Contacts of the helix formed by residues 14 - 26 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I PRO* 5.7 10.9 - - + +
13M PRO* 1.3 78.7 - - + +
15M ASP* 1.3 64.2 + - - +
17M GLN* 3.0 28.0 + - - +
18M MET* 2.9 34.4 + - + +
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Residues in contact with ASP 15 (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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14I LEU* 4.2 12.0 - - - +
13M PRO* 3.2 14.8 - - + +
14M LYS* 1.3 81.3 - - - +
16M ALA* 1.3 57.2 + - - +
18M MET* 3.2 9.0 + - - +
19M MET* 2.9 32.1 + - - +
40M LEU* 3.7 25.0 - - + +
44M PHE* 4.0 29.1 - - - -
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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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13M PRO* 3.4 23.5 + - + +
14M LYS 3.2 0.2 - - - -
15M ASP* 1.3 76.5 - - - +
17M GLN* 1.3 60.0 + - + +
19M MET* 3.4 7.7 + - - +
20M ALA* 2.9 28.8 + - - +
36M ILE* 5.4 4.4 - - + +
37M ASN* 5.1 9.0 - - - +
40M LEU* 4.4 4.5 - - - +
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Residues in contact with GLN 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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13M PRO 3.5 14.7 + - - +
14M LYS* 3.0 31.2 + - - +
16M ALA* 1.3 75.1 - - + +
18M MET* 1.3 63.3 + - - +
20M ALA* 3.2 7.8 + - - +
21M GLN* 2.9 40.4 + - - +
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Residues in contact with MET 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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12I THR* 3.3 28.2 - - + +
13I VAL 3.3 33.0 - - - +
14I LEU* 3.7 27.4 - - + +
15I PRO* 4.6 6.7 - - + -
14M LYS* 2.9 20.6 + - + +
15M ASP* 3.2 11.2 + - - +
17M GLN* 1.3 79.5 - - - +
19M MET* 1.3 56.6 + - + +
21M GLN* 3.3 20.1 + - - +
22M ILE* 2.9 33.4 + - + +
40M LEU* 5.7 2.2 - - + -
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Residues in contact with MET 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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47I ILE* 5.7 6.5 - - + -
15M ASP 2.9 20.5 + - - +
16M ALA 3.8 4.0 - - - +
18M MET* 1.3 72.4 - - - +
20M ALA* 1.3 61.1 + - - +
22M ILE* 3.1 28.3 + - + +
23M LEU* 2.9 41.1 + - + +
36M ILE* 3.4 51.8 - - + +
39M MET* 3.8 22.9 - - + -
40M LEU* 3.6 28.9 - - + -
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Residues in contact with ALA 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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16M ALA 2.9 18.4 + - - +
17M GLN* 3.2 8.7 + - - +
19M MET* 1.3 76.1 - - - +
21M GLN* 1.3 58.2 + - + +
23M LEU* 3.4 5.3 + - - +
24M LYS* 2.9 46.6 + - - +
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Residues in contact with GLN 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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12I THR* 3.7 27.8 + - - +
17M GLN* 2.9 24.0 + - - +
18M MET* 3.4 23.7 - - - +
20M ALA* 1.3 76.1 - - + +
22M ILE* 1.3 58.5 + - - +
24M LYS* 3.7 13.1 - - + +
25M ASP* 2.9 35.3 + - - +
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Residues in contact with ILE 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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12I THR* 3.7 24.9 - - + -
44I SER* 6.5 0.7 - - - -
47I ILE* 4.8 18.2 - - + -
48I LYS* 3.9 23.3 - - + +
51I ALA* 5.4 3.1 - - + -
18M MET* 2.9 23.7 + - + +
19M MET* 3.3 34.5 - - + +
21M GLN* 1.3 75.5 - - - +
23M LEU* 1.3 59.9 + - + +
25M ASP* 2.9 8.5 + - - +
26M MET* 2.5 50.5 + - + +
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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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51I ALA* 5.6 4.0 - - + -
55I LEU* 6.3 0.7 - - + -
66I LEU* 5.6 2.5 - - + -
19M MET* 2.9 26.6 + - + +
20M ALA* 4.1 5.4 - - - +
22M ILE* 1.3 79.3 - - + +
24M LYS* 1.3 61.6 + - - +
26M MET* 3.5 19.0 - - + -
27M GLY* 2.9 19.9 + - - -
28M ILE 3.3 13.6 + - - +
31M TYR* 3.2 48.2 - - + +
36M ILE* 3.8 31.4 - - + -
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Residues in contact with LYS 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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20M ALA* 2.9 32.6 + - - +
21M GLN* 3.7 12.3 - - + +
23M LEU* 1.3 76.6 - - - +
25M ASP* 1.3 59.2 + - - +
27M GLY* 2.9 19.1 + - - +
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Residues in contact with ASP 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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280G ARG* 3.2 27.4 + - - +
8I LYS 4.4 3.3 - - - +
9I LEU* 3.8 29.7 - - + +
10I SER 3.2 19.0 + - - +
12I THR* 3.2 18.5 + - - -
48I LYS* 4.0 11.7 + - + +
21M GLN* 2.9 19.2 + - - +
22M ILE* 2.9 11.1 + - - +
24M LYS* 1.3 77.5 - - - +
26M MET* 1.3 59.2 + - - +
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Residues in contact with MET 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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280G ARG* 3.2 22.1 + - - +
48I LYS* 3.9 22.2 - - - +
51I ALA* 3.6 16.2 - - + -
52I GLN* 3.5 45.8 - - + +
55I LEU* 3.7 21.4 - - + +
22M ILE* 2.5 29.9 + - + +
23M LEU* 3.5 24.5 - - + +
24M LYS 3.1 0.2 - - - -
25M ASP* 1.3 77.9 - - - +
27M GLY* 1.3 55.9 + - - +
28M ILE* 3.0 22.9 + - - +
31M TYR* 4.6 1.6 - - - +
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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