Contacts of the helix formed by residues 4 - 22 (chain B) in PDB entry 3E20
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 THR 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ALA* 1.3 74.8 + - - +
6B GLU 3.9 0.2 - - - -
7B LYS* 3.5 35.5 - - + +
8B ALA* 3.4 22.6 + - - +
279B GLN* 5.3 11.4 + - - +
389B GLU* 5.6 0.9 - - - +
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Residues in contact with ALA 5 (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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4B THR* 1.3 89.4 + - - +
6B GLU* 1.3 67.6 + - + +
7B LYS 3.1 3.3 + - - -
8B ALA* 3.9 4.7 + - - +
9B ILE* 4.0 7.6 + - - +
388B LEU 5.5 1.4 - - - +
389B GLU* 4.9 8.5 - - - +
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Residues in contact with GLU 6 (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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5B ALA* 1.3 84.4 - - + +
7B LYS* 1.3 58.9 + - - +
9B ILE* 3.0 30.2 - - + +
10B GLU* 3.6 10.6 - - - +
381B TYR* 3.4 23.2 + - - +
382B LYS* 3.5 28.6 + - - +
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Residues in contact with LYS 7 (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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4B THR* 3.5 32.8 - - + +
5B ALA 3.1 0.4 - - - -
6B GLU* 1.3 76.1 - - - +
8B ALA* 1.3 58.7 + - + +
9B ILE 3.0 1.3 - - - -
10B GLU* 2.7 29.9 + - + +
11B ILE* 3.1 29.4 + - + +
114B PHE* 6.4 0.2 - - - -
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Residues in contact with ALA 8 (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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4B THR* 3.4 19.4 + - - +
5B ALA 4.4 1.8 - - - +
7B LYS* 1.3 79.3 - - - +
9B ILE* 1.3 56.2 + - - +
11B ILE* 3.2 19.6 + - + +
12B TRP* 2.9 28.6 + - - +
389B GLU* 5.7 4.0 - - - +
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Residues in contact with ILE 9 (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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5B ALA 4.0 4.5 + - - +
6B GLU* 3.0 39.2 - - + +
7B LYS 3.0 0.8 - - - -
8B ALA* 1.3 79.3 - - - +
10B GLU* 1.3 70.9 + - - +
12B TRP* 3.1 31.6 - - + +
13B LYS* 3.7 6.0 + - - +
378B ALA* 5.0 8.3 - - + +
381B TYR* 4.7 19.5 - - + +
388B LEU* 3.9 33.0 - - + +
390B PHE* 3.6 35.0 - - + +
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Residues in contact with GLU 10 (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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6B GLU 3.6 15.4 - - - +
7B LYS* 2.7 9.9 + - + +
9B ILE* 1.3 89.1 - - - +
11B ILE* 1.3 58.0 + - + +
12B TRP 2.9 1.6 - - - -
13B LYS* 2.7 53.4 + - - +
14B ILE* 3.1 15.7 + - + +
114B PHE* 3.6 40.8 - - + -
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Residues in contact with ILE 11 (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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7B LYS* 3.5 30.7 - - + +
8B ALA* 3.5 23.3 - - + +
10B GLU* 1.3 76.3 - - + +
12B TRP* 1.3 63.2 + - - +
14B ILE* 3.4 10.4 + - - +
15B ARG* 3.0 24.2 + - + +
114B PHE* 6.5 0.7 - - + -
136B LEU 3.7 23.3 - - - +
137B LEU* 3.8 29.2 - - + -
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Residues in contact with TRP 12 (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 ALA 2.9 13.2 + - - +
9B ILE 3.1 23.1 - - - +
11B ILE* 1.3 76.5 - - - +
13B LYS* 1.3 84.0 + - + +
15B ARG* 3.2 16.4 + - - +
16B ARG* 3.0 51.0 + - + +
321B ALA* 2.8 51.4 - - + -
374B SER* 2.9 26.2 - - - -
375B GLU* 5.2 3.8 - - + +
378B ALA* 4.0 10.5 - - + +
390B PHE* 3.4 50.5 - + + -
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Residues in contact with LYS 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* 4.2 6.7 - - - +
10B GLU* 2.7 46.5 + - - +
12B TRP* 1.3 96.0 - - + +
14B ILE* 1.3 66.7 + - + +
16B ARG* 3.0 9.3 + - + +
17B LEU* 2.9 23.0 + - - +
375B GLU* 5.9 8.5 - - + -
378B ALA* 4.9 13.1 + - + +
