Contacts of the helix formed by residues 9 - 26 (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 SER 9 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53o THR* 4.2 4.9 - - - -
8p ARG* 1.3 76.7 - - - +
10p TYR* 1.3 64.8 + - - +
11p SER* 2.7 28.5 + - - -
12p GLN* 2.8 23.5 + - - +
13p ARG* 3.0 21.0 + - - +
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Residues in contact with TYR 10 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45o PHE* 5.1 0.9 - + - -
46o GLN* 5.2 14.6 + - - +
49o VAL* 4.6 6.7 - - + -
50o PRO* 3.7 39.7 - - + -
53o THR* 3.1 39.0 - - + +
9p SER* 1.3 75.6 - - - +
11p SER* 1.3 77.0 + - - +
13p ARG* 3.5 6.8 - - - +
14p TYR* 2.8 49.9 + + + -
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Residues in contact with SER 11 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9p SER* 2.7 22.1 + - - -
10p TYR* 1.3 102.8 - - - +
12p GLN* 1.3 59.8 + - - +
14p TYR* 3.7 4.0 + - - +
15p ALA* 2.9 29.5 + - - +
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Residues in contact with GLN 12 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2538 A 4.1 3.1 + - - -
7p SER 4.7 1.7 + - - +
8p ARG* 3.6 26.8 - - - +
9p SER* 2.8 39.5 + - - +
10p TYR 3.1 0.2 - - - -
11p SER* 1.3 84.5 + - - +
13p ARG* 1.3 64.6 + - - +
15p ALA* 3.7 4.8 - - - +
16p LYS* 3.1 26.2 + - - +
40q VAL* 5.0 1.7 - - - +
43q GLN* 5.3 7.4 - - + +
44q ASN* 2.9 33.4 + - - +
47q THR* 4.9 15.4 + - - +
48q ASN* 5.5 3.4 - - - +
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Residues in contact with ARG 13 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977 A 3.9 14.8 + - - -
987 T 4.8 5.3 + - - -
2528 T 3.8 30.8 + - + +
2538 A 3.6 57.7 + - - +
45o PHE* 4.5 7.9 - - + -
49o VAL* 3.8 20.7 + - + +
52o PHE* 4.5 4.2 - - - +
53o THR* 2.7 48.5 + - - +
56o ASN* 4.0 11.2 - - - +
8p ARG* 4.3 7.9 - - + -
9p SER 3.0 20.5 + - - +
10p TYR* 3.5 7.4 - - + +
12p GLN* 1.3 77.1 - - - +
14p TYR* 1.3 57.8 + - - +
17p TRP* 3.0 28.9 + - - +
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Residues in contact with TYR 14 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42o GLN* 3.9 10.3 + - - +
45o PHE* 3.5 33.8 - + + -
46o GLN* 3.4 41.4 + - + -
10p TYR* 2.8 35.7 + + + +
11p SER* 3.9 3.8 - - - +
13p ARG* 1.3 75.1 - - - +
15p ALA* 1.3 72.1 + - + +
17p TRP* 3.0 12.6 + + - +
18p GLN* 2.7 59.7 + - + +
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Residues in contact with ALA 15 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11p SER 2.9 20.5 + - - +
12p GLN* 3.3 8.3 + - - +
14p TYR* 1.3 84.9 - - + +
16p LYS* 1.3 62.2 + - - +
18p GLN* 3.3 5.5 + - - +
19p ALA* 3.1 19.8 + - - +
40q VAL* 4.1 22.9 - - + +
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Residues in contact with LYS 16 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887 T 3.7 33.8 + - - +
897 A 2.8 32.5 + - - -
2528 T 3.3 32.8 + - - +
2538 A 3.9 22.4 + - - +
12p GLN 3.1 12.2 + - - +
15p ALA* 1.3 76.6 - - - +
17p TRP* 1.3 66.1 + - - +
19p ALA* 3.1 4.9 + - - +
20p LYS* 2.9 26.0 + - + +
37q VAL* 4.7 8.1 - - + -
40q VAL* 3.9 19.7 - - + +
44q ASN* 5.5 2.7 - - - +
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Residues in contact with TRP 17 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997 A 3.8 34.3 + - + -
2518 A 3.8 26.9 + - + -
2528 T 3.8 19.4 - - - +
41o ALA* 4.1 20.9 - - + -
42o GLN* 4.2 6.7 - - + -
45o PHE* 3.5 54.4 - + + -
13p ARG 3.0 19.7 + - - +
14p TYR* 3.4 15.3 - + - +
16p LYS* 1.3 76.6 - - - +
18p GLN* 1.3 93.6 + - - +
20p LYS* 3.4 2.1 + - - +
21p PHE* 2.9 53.3 + + + +
