Contacts of the helix formed by residues 15 - 32 (chain M) in PDB entry 6AH0
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 15 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13M LEU 4.1 1.4 + - - -
14M ALA* 1.3 78.9 - - - +
16M ALA* 1.3 61.1 + - - +
17M HIS 3.2 2.7 - - - +
18M LEU* 3.5 4.5 + - - +
19M THR* 2.9 22.1 + - - +
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Residues in contact with ALA 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ASP* 1.3 72.2 - - - +
17M HIS* 1.3 60.7 + - - +
19M THR* 4.0 1.4 - - - +
20M LYS* 3.2 17.0 + - - -
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Residues in contact with HIS 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ASP* 3.2 0.8 - - - +
16M ALA* 1.3 73.9 - - - +
18M LEU* 1.3 66.6 + - - +
20M LYS* 3.1 10.9 + - - -
21M LYS* 3.3 8.8 + - - -
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Residues in contact with LEU 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ALA* 5.4 4.3 - - - +
15M ASP 3.5 9.0 + - - +
17M HIS* 1.3 74.8 - - - +
19M THR* 1.3 62.5 + - - +
21M LYS* 3.0 3.5 + - - +
22M LEU* 2.9 23.6 + - - -
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Residues in contact with THR 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ALA* 4.7 6.0 - - - +
15M ASP 2.9 17.8 + - - -
16M ALA* 4.0 2.9 - - - +
18M LEU* 1.3 76.7 - - - +
20M LYS* 1.3 60.8 + - - +
22M LEU* 4.0 0.8 - - - +
23M LEU* 3.1 20.4 + - - -
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Residues in contact with LYS 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436J LEU* 4.2 19.3 + - - +
16M ALA 3.2 11.5 + - - -
17M HIS 3.1 9.0 + - - -
19M THR* 1.3 74.6 - - - +
21M LYS* 1.3 56.8 + - - +
23M LEU* 3.8 0.7 - - - -
24M ASP* 3.0 25.1 + - - -
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Residues in contact with LYS 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M HIS 3.3 7.9 + - - -
18M LEU* 3.0 6.9 + - - +
20M LYS* 1.3 72.6 - - - +
22M LEU* 1.3 56.2 - - - +
24M ASP* 3.1 2.9 + - - +
25M LEU* 2.8 32.7 + - - -
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Residues in contact with LEU 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M LEU 2.9 14.3 + - - -
19M THR* 4.0 0.9 - - - +
21M LYS* 1.3 73.1 - - - +
23M LEU* 1.3 57.3 + - - +
25M LEU* 3.1 2.9 + - - +
26M VAL* 2.8 27.0 + - - -
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Residues in contact with LEU 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436J LEU* 5.6 0.2 - - - -
437J GLY 4.9 8.4 - - - +
19M THR 3.1 17.0 + - - -
20M LYS* 3.8 1.6 - - - +
22M LEU* 1.3 74.7 - - - +
24M ASP* 1.3 62.0 + - - +
26M VAL* 3.9 1.7 - - - +
27M GLN* 3.0 19.4 + - - -
92M ALA* 4.7 11.3 - - - +
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Residues in contact with ASP 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436J LEU* 4.8 14.1 - - - +
437J GLY* 4.8 4.5 - - - +
20M LYS 3.0 15.2 + - - -
21M LYS* 3.1 4.4 + - - +
23M LEU* 1.3 75.4 - - - +
25M LEU* 1.3 57.5 + - - +
27M GLN* 3.0 4.0 + - - -
28M GLN* 2.9 24.9 + - - -
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Residues in contact with LEU 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LYS 2.8 14.1 + - - -
22M LEU* 3.6 2.7 - - - +
24M ASP* 1.3 72.9 - - - +
26M VAL* 1.3 60.1 + - - +
28M GLN* 3.4 2.8 + - - +
29M SER* 3.0 23.9 + - - -
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Residues in contact with VAL 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M LEU 2.8 14.6 + - - -
23M LEU* 4.0 2.5 - - - +
25M LEU* 1.3 75.2 - - - +
27M GLN* 1.3 58.7 + - - +
29M SER* 3.1 2.8 + - - +
30M CYS* 2.9 26.2 + - - -
92M ALA 3.9 8.0 - - - +
93M CYS* 5.6 0.7 - - - -
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Residues in contact with GLN 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437J GLY 5.9 1.6 - - - -
23M LEU 3.0 15.5 + - - -
24M ASP 3.0 5.1 + - - -
26M VAL* 1.3 77.0 - - - +
28M GLN* 1.3 59.3 + - - +
30M CYS* 3.4 2.6 + - - -
31M ASN* 3.3 15.6 + - - -
92M ALA* 3.3 20.4 + - - +
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Residues in contact with GLN 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M ASP 2.9 13.4 + - - -
25M LEU* 3.8 4.0 - - - +
26M VAL 3.2 0.4 - - - -
27M GLN* 1.3 74.1 - - - +
29M SER* 1.3 59.9 + - - +
30M CYS 3.2 0.2 - - - -
31M ASN* 3.2 3.4 + - - +
32M TYR* 2.9 23.9 + - - -
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Residues in contact with SER 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M LEU 3.0 14.4 + - - -
26M VAL* 3.1 4.7 + - - +
28M GLN* 1.3 75.0 - - - +
30M CYS* 1.3 61.1 + - - +
31M ASN 3.1 0.2 - - - -
32M TYR* 4.3 2.2 - - - +
33M LYS* 2.9 8.3 + - - -
34M GLN* 2.8 36.3 + - - +
35M LEU* 3.7 6.6 + - - +
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Residues in contact with CYS 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M VAL 2.9 13.6 + - - -
27M GLN* 3.4 4.4 + - - +
28M GLN 3.2 0.2 - - - -
29M SER* 1.3 79.5 - - - +
31M ASN* 1.3 58.2 + - - +
33M LYS* 3.5 9.4 + - - +
35M LEU* 5.0 7.5 - - - +
92M ALA 5.4 3.1 - - - -
93M CYS* 6.0 5.2 - - - +
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Residues in contact with ASN 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I U 4.9 10.7 + - - -
7I G 5.7 6.2 - - - +
27M GLN 3.3 8.8 + - - -
28M GLN* 3.2 6.8 + - - +
29M SER 3.1 0.6 - - - -
30M CYS* 1.3 75.0 - - - +
32M TYR* 1.3 56.9 + - - +
33M LYS 3.1 7.5 + - - -
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Residues in contact with TYR 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I U 6.0 0.4 - - - -
28M GLN 2.9 15.7 + - - -
29M SER* 3.5 2.0 + - - +
31M ASN* 1.3 73.5 - - - +
33M LYS* 1.3 63.6 + - - +
34M GLN* 3.3 3.6 + - - -
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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