Contacts of the helix formed by residues 2 - 25 (chain B) in PDB entry 6CMO
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 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B GLN* 1.3 78.9 + - - +
3B GLU* 1.3 66.7 + - - +
4B LEU 3.2 1.8 - - - -
5B ASP* 3.2 27.0 + - - +
6B GLN* 3.3 24.1 + - - +
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Residues in contact with GLU 3 (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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1B GLN* 2.5 34.1 + - - -
2B SER* 1.3 80.6 + - - +
4B LEU* 1.3 60.0 + - - +
6B GLN* 3.1 23.8 + - - +
7B LEU* 2.9 41.1 + - + +
9G ILE* 4.0 14.9 - - + +
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Residues in contact with LEU 4 (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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1B GLN* 3.3 23.3 - - + +
2B SER 3.2 0.6 - - - -
3B GLU* 1.3 78.4 - - - +
5B ASP* 1.3 84.2 + - - +
7B LEU* 3.6 3.6 + - - +
8B ARG* 2.9 28.5 + - + +
5G ASN 5.1 5.8 - - - +
8G SER* 5.1 7.4 - - - +
9G ILE* 3.6 40.0 - - + +
12G ALA* 4.5 17.3 - - + +
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Residues in contact with ASP 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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1B GLN 5.1 0.3 - - - +
2B SER* 3.2 20.6 + - - +
4B LEU* 1.3 92.6 - - - +
6B GLN* 1.3 60.6 + - - +
8B ARG* 3.2 43.3 + - - +
9B GLN* 2.8 39.9 + - - +
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Residues in contact with GLN 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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2B SER* 3.3 19.7 + - - +
3B GLU* 3.1 30.5 + - - +
5B ASP* 1.3 75.6 - - - +
7B LEU* 1.3 63.8 + - + +
9B GLN* 3.0 29.7 + - - +
10B GLU* 3.0 12.7 + - - +
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Residues in contact with LEU 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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3B GLU* 2.9 28.8 + - + +
4B LEU* 4.1 5.4 - - - +
6B GLN* 1.3 79.9 - - + +
8B ARG* 1.3 60.8 + - - +
10B GLU* 3.8 15.5 - - + +
11B ALA* 2.9 27.2 + - - +
12G ALA* 5.3 9.9 - - + +
13G ARG* 6.4 0.2 - - - -
16G VAL* 3.7 42.6 - - + +
20G LYS* 6.1 1.8 - - - +
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Residues in contact with ARG 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 LEU* 2.9 18.6 + - + +
5B ASP* 3.2 44.9 + - - +
6B GLN 3.2 0.2 - - - -
7B LEU* 1.3 75.0 - - - +
9B GLN* 1.3 71.9 + - - +
11B ALA* 3.5 7.7 - - + +
12B GLU* 2.9 38.6 + - + +
15B LYS* 6.2 1.1 - - - +
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Residues in contact with GLN 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 ASP* 2.8 35.1 + - - +
6B GLN* 3.0 19.1 + - - +
8B ARG* 1.3 91.4 - - - +
10B GLU* 1.3 60.2 + - - +
12B GLU* 3.3 9.2 + - + +
13B GLN* 2.9 35.1 + - - +
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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 GLN 3.0 12.4 + - - +
7B LEU* 3.9 16.4 - - + +
9B GLN* 1.3 72.8 - - - +
11B ALA* 1.3 62.6 + - - +
13B GLN* 3.2 22.8 + - - +
14B LEU* 2.9 36.8 + - - +
16G VAL* 3.3 28.3 - - - +
20G LYS* 4.5 15.2 - - - +
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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
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7B LEU 2.9 19.9 + - - +
8B ARG* 3.5 10.5 - - + +
9B GLN 3.3 0.2 - - - -
10B GLU* 1.3 81.8 + - - +
12B GLU* 1.3 56.8 + - + +
14B LEU* 3.1 10.0 + - - +
15B LYS* 2.9 39.8 + - - +
15G LEU* 5.1 11.9 - - + -
16G VAL* 5.8 4.3 - - + -
19G LEU* 4.4 19.9 - - + +
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Residues in contact with GLU 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 ARG* 2.9 29.7 + - + +
9B GLN* 3.6 8.7 - - + +
11B ALA* 1.3 73.4 - - - +
13B GLN* 1.3 60.4 + - - +
15B LYS* 2.9 42.2 + - - +
16B ASN* 2.9 29.5 + - - +
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Residues in contact with GLN 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 GLN* 2.9 23.5 + - - +
10B GLU* 3.3 23.8 - - + +
12B GLU* 1.3 75.8 - - + +
14B LEU* 1.3 57.7 + - - +
16B ASN* 2.8 34.0 - - - +
17B GLN* 3.0 22.0 + - - +
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Residues in contact with LEU 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* 2.9 25.4 + - - +