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Residues in contact with GLN 18 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42o GLN* 3.2 39.8 - - - +
14p TYR* 2.7 57.9 + - + +
15p ALA* 3.5 6.7 - - - +
17p TRP* 1.3 82.8 - - - +
19p ALA* 1.3 63.8 + - - +
21p PHE* 3.2 5.7 + - - +
22p ASN* 2.9 63.5 + - - +
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Residues in contact with ALA 19 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15p ALA 3.1 8.8 + - - +
16p LYS* 3.1 10.4 + - - +
18p GLN* 1.3 79.7 - - - +
20p LYS* 1.3 58.1 + - - +
22p ASN* 3.5 10.0 + - - +
23p ALA* 3.0 25.6 + - - +
36q ASN* 3.4 35.2 - - - +
37q VAL* 3.7 17.3 - - + -
40q VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 20 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897 A 2.8 30.9 + - - +
907 T 3.1 25.1 + - - -
2518 A 3.4 43.5 + - + +
2528 T 3.2 21.1 + - - +
16p LYS* 2.9 21.8 + - + +
17p TRP 3.9 3.1 - - - +
19p ALA* 1.3 74.1 - - - +
21p PHE* 1.3 66.9 + - - +
23p ALA* 3.3 4.3 + - + +
24p PHE* 3.0 24.4 + - - +
33q ILE* 3.9 20.0 - - + -
37q VAL* 3.6 17.3 - - + -
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Residues in contact with PHE 21 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997 A 5.7 2.7 - + - -
1007 T 4.4 24.0 - - + -
2508 T 6.0 1.6 - - - -
2518 A 5.2 2.4 - - - -
34o LEU* 3.9 30.5 - - + -
37o VAL* 4.5 4.9 - - + -
38o SER* 3.5 36.8 - - - -
41o ALA* 4.5 9.4 - - + -
42o GLN* 5.6 0.4 - - + -
17p TRP* 2.9 47.9 + + + +
18p GLN* 3.6 12.1 - - - +
20p LYS* 1.3 77.0 - - - +
22p ASN* 1.3 72.5 + - - +
24p PHE* 3.3 12.1 + + + +
25p SER* 3.0 23.2 + - - -
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Residues in contact with ASN 22 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38o SER* 5.5 2.4 + - - -
42o GLN* 4.6 3.1 + - - -
18p GLN* 2.9 51.3 + - - +
19p ALA* 3.5 7.5 - - - +
21p PHE* 1.3 80.5 - - - +
23p ALA* 1.3 62.7 + - - +
25p SER* 2.6 25.9 + - - -
26p ASN* 3.6 4.2 + - - +
36q ASN* 4.0 11.9 - - - +
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Residues in contact with ALA 23 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19p ALA 3.0 14.2 + - - +
20p LYS* 3.5 9.2 - - + +
22p ASN* 1.3 79.6 - - - +
24p PHE* 1.3 63.5 + - - +
26p ASN* 3.1 22.2 + - - +
29p VAL* 3.3 11.2 - - - +
32q THR* 3.6 14.6 - - + -
33q ILE* 3.8 28.5 - - + -
36q ASN* 3.5 16.1 - - - +
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Residues in contact with PHE 24 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017 A 6.0 0.2 - - - -
2508 T 3.7 51.6 - - + +
2518 A 5.4 2.5 - - - +
24o PHE* 4.4 9.6 - + - -
34o LEU* 3.5 30.7 - - + -
20p LYS 3.0 16.5 + - - +
21p PHE* 3.3 12.1 + + - +
23p ALA* 1.3 76.7 - - - +
25p SER* 1.3 62.0 + - - +
26p ASN 3.0 1.4 + - - -
29p VAL* 3.8 5.8 - - - -
30p ALA* 3.3 45.0 + - - +
33p ILE* 4.2 20.2 - - + -
34p LEU* 4.0 24.9 - - + -
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Residues in contact with SER 25 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31o SER* 3.4 21.7 - - - +
34o LEU* 3.8 37.2 - - - -
35o SER* 4.5 6.9 - - - -
38o SER* 4.7 7.8 + - - -
21p PHE* 3.0 15.5 + - - -
22p ASN* 2.6 23.5 + - - -
24p PHE* 1.3 75.9 - - - +
26p ASN* 1.3 61.0 + - - +
27p PRO* 3.2 4.7 - - - +
30p ALA* 4.9 0.7 - - - -
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Residues in contact with ASN 26 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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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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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