2 6.7 + - + +
12H GLN* 1.3 76.9 - - - +
14H TYR* 1.3 57.7 + - - +
17H TRP* 3.0 29.6 + - - +
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Residues in contact with TYR 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G GLN* 3.9 10.9 + - - +
45G PHE* 3.5 34.2 - + + -
46G GLN* 3.4 42.1 + - + -
10H TYR* 2.8 35.0 + + + +
11H SER* 3.9 4.5 - - - +
13H ARG* 1.3 74.7 - - - +
15H ALA* 1.3 71.2 + - - +
17H TRP* 3.0 14.3 + + - +
18H GLN* 2.7 58.9 + - + +
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Residues in contact with ALA 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H SER 2.9 21.3 + - - +
12H GLN* 3.7 8.1 - - - +
14H TYR* 1.3 83.7 - - + +
16H LYS* 1.3 63.0 + - - +
18H GLN* 3.3 6.0 + - - +
19H ALA* 3.1 19.9 + - - +
40I VAL* 4.1 20.8 - - + +
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Residues in contact with LYS 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2927 T 3.7 33.4 + - - +
2937 A 2.8 32.0 + - - -
488 T 3.3 32.4 + - - +
498 A 3.9 22.2 + - - +
12H GLN 3.1 13.5 + - - +
15H ALA* 1.3 75.9 - - - +
17H TRP* 1.3 66.5 + - - +
19H ALA* 3.1 5.0 + - - +
20H LYS* 3.0 25.7 + - + +
37I VAL* 4.7 8.1 - - + -
40I VAL* 3.9 19.0 - - + +
44I ASN* 5.5 2.7 - - - +
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Residues in contact with TRP 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3037 A 3.8 34.3 + - + -
478 A 3.8 26.9 + - + -
488 T 3.8 19.2 - - - +
41G ALA* 4.1 20.6 - - + -
42G GLN* 4.2 7.0 - - + -
45G PHE* 3.5 55.3 - + + -
13H ARG 3.0 21.0 + - - +
14H TYR* 3.0 15.2 + + - +
16H LYS* 1.3 75.7 - - - +
18H GLN* 1.3 92.7 + - - +
20H LYS* 3.4 2.5 + - - +
21H PHE* 2.9 53.4 + + + +
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Residues in contact with GLN 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G GLN* 3.2 39.9 - - - +
14H TYR* 2.7 57.1 + - + +
15H ALA* 3.5 6.7 - - - +
17H TRP* 1.3 83.8 - - - +
19H ALA* 1.3 62.6 + - - +
21H PHE* 3.2 6.3 + - - +
22H ASN* 2.9 62.7 + - - +
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Residues in contact with ALA 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ALA 3.1 9.8 + - - +
16H LYS* 3.1 11.5 + - - +
18H GLN* 1.3 78.7 - - - +
20H LYS* 1.3 59.2 + - - +
22H ASN* 3.5 10.0 + - - +
23H ALA* 3.0 26.9 + - - +
36I ASN* 3.4 35.1 - - - +
37I VAL* 3.7 16.4 - - + -
40I VAL* 4.5 4.3 - - + -
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Residues in contact with LYS 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2937 A 2.8 31.3 + - - +
2947 T 3.1 25.1 + - - -
478 A 3.4 45.3 + - + +
488 T 3.2 21.1 + - - +
16H LYS* 3.0 20.9 + - + +
17H TRP 3.9 3.1 - - - +
19H ALA* 1.3 74.7 - - - +
21H PHE* 1.3 65.5 + - - +
23H ALA* 3.3 4.6 + - + +
24H PHE* 3.0 25.1 + - - +
33I ILE* 3.9 19.3 - - + -
37I VAL* 3.6 17.5 - - + -
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Residues in contact with PHE 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3037 A 5.7 2.5 - + - -
3047 T 4.5 23.3 - - - -
468 T 6.0 2.0 - - - -
478 A 5.2 2.8 - - - -
34G LEU* 3.9 30.3 - - + -
37G VAL* 4.5 5.2 - - + -
38G SER* 3.5 38.6 - - - -
41G ALA* 4.5 9.4 - - + -
42G GLN* 5.8 0.2 - - + -
17H TRP* 2.9 49.7 + + + +
18H GLN* 3.6 11.2 - - - +
20H LYS* 1.3 77.6 - - - +
22H ASN* 1.3 71.7 + - - +
24H PHE* 3.3 11.6 + + - +
25H SER* 3.0 22.8 + - - -
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Residues in contact with ASN 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G SER* 5.5 2.1 + - - -
42G GLN* 4.6 3.5 + - - -
18H GLN* 2.9 52.0 + - - +
19H ALA* 3.5 8.5 - - - +
21H PHE* 1.3 79.8 - - - +
23H ALA* 1.3 62.5 + - - +
25H SER* 2.6 26.2 + - - -
26H ASN* 3.6 4.0 + - - +
36I ASN* 4.0 11.2 - - - +
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Residues in contact with ALA 23 (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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19H ALA 3.0 14.6 + - - +
20H LYS* 3.5 9.0 - - + +
21H PHE 3.2 0.2 - - - -
22H ASN* 1.3 79.4 - - - +
24H PHE* 1.3 63.4 + - - +
26H ASN* 3.1 21.5 + - - +
29H VAL* 3.3 10.9 - - - +
32I THR* 3.6 14.6 - - + -
33I ILE* 3.8 27.6 - - + -
36I ASN* 3.5 16.1 - - - +
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Residues in contact with PHE 24 (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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3057 A 6.0 0.4 - - - -
468 T 3.7 50.3 - - + +
478 A 5.4 2.9 - - - +
24G PHE* 4.4 8.5 - + - -
34G LEU* 3.5 31.0 - - + -
20H LYS 3.0 16.6 + - - +
21H PHE* 3.7 11.7 - + - +
23H ALA* 1.3 77.1 - - - +
25H SER* 1.3 62.1 + - - +
26H ASN 3.0 1.6 + - - -
29H VAL* 3.8 6.1 - - + -
30H ALA* 3.3 45.5 + - - +
33H ILE* 4.2 18.8 - - + -
34H LEU* 4.0 26.2 - - + -
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Residues in contact with SER 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G SER* 3.4 21.8 - - - +
34G LEU* 3.8 37.2 - - - -
35G SER* 4.5 7.0 - - - -
38G SER* 4.7 7.5 + - - -
21H PHE* 3.0 14.8 + - - -
22H ASN* 2.6 23.6 + - - -
24H PHE* 1.3 75.7 - - - +
26H ASN* 1.3 60.8 + - - +
27H PRO* 3.2 4.5 - - - +
30H ALA* 4.9 0.7 - - - -
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Residues in contact with ASN 26 (chain H).
Click here for Legend to table.
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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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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) + - + + + + + -
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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