Contacts of the helix formed by residues 10 - 28 (chain B) in PDB entry 3CJD
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 ALA 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 1.3 69.0 + - - +
12B LEU* 3.5 3.0 - - - +
13B ARG* 3.9 10.9 + - - +
14B GLU* 3.6 26.0 + - - +
51B HIS* 5.7 4.6 + - - -
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 1.3 79.6 - - - +
12B LEU* 1.3 57.3 + - - +
14B GLU* 3.5 3.2 + - - +
15B LYS* 2.9 31.8 + - + +
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA 3.5 1.8 - - - +
11B ALA* 1.3 77.3 - - - +
13B ARG* 1.3 59.0 + - - +
15B LYS* 4.2 9.2 - - + -
16B LEU* 2.9 51.7 + - + +
41B ALA* 3.9 24.2 - - + +
43B CYS* 3.9 15.3 - - + -
47B ALA* 3.8 27.8 - - + -
51B HIS* 4.2 16.2 - - + -
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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
----------------------------------------------------------
10B ALA* 3.9 13.4 + - - +
11B ALA 3.4 0.6 - - - -
12B LEU* 1.3 78.7 - - - +
14B GLU* 1.3 81.3 + - + +
16B LEU* 3.4 1.2 + - - -
17B ILE* 3.3 32.5 + - - +
51B HIS* 3.8 47.2 + - + -
52B PHE* 3.6 27.8 - - + -
61B GLU* 3.3 27.7 + - - -
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA 3.6 17.2 + - - +
11B ALA* 3.5 4.6 + - - +
12B LEU 3.3 0.2 - - - -
13B ARG* 1.3 92.5 + - + +
15B LYS* 1.3 58.7 + - - +
17B ILE* 3.2 14.0 + - - +
18B ASP* 3.0 37.0 + - - +
65B ARG* 3.2 24.7 + - - +
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Residues in contact with LYS 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 ALA* 2.9 20.8 + - + +
12B LEU* 3.4 11.6 + - + +
14B GLU* 1.3 74.2 - - - +
16B LEU* 1.3 57.0 + - - +
18B ASP* 3.3 11.8 + - + +
19B LEU* 2.9 50.1 + - + +
40B GLN 4.6 4.1 + - - -
41B ALA* 3.6 35.2 + - + +
42B ASP* 5.2 3.4 - - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 2.9 39.4 + - + +
13B ARG 3.7 5.2 - - - +
14B GLU 3.3 0.2 - - - -
15B LYS* 1.3 76.2 - - - +
17B ILE* 1.3 54.9 + - - +
19B LEU* 3.8 3.7 - - + +
20B ALA* 2.9 31.2 + - - +
37B LEU* 4.2 16.8 - - + +
41B ALA* 3.7 25.1 - - + -
43B CYS* 4.3 2.5 - - - -
47B ALA 4.3 4.9 - - - +
48B ILE* 3.9 41.7 - - + +
51B HIS* 4.4 3.1 - - - +
52B PHE* 3.7 24.7 - - + -
58B LEU* 4.0 8.0 - - + +
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Residues in contact with ILE 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 ARG* 3.3 37.4 + - - +
14B GLU* 3.2 21.4 + - - +
16B LEU* 1.3 72.1 - - - +
18B ASP* 1.3 59.9 + - - +
20B ALA* 3.3 2.2 + - - +
21B GLU* 3.0 29.3 + - - +
52B PHE* 3.7 15.5 - - + -
58B LEU* 3.9 11.4 - - + -
61B GLU* 3.9 35.7 - - + +
62B VAL* 4.0 5.2 - - + +
65B ARG* 3.4 33.7 - - - +
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Residues in contact with ASP 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 GLU* 3.0 25.0 + - - +
15B LYS* 3.5 13.1 - - + +
17B ILE* 1.3 74.2 - - - +
19B LEU* 1.3 59.3 + - + +
21B GLU* 3.5 5.5 + - - +
22B ALA* 3.0 27.7 + - - +
65B ARG* 2.9 32.8 + - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 2.9 32.6 + - + +
16B LEU* 3.9 2.5 - - - +
18B ASP* 1.3 77.2 - - + +
20B ALA* 1.3 59.0 + - - +
22B ALA* 3.3 9.9 + - + +
23B GLN* 2.9 29.3 + - - +
37B LEU* 3.8 18.2 - - + +
40B GLN* 3.9 30.8 - - + +
41B ALA* 3.6 44.2 - - + +
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Residues in contact with ALA 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 LEU 2.9 22.8 + - - +
