Contacts of the helix formed by residues 2 - 23 (chain A) in PDB entry 3BT9
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 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 1.3 62.4 + - - +
4A LYS* 3.1 2.9 - - - +
5A ASP* 3.5 22.1 + - - +
6A LYS* 2.7 40.5 + - - +
279A SO4 3.4 19.4 + - - +
599A SO4 2.8 24.9 + - - -
601A SO4 2.8 48.9 + - - +
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Residues in contact with LEU 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 1.3 82.2 + - - +
4A LYS* 1.3 57.5 + - - +
6A LYS* 3.5 6.4 + - + +
7A ILE* 3.0 35.3 + - - +
32A SER 4.0 21.1 - - - +
33A GLU* 4.1 11.9 - - + +
34A SER* 4.0 5.4 - - - +
38A ASN* 3.7 29.8 - - + +
279A SO4 3.1 22.1 + - - +
13E GLU* 5.8 0.4 - - - +
90E GLU* 3.3 29.8 - - + +
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Residues in contact with LYS 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN 4.8 1.8 - - - +
3A LEU* 1.3 78.4 - - - +
5A ASP* 1.3 66.9 + - - +
7A ILE* 3.3 5.8 + - - +
8A LEU* 3.0 36.9 + - + +
42A HIS* 3.6 21.3 - - + +
43A PHE* 3.5 33.4 - - + -
52A GLU* 5.5 5.6 + - - +
279A SO4 2.7 17.5 + - - +
299A SO4 3.0 45.4 + - - +
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Residues in contact with ASP 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 3.2 17.9 + - - +
4A LYS* 1.3 86.2 - - - +
6A LYS* 1.3 56.1 + - - +
8A LEU* 3.5 14.9 + - - +
9A GLY* 3.0 21.8 + - - -
599A SO4 3.3 31.1 + - - +
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 2.7 24.5 + - - +
3A LEU* 3.7 10.5 - - + +
4A LYS 3.2 0.2 - - - -
5A ASP* 1.3 72.0 - - - +
7A ILE* 1.3 65.1 + - - +
9A GLY* 3.1 0.8 + - - -
10A VAL* 2.9 37.4 + - + +
31A LEU 3.4 21.8 + - - -
32A SER* 3.6 25.4 - - - +
33A GLU* 4.7 12.0 + - - -
599A SO4 3.3 22.4 - - - +
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Residues in contact with ILE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU 3.0 25.4 + - - +
4A LYS* 3.3 6.9 + - - +
6A LYS* 1.3 74.7 - - - +
8A LEU* 1.3 59.7 + - - +
11A ALA* 2.9 34.5 + - - +
28A ILE* 3.6 14.8 - - + +
29A VAL* 6.2 0.4 - - - -
32A SER* 3.5 24.0 - - - +
34A SER* 3.7 10.1 - - - +
38A ASN* 3.2 27.6 - - - +
39A LEU* 3.5 38.8 - - + -
42A HIS* 4.7 0.9 - - + -
43A PHE* 3.9 16.4 - - + -
49A LEU* 4.1 9.0 - - + -
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 3.0 27.1 + - + +
5A ASP* 3.6 19.3 - - - +
7A ILE* 1.3 77.6 - - - +
9A GLY* 1.3 62.7 + - - +
11A ALA* 3.9 2.8 - - - +
12A LYS* 3.0 26.5 + - - +
43A PHE* 3.8 20.6 - - + -
49A LEU* 3.5 28.0 - - + -
52A GLU* 4.2 11.2 - - + -
53A ILE* 3.7 18.1 - - + +
56A ILE* 3.5 28.0 - - + -
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Residues in contact with GLY 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP 3.0 15.7 + - - -
6A LYS* 3.1 2.9 + - - -
8A LEU* 1.3 76.7 - - - +
10A VAL* 1.3 60.7 + - - +
12A LYS* 3.5 6.3 + - - +
13A GLU* 3.2 26.9 + - - +
599A SO4 5.4 3.1 - - - -
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 2.9 42.0 + - + +
7A ILE 4.2 1.6 - - - +
9A GLY* 1.3 72.4 - - - +
11A ALA* 1.3 67.2 + - - +
13A GLU* 3.0 9.8 + - - +
14A LEU* 2.9 37.2 + - + +
28A ILE* 4.6 5.4 - - - +
31A LEU* 3.8 36.3 - - + +
32A SER* 4.2 7.0 - - - +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE 2.9 20.5 + - - +
10A VAL* 1.3 77.6 - - - +
12A LYS* 1.3 58.9 + - - +
14A LEU* 3.1 3.3 + - - +
15A PHE* 2.9 40.3 + - + -
28A ILE* 4.0 20.8 - - + +
49A LEU* 3.8 21.5 - - + -
53A ILE* 3.8 16.6 - - + -
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Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU 3.0 19.0 + - - +
9A GLY* 3.7 7.2 - - - +
10A VAL 3.2 0.2 - - - -
11A ALA* 1.3 77.6 - - - +