379B GLU* 4.6 22.7 + - + +
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Residues in contact with ILE 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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10B GLU* 3.1 16.9 + - + +
11B ILE* 3.6 12.3 - - - +
13B LYS* 1.3 77.1 - - + +
15B ARG* 1.3 59.2 + - - +
17B LEU* 3.1 9.3 + - + +
18B VAL* 2.9 43.6 + - + +
111B PHE* 4.2 25.1 - - + -
113B PRO* 5.5 1.8 - - + -
114B PHE* 5.4 11.9 - - + -
133B LEU* 4.5 14.8 - - + -
136B LEU* 4.5 26.7 - - + +
137B LEU* 3.8 20.0 - - + -
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Residues in contact with ARG 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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11B ILE* 3.0 14.1 + - + +
12B TRP* 3.4 25.4 - - - +
13B LYS 3.2 0.2 - - - -
14B ILE* 1.3 78.2 - - - +
16B ARG* 1.3 93.2 + - - +
18B VAL* 3.1 25.4 - - + +
19B LYS* 3.2 20.0 - - + +
137B LEU* 4.2 11.0 - - + +
321B ALA* 4.0 8.3 - - - +
322B ASP* 2.7 34.4 + - - -
392B SER* 5.7 2.8 + - - -
394B ARG* 5.1 14.6 - - - +
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Residues in contact with ARG 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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12B TRP* 3.0 46.1 + - + +
13B LYS* 3.0 11.7 + - + +
15B ARG* 1.3 90.5 - - - +
17B LEU* 1.3 67.7 + - - +
19B LYS* 3.3 27.3 - - - +
20B GLN* 3.3 25.5 + - - +
321B ALA 3.8 4.9 + - - -
322B ASP* 2.9 47.5 + - - +
323B LEU 5.6 2.0 + - - -
372B LEU* 5.1 14.5 - - - +
374B SER* 5.9 0.4 - - - -
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Residues in contact with LEU 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 LYS 2.9 12.3 + - - +
14B ILE* 3.1 13.0 + - + +
16B ARG* 1.3 72.4 - - - +
18B VAL* 1.3 66.7 + - + +
19B LYS 2.8 4.5 - - - -
20B GLN* 2.7 41.8 + - + +
21B LEU* 3.0 40.7 + - + +
109B ILE* 4.8 19.3 - - + -
111B PHE* 3.8 37.5 - - + -
133B LEU* 4.8 5.8 - - + -
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Residues in contact with VAL 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 ILE* 2.9 27.5 + - + +
15B ARG* 3.1 24.0 - - + +
17B LEU* 1.3 72.8 - - - +
19B LYS* 1.3 66.4 + - + +
21B LEU* 4.6 0.4 - - - -
22B ILE* 3.2 33.6 + - + +
130B THR* 4.1 20.2 - - - +
133B LEU* 3.6 37.2 - - + -
137B LEU* 5.0 13.7 - - + -
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Residues in contact with LYS 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 ARG* 3.2 23.2 - - + +
16B ARG* 3.3 39.7 - - - +
17B LEU 2.7 1.8 + - - -
18B VAL* 1.3 85.4 - - + +
20B GLN* 1.3 56.1 + - + +
22B ILE* 3.8 11.0 - - - +
23B ASN* 3.2 32.6 + - - +
322B ASP* 3.3 24.4 + - - +
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Residues in contact with GLN 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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16B ARG* 3.5 11.3 - - - +
17B LEU* 2.7 51.4 + - + +
19B LYS* 1.3 74.8 - - + +
21B LEU* 1.3 63.3 + - + +
23B ASN* 3.3 8.9 - - - +
24B CYS* 3.2 23.7 + - - +
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Residues in contact with LEU 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 LEU* 3.0 42.5 + - + +
20B GLN* 1.3 77.7 - - + +
22B ILE* 1.3 59.7 + - - +
23B ASN 2.9 4.6 + - - -
24B CYS* 3.0 31.3 + - - +
93B TYR* 3.6 45.1 - - + -
107B LEU* 4.4 15.5 - - + -
109B ILE* 4.5 7.6 - - + -
128B PHE* 3.8 34.5 + - + +
130B THR* 3.9 18.2 - - + -
133B LEU* 4.5 1.8 - - + -
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Residues in contact with ILE 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 VAL* 3.2 21.9 + - + +
19B LYS* 3.8 10.8 - - - +
21B LEU* 1.3 74.2 - - - +
23B ASN* 1.3 63.4 + - - +
24B CYS 3.5 3.5 - - - +
25B HIS* 6.0 0.2 - - - +
127B LYS* 6.3 3.1 - - - -
128B PHE 4.4 10.8 - - - +
130B THR* 3.0 32.1 - - + +
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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