Contacts of the helix formed by residues 9 - 26 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR* 4.2 5.2 - - - -
8B ARG* 1.3 76.0 - - - +
10B TYR* 1.3 65.2 + - - +
11B SER* 2.7 28.3 + - - -
12B GLN* 2.8 24.3 + - - +
13B ARG* 3.0 20.8 + - - +
47f THR* 5.8 6.3 - - - -
50f PRO* 6.4 2.7 - - - -
51f LYS* 6.4 2.7 - - - -
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Residues in contact with TYR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 5.1 0.7 - + - -
46A GLN* 5.2 12.6 + - + +
49A VAL* 4.6 6.7 - - + -
50A PRO* 3.7 35.0 - - + -
53A THR* 3.1 39.2 - - + +
9B SER* 1.3 76.0 - - - +
11B SER* 1.3 77.2 + - - +
13B ARG* 3.4 6.2 - - - +
14B TYR* 2.8 49.8 + + + +
10e TYR* 2.8 47.6 + + - -
11e SER* 5.0 3.6 + - - -
14e TYR* 5.5 1.9 - - - -
50f PRO* 4.1 17.5 - - + -
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Residues in contact with SER 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 2.7 21.3 + - - -
10B TYR* 1.3 100.6 - - - +
12B GLN* 1.3 58.8 + - - +
14B TYR* 3.9 4.1 - - - +
15B ALA* 2.9 29.1 + - - +
43f GLN* 5.2 5.4 + - - -
46f GLN* 4.3 39.7 + - - +
47f THR* 5.0 3.8 - - - -
50f PRO* 5.7 0.7 - - - -
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 A 4.1 3.0 + - - -
7B SER 4.7 1.7 + - - +
8B ARG* 3.6 27.4 - - - +
9B SER* 2.8 39.0 + - - +
10B TYR 3.1 0.2 - - - -
11B SER* 1.3 82.7 + - - +
13B ARG* 1.3 65.4 + - - +
15B ALA* 3.7 6.4 - - - +
16B LYS* 3.1 25.6 + - - +
40C VAL* 5.0 2.1 - - - +
43C GLN* 5.3 7.4 - - + +
44C ASN* 2.9 32.4 + - - +
47C THR* 4.9 15.0 + - - +
48C ASN* 5.5 3.4 - - - +
43f GLN* 6.2 1.8 - - - +
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3377 A 3.9 15.2 + - - -
3387 T 4.8 5.1 + - - -
128 T 3.8 30.8 + - + +
138 A 3.6 56.6 + - - +
45A PHE* 4.5 9.3 - - + -
49A VAL* 3.8 20.1 + - + +
52A PHE* 4.5 4.8 - - - +
53A THR* 2.7 49.0 + - - +
56A ASN* 4.0 11.8 - - - +
8B ARG* 4.3 8.5 - - + -
9B SER 3.0 19.7 + - - +
10B TYR* 3.2 7.2 + - + +
12B GLN* 1.3 78.4 - - - +
14B TYR* 1.3 55.7 + - - +
17B TRP* 3.0 29.2 + - - +
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Residues in contact with TYR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.9 10.7 + - - +
45A PHE* 3.5 33.8 - + + -
46A GLN* 3.4 40.3 + - + -
10B TYR* 2.8 34.1 + + + +
11B SER* 3.9 4.5 - - - +
13B ARG* 1.3 74.8 - - - +
15B ALA* 1.3 71.3 + - - +
17B TRP* 3.0 14.4 + + - -
18B GLN* 2.7 59.2 + - + +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER 2.9 21.3 + - - +
12B GLN* 3.7 8.1 - - - +
14B TYR* 1.3 83.8 - - + +
16B LYS* 1.3 62.2 + - - +
18B GLN* 3.3 5.7 + - - +
19B ALA* 3.1 19.6 + - - +
40C VAL* 4.1 22.5 - - + +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3287 T 3.7 34.7 + - - +
3297 A 2.8 31.8 + - - -
128 T 3.3 33.7 + - - +
138 A 3.9 21.7 + - - +
12B GLN 3.1 13.0 + - - +
15B ALA* 1.3 76.6 - - - +
17B TRP* 1.3 66.8 + - - +
19B ALA* 3.1 5.7 + - - +
20B LYS* 3.0 25.5 + - + +
37C VAL* 4.7 8.3 - - + -
40C VAL* 3.9 19.2 - - + +
44C ASN* 5.5 2.7 - - - +
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Residues in contact with TRP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3397 A 3.8 33.6 + - + -
118 A 3.8 26.9 + - + -
128 T 3.8 19.8 - - - +
41A ALA* 4.1 20.0 - - + -
