Contacts of the helix formed by residues 12 - 28 (chain B) in PDB entry 3LB2
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 ASP 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR 3.6 1.6 + - - +
9B ILE 3.1 6.4 + - - -
11B GLY* 1.3 81.0 - - - +
13B LEU* 1.3 64.4 + - - +
14B ARG* 3.4 2.1 - - - +
15B THR* 3.2 32.1 + - - +
16B TYR* 3.1 39.0 + - + -
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Residues in contact with LEU 13 (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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9B ILE* 3.1 37.5 - - + +
10B ARG* 3.8 16.9 + - + +
12B ASP* 1.3 75.7 - - - +
14B ARG* 1.3 54.2 + - - +
16B TYR* 3.3 0.7 + - - +
17B ALA* 2.7 38.7 + - + +
57B GLU* 3.4 55.4 - - + +
60B PHE* 4.0 25.8 - - + +
61B ASN 4.3 3.4 - - - +
64B MET* 4.3 6.5 - - + -
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Residues in contact with ARG 14 (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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12B ASP* 3.4 1.0 - - - +
13B LEU* 1.3 83.2 - - - +
15B THR* 1.3 63.8 + - - +
17B ALA* 3.9 2.8 - - - +
18B GLN* 3.0 45.8 + - + +
50B ALA 5.4 3.0 + - - -
53B GLY* 3.5 23.5 - - - -
54B ASP* 3.3 38.0 + - - +
56B THR* 5.6 0.2 - - - -
57B GLU* 2.9 31.2 + - - +
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Residues in contact with THR 15 (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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12B ASP* 3.2 33.3 + - - +
13B LEU 3.2 0.6 - - - -
14B ARG* 1.3 78.3 - - - +
16B TYR* 1.3 67.5 + - + +
18B GLN* 3.9 5.8 - - - +
19B ASP* 3.0 45.1 + - - +
47B LYS* 6.0 2.2 - - - +
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Residues in contact with TYR 16 (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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8B THR* 3.6 27.0 - - + +
9B ILE* 3.7 34.1 - - + -
12B ASP* 3.1 39.8 + - + +
13B LEU 4.0 2.2 - - - +
15B THR* 1.3 80.0 - - + +
17B ALA* 1.3 58.5 + - - +
19B ASP* 3.3 2.9 + - - +
20B ILE* 2.9 42.0 + - + +
107B TYR* 3.3 31.2 - + - -
111B SER* 6.0 0.4 - - - -
113B GLN* 3.5 26.4 - - + +
115B PHE* 3.7 24.2 - + - -
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Residues in contact with ALA 17 (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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13B LEU* 2.7 26.2 + - + +
14B ARG 3.9 3.4 - - - +
16B TYR* 1.3 73.5 - - - +
18B GLN* 1.3 58.1 + - - +
21B PHE* 2.9 32.1 + - - +
56B THR* 3.8 18.6 - - - +
57B GLU 4.4 0.7 - - - +
60B PHE* 3.6 45.1 - - + -
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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
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14B ARG* 3.0 35.9 + - + +
15B THR* 4.0 4.7 + - - +
17B ALA* 1.3 75.5 - - - +
19B ASP* 1.3 59.8 + - - +
21B PHE* 4.0 2.1 - - - +
22B LEU* 2.8 36.2 + - - +
47B LYS* 3.7 39.8 + - - +
52B PHE* 3.5 26.7 - - + -
53B GLY* 3.5 22.8 - - - +
56B THR* 3.4 18.8 - - - +
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Residues in contact with ASP 19 (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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15B THR* 3.0 35.9 + - - +
16B TYR 4.0 1.8 - - - +
18B GLN* 1.3 78.1 - - - +
20B ILE* 1.3 57.7 + - - +
22B LEU* 3.5 6.9 + - - +
23B ALA* 3.0 27.9 + - - +
47B LYS* 3.3 29.3 + - - -
107B TYR* 3.9 30.2 + - + +
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Residues in contact with ILE 20 (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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9B ILE* 5.2 9.6 - - + -
16B TYR* 2.9 31.1 + - + +
19B ASP* 1.3 72.4 - - - +
21B PHE* 1.3 63.2 + - - +
23B ALA* 3.2 8.0 + - - +
24B PHE* 2.9 26.9 + - - +
60B PHE* 3.7 29.4 - - + -