13A GLU* 1.3 68.7 + - - +
15A PHE* 3.6 4.5 + - - +
16A ILE* 3.0 50.1 + - + +
53A ILE* 3.7 16.7 - - + +
57A GLN* 3.1 40.1 + - - +
60A LYS* 3.9 15.7 - - - +
93A TYR* 5.9 2.2 - - - -
95A LEU* 4.3 16.6 - - + +
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY 3.2 14.7 + - - +
10A VAL* 3.0 11.0 + - + +
12A LYS* 1.3 85.2 - - - +
14A LEU* 1.3 57.9 + - + +
16A ILE* 3.0 22.7 + - - +
17A LYS* 2.7 31.4 + - - +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 2.9 31.9 + - + +
11A ALA 3.1 5.1 + - - +
13A GLU* 1.3 76.9 - - + +
15A PHE* 1.3 57.4 + - - +
17A LYS* 3.0 6.0 + - + +
18A ASN* 2.8 45.0 + - - +
23A THR* 3.6 20.0 + - + +
27A GLU* 4.2 16.4 - - + +
28A ILE* 3.7 35.9 - - + +
31A LEU* 4.1 21.5 - - + -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 2.9 31.5 + - + +
12A LYS* 4.0 3.8 - - - +
14A LEU* 1.3 72.4 - - - +
16A ILE* 1.3 57.7 + - - +
19A GLY* 2.7 39.4 + - - -
20A TYR* 3.8 26.5 - + - -
23A THR* 3.6 28.0 - - + -
28A ILE* 4.3 12.3 - - + -
46A LYS* 4.1 20.4 - - + -
49A LEU* 4.6 4.9 - - + -
50A PHE* 3.5 31.0 - + + -
53A ILE* 3.6 24.9 - - + -
95A LEU* 4.1 7.2 - - + -
98A ALA* 3.8 20.6 + - + +
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.0 48.1 + - - +
13A GLU* 3.3 22.7 - - - +
15A PHE* 1.3 78.2 - - - +
17A LYS* 1.3 63.3 + - + +
19A GLY 4.7 0.5 + - - -
94A PRO* 3.7 45.8 - - + +
95A LEU* 3.9 20.6 - - + +
97A ASN* 5.8 1.0 + - - -
98A ALA* 5.4 0.2 - - - -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU 2.7 19.6 + - - +
14A LEU* 3.9 6.5 - - + +
16A ILE* 1.3 80.3 - - + +
18A ASN* 1.3 85.1 + - - +
19A GLY 3.7 0.2 - - - -
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 2.8 29.0 + - + +
17A LYS* 1.3 108.8 + - - +
19A GLY* 1.3 63.3 + - - +
22A ALA* 3.3 30.5 + - + +
23A THR* 4.4 5.2 - - - +
27A GLU* 5.2 4.9 - - - +
101A GLU* 4.9 0.5 - - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 2.7 29.9 + - - -
16A ILE 4.6 0.8 + - - -
17A LYS 3.7 1.4 - - - -
18A ASN* 1.3 72.8 - - - +
20A TYR* 1.3 59.7 + - - -
21A ASN 3.6 1.1 - - - -
23A THR* 2.7 29.3 + - - -
97A ASN* 5.5 1.8 - - - -
98A ALA* 4.5 6.3 - - - -
101A GLU* 3.5 17.0 - - - -
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.8 9.9 - + - -
19A GLY* 1.3 70.8 - - - +
21A ASN* 1.3 70.9 + - - +
23A THR* 3.4 9.5 + - - +
46A LYS* 2.7 60.1 + - + +
47A GLU* 3.3 18.5 + - - -
50A PHE* 3.7 31.6 - + + -
98A ALA* 3.6 24.6 - - + +
101A GLU* 3.1 13.7 + - + +
102A PHE* 3.6 24.2 - + + -
105A GLU* 4.0 11.7 - - + -
106A TYR* 3.1 43.1 + + - -
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Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 1.3 76.6 - - - +
22A ALA* 1.3 58.5 + - - +
23A THR 3.5 1.6 + - - +
24A THR* 5.9 0.3 - - - +
46A LYS* 3.5 13.1 + - - +
101A GLU* 2.7 39.4 + - - +
105A GLU* 3.6 29.2 - - - +
800A SO4 4.8 0.9 + - - -
21B ASN* 4.9 13.9 - - - +
22B ALA* 5.7 4.8 - - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN* 3.3 30.7 + - + +
19A GLY 4.1 1.6 + - - -
20A TYR 3.4 0.8 - - - -
21A ASN* 1.3 75.2 - - - +
23A THR* 1.3 60.7 + - - +
24A THR* 3.8 7.9 + - - +
27A GLU* 3.6 12.1 - - - +
101A GLU* 4.6 0.4 + - - -
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Residues in contact with THR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 5.1 0.2 - - - +
14A LEU* 3.6 36.2 + - + +
15A PHE* 3.6 26.2 - - + -
18A ASN* 4.4 4.4 - - - +
19A GLY 2.7 24.3 + - - -
20A TYR 3.8 0.7 - - - -
21A ASN 3.3 1.7 - - - +
22A ALA* 1.3 78.3 - - - +
24A THR* 1.3 55.6 + - - +
27A GLU* 3.4 7.6 - - - +
28A ILE* 3.8 22.0 - - + -
46A LYS* 2.7 19.2 + - - +
800A SO4 2.7 21.8 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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