17B ILE 3.3 0.9 + - - +
19B LEU* 1.3 72.0 - - - +
21B GLU* 1.3 57.3 + - - +
23B GLN* 3.4 2.1 + - - +
24B ILE* 3.0 33.8 + - - +
32B LEU* 4.0 14.1 - - + -
37B LEU* 3.6 8.4 - - + +
58B LEU* 3.8 25.1 - - + -
62B VAL* 3.6 21.3 - - + -
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Residues in contact with GLU 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 ILE 3.0 16.8 + - - +
18B ASP* 3.6 5.8 - - - +
20B ALA* 1.3 77.0 - - - +
22B ALA* 1.3 56.5 + - - +
24B ILE* 3.4 2.1 + - - +
25B GLU* 3.0 47.2 + - - +
62B VAL* 3.7 25.5 - - + +
65B ARG* 3.2 43.4 + - - +
66B THR* 5.2 0.5 + - - -
69B ARG* 3.3 30.4 + - - -
107B LEU* 4.0 7.2 - - + +
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Residues in contact with ALA 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 ASP 3.0 17.8 + - - +
19B LEU* 3.3 12.5 + - + +
21B GLU* 1.3 76.1 - - - +
23B GLN* 1.3 56.6 + - - +
25B GLU* 3.5 16.2 + - - +
26B ALA* 3.0 29.7 + - - +
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Residues in contact with GLN 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 LEU 2.9 16.8 + - - +
20B ALA 3.6 4.0 - - - +
22B ALA* 1.3 73.9 - - - +
24B ILE* 1.3 60.7 + - - +
26B ALA* 3.8 4.2 - - - +
27B GLU* 2.9 60.8 + - - +
28B GLY 3.6 2.6 + - - -
31B SER* 3.0 33.1 + - - +
32B LEU* 3.8 28.3 - - + -
33B ARG 5.4 0.7 - - - +
36B GLU* 4.5 14.2 - - - +
37B LEU* 5.0 4.7 - - + -
40B GLN* 4.3 18.5 + - - +
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Residues in contact with ILE 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 ALA 3.0 20.4 + - - +
21B GLU 3.8 4.0 - - - +
23B GLN* 1.3 74.8 - - - +
25B GLU* 1.3 59.1 + - - +
28B GLY* 2.8 32.4 + - - +
29B LEU* 3.9 39.9 - - + +
32B LEU* 4.4 15.9 - - + -
59B THR* 4.6 5.8 - - + -
62B VAL* 3.9 28.0 - - + -
106B LYS* 3.3 29.8 - - - +
107B LEU* 3.8 15.9 - - + -
110B ALA* 4.2 10.5 - - + -
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Residues in contact with GLU 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 GLU* 3.0 33.4 + - - +
22B ALA* 3.5 14.6 - - - +
24B ILE* 1.3 77.3 - - - +
26B ALA* 1.3 60.5 + - - +
69B ARG* 3.3 26.0 + - - -
106B LYS* 3.6 13.7 + - - +
107B LEU* 3.7 19.1 - - + +
202B CL 4.1 15.3 - - + -
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Residues in contact with ALA 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 ALA 3.0 18.2 + - - +
23B GLN* 3.3 5.6 + - - +
25B GLU* 1.3 76.7 - - - +
27B GLU* 1.3 71.3 + - + +
106B LYS* 2.7 22.4 + - - -
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Residues in contact with GLU 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 GLN* 2.9 29.4 + - - +
26B ALA* 1.3 87.5 - - + +
28B GLY* 1.3 62.4 + - - +
30B ALA* 5.7 0.9 - - - +
31B SER* 3.1 27.5 + - - +
106B LYS* 4.0 7.2 - - - +
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Residues in contact with GLY 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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23B GLN 3.6 0.4 + - - -
24B ILE* 2.8 34.0 + - - +
27B GLU* 1.3 71.4 - - - +
29B LEU* 1.3 64.8 + - - +
30B ALA* 3.3 3.4 - - - -
31B SER* 2.6 26.2 + - - -
32B LEU 4.0 0.9 + - - -
106B LYS* 3.6 16.1 - - - +
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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