Contacts of the helix formed by residues 14 - 27 (chain L) 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 LYS 14 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15H PRO* 5.8 8.1 - - + -
13L PRO* 1.3 80.5 - - + +
15L ASP* 1.3 61.4 + - - +
17L GLN* 3.0 21.5 + - - +
18L MET* 2.9 34.8 + - + +
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Residues in contact with ASP 15 (chain L).
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* 4.3 12.3 - - - +
13L PRO* 3.3 13.3 - - + +
14L LYS* 1.3 77.4 - - - +
16L ALA* 1.3 59.9 + - - +
18L MET* 3.6 7.9 - - - +
19L MET* 2.9 32.4 + - - +
40L LEU* 3.7 25.1 - - + +
44L PHE* 3.5 34.7 - - - -
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Residues in contact with ALA 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L PRO* 3.6 24.2 + - + +
14L LYS 3.2 0.4 - - - -
15L ASP* 1.3 78.6 - - - +
17L GLN* 1.3 56.2 + - + +
19L MET* 3.5 6.5 + - - +
20L ALA* 2.9 27.4 + - - +
36L ILE* 5.2 5.1 - - + +
37L ASN* 5.3 7.6 - - - +
40L LEU* 4.4 4.8 - - - +
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Residues in contact with GLN 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L PRO 3.9 13.7 + - - +
14L LYS* 3.0 20.0 + - - +
16L ALA* 1.3 74.4 - - + +
18L MET* 1.3 63.6 + - + +
20L ALA* 3.2 8.3 + - - +
21L GLN* 2.9 36.6 + - - +
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Residues in contact with MET 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H THR* 3.5 24.5 - - + +
13H VAL 3.3 35.7 - - - +
14H LEU* 3.8 30.1 - - + -
15H PRO* 4.5 9.9 - - + -
14L LYS* 2.9 25.3 + - + +
15L ASP* 3.3 9.2 + - - +
17L GLN* 1.3 78.2 - - - +
19L MET* 1.3 57.9 + - + +
21L GLN* 3.2 17.5 + - - +
22L ILE* 2.9 34.5 + - + +
40L LEU* 5.9 1.3 - - + -
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Residues in contact with MET 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ILE* 5.2 12.1 - - + -
15L ASP 2.9 20.2 + - - +
16L ALA 3.9 2.7 - - - +
18L MET* 1.3 73.6 - - - +
20L ALA* 1.3 60.6 + - - +
22L ILE* 3.6 25.4 - - + +
23L LEU* 2.9 51.9 + - + +
36L ILE* 3.7 43.3 - - + +
39L MET* 4.4 17.5 - - + -
40L LEU* 3.7 28.7 - - + -
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Residues in contact with ALA 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ALA 2.9 18.5 + - - +
17L GLN* 3.4 10.3 - - - +
18L MET 3.2 0.2 - - - -
19L MET* 1.3 76.8 - - - +
21L GLN* 1.3 57.9 + - + +
23L LEU* 3.5 5.0 + - - +
24L LYS* 2.9 45.4 + - + +
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Residues in contact with GLN 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H THR* 3.7 26.5 + - - +
17L GLN* 2.9 21.7 + - - +
18L MET* 3.2 22.7 + - - +
20L ALA* 1.3 73.3 - - + +
22L ILE* 1.3 58.1 + - - +
24L LYS* 3.4 9.5 + - + +
25L ASP* 3.0 33.9 + - - +
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Residues in contact with ILE 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H THR* 3.7 27.6 - - + +
14H LEU* 6.5 0.7 - - + -
44H SER* 5.9 4.9 - - - -
47H ILE* 4.6 21.5 - - + -
48H LYS* 4.2 27.1 - - + +
51H ALA* 5.8 3.1 - - + -
18L MET* 2.9 20.1 + - + +
19L MET* 3.6 34.1 - - + +
20L ALA 3.3 0.2 - - - -
21L GLN* 1.3 76.4 - - - +
23L LEU* 1.3 64.5 + - + +
25L ASP* 3.0 10.0 + - - +
26L MET* 2.9 36.6 + - + +
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Residues in contact with LEU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ALA* 5.7 5.6 - - + -
55H LEU* 6.3 0.4 - - + -
66H LEU* 5.8 1.8 - - + -
19L MET* 2.9 32.0 + - + +
20L ALA* 4.2 4.7 - - - +
22L ILE* 1.3 79.1 - - + +
24L LYS* 1.3 63.2 + - - +
26L MET* 3.3 15.6 + - + +
27L GLY* 3.3 16.1 + - - -
28L ILE 3.6 12.0 + - - +
31L TYR* 3.5 54.1 - - + +
36L ILE* 3.9 29.2 - - + -
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Residues in contact with LYS 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L ALA* 2.9 30.6 + - - +
21L GLN* 3.8 9.4 - - + +
22L ILE 3.3 0.2 - - - -
23L LEU* 1.3 75.7 - - - +
25L ASP* 1.3 66.5 - - - +
26L MET 3.2 0.2 - - - -
27L GLY* 3.4 11.8 + - - -
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Residues in contact with ASP 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F ARG* 2.9 26.9 + - + +
8H LYS 4.2 4.3 - - - +
9H LEU* 3.8 29.0 - - + +
10H SER 3.2 19.3 + - - +
12H THR* 3.2 18.7 + - - -
48H LYS* 3.7 13.5 + - + +
21L GLN* 3.0 20.6 + - - +
22L ILE* 3.0 9.8 + - - +
24L LYS* 1.3 77.3 - - - +
26L MET* 1.3 60.3 + - + +
27L GLY 3.3 0.4 + - - -
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Residues in contact with MET 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F ARG* 3.0 31.5 + - - +
48H LYS* 4.0 22.4 - - - +
51H ALA* 3.8 21.5 - - + -
52H GLN* 3.7 31.4 - - + +
55H LEU* 3.7 25.4 - - + +
22L ILE* 2.9 22.1 + - + +
23L LEU* 3.7 24.0 - - + +
24L LYS 3.2 0.6 - - - -
25L ASP* 1.3 81.5 - - - +
27L GLY* 1.3 56.6 + - - +
28L ILE* 3.2 16.1 + - - +
31L TYR* 4.2 9.9 - - - +
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Residues in contact with GLY 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F ARG* 3.5 13.7 - - - -
23L LEU 3.3 7.7 + - - -
24L LYS* 3.4 9.2 + - - -
25L ASP 3.3 3.2 - - - -
26L MET* 1.3 75.6 - - - +
28L ILE* 1.3 63.3 + - - +
29L THR* 4.2 9.1 + - - +
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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