100B LEU* 4.8 6.3 - - + -
103B ALA* 4.8 1.2 - - - +
104B LEU* 3.3 52.9 - - + +
107B TYR* 3.6 31.4 - - + -
108B MET* 5.2 0.9 - - + -
115B PHE* 6.5 0.7 - - + -
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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
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17B ALA 2.9 18.8 + - - +
18B GLN 4.0 2.2 - - - +
20B ILE* 1.3 78.3 - - - +
22B LEU* 1.3 56.7 + - - +
24B PHE* 3.2 30.1 + + + +
25B LEU* 2.9 45.6 + - + +
35B PHE* 3.8 23.8 - + - -
38B TYR* 3.8 11.9 - + - -
52B PHE* 3.6 28.9 - + - -
56B THR* 3.4 22.7 - - + -
60B PHE* 4.5 6.9 - - + -
100B LEU* 5.1 1.3 - - + -
192B BML 3.3 47.8 - + + -
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Residues in contact with LEU 22 (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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18B GLN 2.8 22.6 + - - +
19B ASP* 3.8 7.4 - - - +
21B PHE* 1.3 75.9 - - - +
23B ALA* 1.3 56.8 + - - +
25B LEU* 3.3 6.8 + - + +
26B ASN* 2.8 44.0 + - - +
43B ASP* 3.7 33.4 - - + +
46B LEU* 3.6 32.1 - - + -
47B LYS* 3.6 34.3 - - + +
52B PHE* 3.7 17.0 - - + -
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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 ASP 3.0 15.5 + - - +
20B ILE* 3.4 11.9 - - - +
22B LEU* 1.3 76.4 - - - +
24B PHE* 1.3 56.3 + - - +
26B ASN* 4.0 4.9 - - - +
27B LYS* 3.0 31.9 + - - +
103B ALA* 4.1 17.0 - - + +
107B TYR* 4.6 12.1 - - + -
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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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20B ILE 2.9 13.0 + - - +
21B PHE* 3.3 32.3 - + - +
23B ALA* 1.3 75.5 - - - +
25B LEU* 1.3 66.4 + - + +
27B LYS 3.3 0.9 + - - -
28B TYR* 2.9 44.5 + + - +
31B GLU* 3.6 37.0 - - + -
35B PHE* 4.6 1.1 - + - -
96B ASN 4.1 3.1 - - - -
99B LYS* 3.8 14.1 - - + -
100B LEU* 3.5 49.6 - - + -
103B ALA* 3.6 13.8 - - + +
139B HEM 3.7 21.1 - - + -
192B BML 5.0 2.0 - - + -
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Residues in contact with LEU 25 (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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21B PHE* 2.9 65.3 + - + +
22B LEU* 3.9 5.6 - - + +
24B PHE* 1.3 85.0 - - + +
26B ASN* 1.3 60.3 + - - +
28B TYR 4.2 2.5 - - - -
29B PRO* 3.1 32.7 - - - +
31B GLU* 4.6 1.8 - - + -
32B ARG* 3.9 35.0 + - + +
35B PHE* 4.2 10.3 - - + -
38B TYR* 4.3 13.0 - - + -
46B LEU* 4.5 14.1 - - + -
52B PHE* 4.5 8.3 - - + -
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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
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22B LEU* 2.8 27.6 + - - +
23B ALA* 4.1 4.4 - - - +
25B LEU* 1.3 78.0 - - - +
27B LYS* 1.3 64.5 + - - +
29B PRO* 3.6 11.2 - - - +
43B ASP* 3.1 33.5 + - - +
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Residues in contact with LYS 27 (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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23B ALA 3.0 18.3 + - - +
24B PHE* 4.8 0.7 - - - -
26B ASN* 1.3 77.5 - - - +
28B TYR* 1.3 102.9 + - + +
29B PRO* 3.5 6.7 - - - +
102B VAL* 3.9 6.7 - - + -
103B ALA* 4.7 7.2 - - + -
106B GLU* 3.2 40.5 + - - +
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Residues in contact with TYR 28 (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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24B PHE* 2.9 30.6 + + - +
25B LEU* 3.3 6.4 - - - +
27B LYS* 1.3 111.2 - - + +
29B PRO* 1.3 66.2 - - - +
30B ASP* 3.2 8.7 - - - +
31B GLU* 2.9 35.3 + - + +
32B ARG 4.4 0.3 + - - -
99B LYS* 3.3 57.3 - - + +
102B VAL* 3.3 30.7 - - - +
103B ALA* 4.5 2.2 - - + -
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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