42A GLN* 4.2 6.7 - - + -
45A PHE* 3.5 54.2 - + + -
13B ARG 3.0 20.5 + - - +
14B TYR* 3.4 14.6 - + - +
16B LYS* 1.3 76.4 - - - +
18B GLN* 1.3 93.0 + - - +
20B LYS* 3.4 2.7 + - - +
21B PHE* 2.9 52.8 + + + +
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.2 39.6 - - - +
14B TYR* 2.7 57.6 + - + +
15B ALA* 3.5 7.2 - - - +
17B TRP* 1.3 83.4 - - - +
19B ALA* 1.3 62.6 + - - +
21B PHE* 3.2 6.3 + - - -
22B ASN* 2.9 64.1 + - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA 3.1 9.2 + - - +
16B LYS* 3.1 10.4 + - - +
18B GLN* 1.3 79.7 - - - +
20B LYS* 1.3 59.2 + - - +
22B ASN* 3.5 9.5 - - - +
23B ALA* 3.0 26.7 + - - +
36C ASN* 3.4 35.7 - - - +
37C VAL* 3.7 16.2 - - + -
40C VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3297 A 2.8 32.6 + - - +
3307 T 3.1 25.3 + - - -
118 A 3.4 45.1 + - + +
128 T 3.2 21.5 + - - +
16B LYS* 3.0 21.5 + - + +
17B TRP 3.9 3.1 - - - +
19B ALA* 1.3 74.1 - - - +
21B PHE* 1.3 65.6 + - - +
23B ALA* 3.3 4.0 + - + +
24B PHE* 3.0 24.8 + - - +
33C ILE* 3.9 19.5 - - + -
37C VAL* 3.6 16.8 - - + -
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3397 A 5.7 2.7 - + - -
3407 T 4.5 23.6 - - - -
108 T 6.0 2.0 - - - -
118 A 5.2 2.4 - - - -
34A LEU* 3.9 30.7 - - + -
37A VAL* 4.5 5.4 - - + -
38A SER* 3.5 38.4 - - - -
41A ALA* 4.5 9.4 - - + -
17B TRP* 2.9 48.8 + + + +
18B GLN* 3.6 12.3 - - - +
20B LYS* 1.3 78.6 - - - +
22B ASN* 1.3 71.6 + - - +
24B PHE* 3.3 11.4 + + - +
25B SER* 3.0 23.3 + - - -
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 5.5 2.1 + - - -
42A GLN* 4.6 3.6 + - - -
18B GLN* 2.9 50.9 + - - +
19B ALA* 3.5 9.1 - - - +
21B PHE* 1.3 80.6 - - - +
23B ALA* 1.3 63.4 + - - +
25B SER* 2.6 25.7 + - - -
26B ASN* 3.6 4.2 + - - +
36C ASN* 4.0 11.0 - - - +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 3.0 14.9 + - - +
20B LYS* 3.5 8.7 - - + +
22B ASN* 1.3 79.3 - - - +
24B PHE* 1.3 62.8 - - - +
26B ASN* 3.1 21.7 + - - +
29B VAL* 3.3 11.1 - - - +
32C THR* 3.6 14.8 - - + -
33C ILE* 3.8 27.4 - - + -
36C ASN* 3.5 16.1 - - + +
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3417 A 6.0 0.7 - - - -
108 T 3.7 52.0 - - + +
118 A 5.4 2.9 - - - +
24A PHE* 4.4 8.5 - + - -
34A LEU* 3.5 31.2 - - + -
20B LYS 3.0 17.8 + - - +
21B PHE* 3.7 11.4 - + - +
23B ALA* 1.3 76.4 - - - +
25B SER* 1.3 61.9 + - - +
26B ASN 3.0 1.8 + - - -
29B VAL* 3.8 6.3 - - - +
30B ALA* 3.3 44.2 + - - +
33B ILE* 4.2 19.7 - - + -
34B LEU* 4.0 24.9 - - + -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.4 21.7 - - - +
34A LEU* 3.8 38.1 - - - -
35A SER* 4.5 6.1 - - - -
38A SER* 4.7 7.7 + - - -
21B PHE* 3.0 14.8 + - - -
22B ASN* 2.6 23.4 + - - -
24B PHE* 1.3 75.5 - - - +
26B ASN* 1.3 61.0 + - - +
27B PRO* 3.2 3.8 - - - +
30B ALA* 4.9 0.4 - - - +
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN 3.6 2.4 + - - +
23B ALA 3.1 16.0 + - - +
24B PHE 3.0 1.0 + - - -
25B SER* 1.3 78.1 + - - +
27B PRO* 1.4 68.3 - - - +
28B THR* 2.9 24.9 + - - -
29B VAL* 2.7 37.6 + - + -
30B ALA* 2.8 11.8 + - - -
32C THR* 4.0 19.0 + - + +
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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
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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