11B ALA* 3.1 10.3 + - - +
13B GLN* 1.3 76.3 - - - +
15B LYS* 1.3 57.7 + - + +
17B GLN* 3.3 21.5 - - - +
18B ILE* 2.9 50.9 + - + +
16G VAL* 6.3 0.4 - - + -
19G LEU* 3.4 56.8 - - + +
20G LYS* 4.2 9.2 - - + +
22G GLU* 4.2 7.6 - - - +
23G ALA* 4.6 11.2 - - + -
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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
----------------------------------------------------------
8B ARG* 6.2 1.2 - - - +
11B ALA* 2.9 25.4 + - - +
12B GLU* 2.9 45.2 + - - +
14B LEU* 1.3 76.7 - - + +
16B ASN* 1.3 59.6 + - - +
18B ILE* 3.0 18.3 + - + +
19B ARG* 2.9 26.7 + - - +
15G LEU* 6.5 0.7 - - - -
19G LEU* 5.7 7.2 - - + -
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Residues in contact with ASN 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 GLU 2.9 10.7 + - - +
13B GLN* 2.8 37.7 - - - +
15B LYS* 1.3 73.9 - - - +
17B GLN* 1.3 72.8 + - - +
19B ARG* 3.3 19.7 - - - +
20B ASP* 2.9 41.6 + - - +
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Residues in contact with GLN 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 GLN* 3.0 18.4 + - - +
14B LEU* 3.3 26.9 - - + +
16B ASN* 1.3 88.2 + - - +
18B ILE* 1.3 55.9 + - + +
20B ASP* 3.9 6.6 - - - +
21B ALA* 3.0 30.7 + - - +
23G ALA* 5.6 4.3 - - - +
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Residues in contact with ILE 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 LEU* 2.9 39.2 + - + +
15B LYS* 3.0 18.6 + - + +
17B GLN* 1.3 76.9 - - + +
19B ARG* 1.3 59.4 + - - +
21B ALA* 3.3 4.4 + - - +
22B ARG* 2.9 67.4 + - + +
258B ASP* 5.7 2.5 - - - +
19G LEU* 5.2 4.5 - - + -
22G GLU* 4.3 15.0 - - - +
27G ARG* 5.3 9.0 - - - +
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Residues in contact with ARG 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 LYS 2.9 9.9 + - - +
16B ASN* 3.3 31.9 - - + +
18B ILE* 1.3 77.6 - - - +
20B ASP* 1.3 64.4 + - - +
22B ARG* 3.8 6.1 - - - +
23B LYS* 2.9 28.6 + - - +
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Residues in contact with ASP 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 ASN* 2.9 28.9 + - - +
17B GLN* 3.9 6.4 - - - +
19B ARG* 1.3 80.5 - - - +
21B ALA* 1.3 59.5 + - - +
23B LYS* 3.3 23.8 + - - +
24B ALA* 2.9 27.3 + - - +
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Residues in contact with ALA 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 GLN 3.0 19.1 + - - +
18B ILE* 3.8 5.2 - - - +
20B ASP* 1.3 75.8 - - - +
22B ARG* 1.3 59.5 + - + +
24B ALA* 3.1 9.5 + - - +
25B CYS* 2.9 32.9 + - - -
27G ARG* 4.3 29.8 - - - +
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Residues in contact with ARG 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 ILE* 2.9 44.8 + - + +
19B ARG* 4.1 6.1 - - - +
21B ALA* 1.3 74.6 - - + +
23B LYS* 1.3 60.4 + - - +
25B CYS* 3.8 4.3 - - - +
26B ALA* 2.9 28.2 + - - +
221B THR 3.9 15.0 + - - -
222B PHE* 5.2 5.6 - - - +
223B THR* 5.1 11.3 + - - +
257B ALA 5.4 1.3 - - - +
258B ASP* 2.7 51.7 + - + +
259B GLN* 2.9 33.2 + - + +
27G ARG* 6.3 0.7 - - - +
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Residues in contact with LYS 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 ARG 2.9 20.0 + - - +
20B ASP* 3.5 24.0 + - - +
22B ARG* 1.3 75.5 - - - +
24B ALA* 1.3 60.9 + - - +
26B ALA* 2.8 26.1 + - + +
27B ASP* 3.0 13.5 + - - +
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Residues in contact with ALA 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 ASP 2.9 14.7 + - - +
21B ALA* 3.1 12.5 + - - +
23B LYS* 1.3 82.2 - - + +
25B CYS* 1.3 60.1 + - - +
27B ASP* 3.2 24.7 - - - +
29G LYS* 3.4 11.8 + - - +
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Residues in contact with CYS 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 ALA 2.9 18.3 + - - +
22B ARG* 4.2 2.2 - - - +
24B ALA* 1.3 76.4 - - - +
26B ALA* 1.3 55.2 + - - +
27B ASP* 3.4 6.5 - - - -
28B ALA 5.3 0.3 - - - +
257B ALA 4.3 17.9 - - - +
259B GLN* 3.6 13.8 - - + +
27G ARG* 4.6 20.4 - - - -
28G ILE 4.3 16.4 - - - -
29G LYS* 4.9 11.9 - - - +
30G VAL* 3.3 40.4 - - + +
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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