Contacts of the helix formed by residues 15 - 26 (chain H) in PDB entry 6MZL
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 PRO 15 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13H VAL 3.7 2.7 - - - +
14H LEU* 1.3 88.0 - - + +
16H SER* 1.3 64.0 + - - +
17H GLU* 3.2 4.7 - - + +
18H SER* 2.7 41.5 + - - +
19H MET* 3.3 8.4 + - - +
14L LYS* 5.8 8.5 - - + +
18L MET* 4.5 11.4 - - + -
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Residues in contact with SER 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LEU 3.3 4.8 + - - -
15H PRO* 1.3 72.3 - - - +
17H GLU* 1.3 63.3 + - - +
19H MET* 3.3 12.5 + - - +
20H LYS* 2.9 33.7 + - - +
33H GLU* 4.1 29.1 + - - +
36H CYS* 3.9 21.4 - - - +
37H GLN* 4.2 18.0 + - - +
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Residues in contact with GLU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PRO* 3.2 3.9 - - + +
16H SER* 1.3 80.8 + - - +
18H SER* 1.3 59.1 + - - +
20H LYS* 3.2 16.3 + - + +
21H VAL* 2.9 31.6 + - + +
33H GLU* 4.9 11.6 - - + +
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Residues in contact with SER 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 5.4 0.2 - - - +
15H PRO* 2.7 38.8 + - - +
17H GLU* 1.3 78.7 - - - +
19H MET* 1.3 61.8 + - - +
21H VAL* 3.2 11.6 + - - +
22H VAL* 2.9 34.2 + - - +
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Residues in contact with MET 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 3.8 16.4 - - + -
15H PRO 3.3 14.6 - - - +
16H SER* 3.5 11.0 - - - +
17H GLU 3.2 0.8 - - - -
18H SER* 1.3 82.9 + - - +
20H LYS* 1.3 56.5 + - - +
22H VAL* 3.4 8.8 + - + +
23H ALA* 2.9 28.1 + - - +
36H CYS* 4.5 14.9 - - + -
39H LEU* 6.1 2.9 - - + -
40H THR* 3.7 31.9 - - + +
43H VAL* 6.5 0.2 - - + -
44L PHE* 3.7 30.5 - - + -
47L VAL* 3.7 35.2 - - + -
51L LEU* 5.1 1.9 - - - +
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Residues in contact with LYS 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H SER* 2.9 21.3 + - - +
17H GLU* 3.2 16.4 + - + +
19H MET* 1.3 73.3 - - - +
21H VAL* 1.3 60.6 + - - +
23H ALA* 4.1 6.3 - - - -
24H GLU* 2.8 44.6 + - - +
31H ILE* 2.9 40.7 + - + +
32H GLN* 3.3 27.7 - - - +
33H GLU* 3.4 24.9 - - - +
36H CYS* 3.7 14.1 - - - -
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Residues in contact with VAL 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 2.9 19.6 + - + +
18H SER* 3.2 13.7 + - - +
20H LYS* 1.3 76.4 - - - +
22H VAL* 1.3 60.7 + - + +
24H GLU* 3.7 4.6 - - - -
25H SER* 2.9 30.0 + - - -
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Residues in contact with VAL 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H SER* 2.9 22.6 + - - +
19H MET* 3.7 9.6 - - + +
21H VAL* 1.3 77.7 - - + +
23H ALA* 1.3 59.3 + - - +
25H SER* 2.4 26.6 + - - +
26H MET* 4.0 4.5 + - - +
44L PHE* 5.0 26.2 - - + +
47L VAL* 5.5 4.3 - - + -
48L THR* 4.3 23.0 - - + +
51L LEU* 4.8 4.7 - - + +
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Residues in contact with ALA 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H MET 2.9 17.4 + - - +
20H LYS* 3.7 4.5 - - - +
22H VAL* 1.3 77.9 - - - +
24H GLU* 1.3 58.2 + - - +
25H SER 3.2 0.2 - - - -
26H MET* 3.0 24.3 + - - +
27H GLY 3.4 4.9 + - - -
28H ILE* 3.6 14.6 - - + +
31H ILE* 3.7 24.7 - - + -
36H CYS* 5.7 2.2 - - - -
51L LEU* 3.7 28.5 - - + -
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Residues in contact with GLU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LYS* 2.8 32.4 + - - +
21H VAL* 3.7 4.0 - - - +
23H ALA* 1.3 67.7 - - - +
25H SER* 1.3 61.6 + - - +
26H MET 3.2 0.9 - - - -
27H GLY* 3.1 21.6 + - - +
28H ILE 4.3 4.3 - - - +
29H ALA 3.0 26.6 - - - +
30H GLN* 4.1 9.7 - - - +
31H ILE* 4.3 13.1 + - + +
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Residues in contact with SER 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H VAL* 2.9 16.5 + - - -
22H VAL* 2.4 28.4 + - - +
24H GLU* 1.3 78.3 - - - +
26H MET* 1.3 66.2 + - - +
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Residues in contact with MET 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H VAL 4.6 3.1 - - - +
23H ALA* 3.0 12.5 + - - +
25H SER* 1.3 85.0 + - - +
27H GLY* 1.3 64.1 + - - +
28H ILE* 4.7 1.8 - - + -
48L THR* 5.5 13.0 - - + +
51L LEU* 6.3 3.8 - - + -
52L ASP* 4.4 12.8 - - - +
55L LYS* 3.5 38.4 + - - +
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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
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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