Contacts of the helix formed by residues 15 - 26 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I VAL 3.6 4.2 - - - +
14I LEU* 1.3 89.8 - - + +
16I SER* 1.3 60.9 - - - +
17I GLU* 3.2 4.3 - - + +
18I SER* 2.4 51.7 + - - +
19I MET* 3.2 4.3 + - - +
14M LYS* 5.7 11.9 - - + +
18M MET* 4.6 9.2 - - + -
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Residues in contact with SER 16 (chain I).
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 3.2 6.3 + - - -
15I PRO* 1.3 70.7 - - - +
17I GLU* 1.3 61.7 + - - +
19I MET* 3.2 12.9 + - - +
20I LYS* 2.8 34.1 + - - +
33I GLU* 4.1 26.3 + - - +
36I CYS* 3.7 22.1 - - - +
37I GLN* 4.2 19.4 + - - +
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Residues in contact with GLU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PRO* 3.2 3.9 - - + -
16I SER* 1.3 78.9 + - - +
18I SER* 1.3 60.4 + - - +
20I LYS* 3.2 15.1 + - + +
21I VAL* 2.9 33.4 + - + +
33I GLU* 5.0 11.0 - - + +
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Residues in contact with SER 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 4.8 0.5 - - - +
15I PRO* 2.4 44.8 + - - +
17I GLU* 1.3 78.1 - - - +
19I MET* 1.3 66.7 + - - +
21I VAL* 3.2 10.7 + - - +
22I VAL* 2.9 33.9 + - - +
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Residues in contact with MET 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 3.7 31.2 - - + -
15I PRO 3.2 14.1 + - - +
16I SER* 3.4 11.2 - - - +
17I GLU 3.2 0.4 - - - -
18I SER* 1.3 84.6 - - - +
20I LYS* 1.3 55.6 - - - +
22I VAL* 3.4 7.8 + - + +
23I ALA* 2.8 28.0 + - - +
36I CYS* 4.3 14.3 - - + -
40I THR* 3.7 26.2 - - + -
44M PHE* 3.7 28.3 - - + -
47M VAL* 4.1 28.0 - - + +
51M LEU* 5.1 1.6 - - - +
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Residues in contact with LYS 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I SER* 2.8 19.8 + - - +
17I GLU* 3.2 16.3 + - + +
19I MET* 1.3 74.1 - - - +
21I VAL* 1.3 60.2 + - + +
23I ALA* 3.9 7.6 - - - -
24I GLU* 2.8 43.8 + - - +
31I ILE* 2.7 44.8 + - + +
32I GLN* 3.2 28.7 - - - +
33I GLU* 3.3 24.1 - - - +
36I CYS* 3.7 14.8 - - - -
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Residues in contact with VAL 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLU* 2.9 22.0 + - + +
18I SER* 3.2 12.3 + - - +
20I LYS* 1.3 77.8 - - + +
22I VAL* 1.3 60.1 + - + +
24I GLU* 3.7 2.8 - - - -
25I SER* 2.9 30.3 + - - -
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I SER* 2.9 22.1 + - - +
19I MET* 3.7 10.3 - - + +
21I VAL* 1.3 78.6 - - + +
23I ALA* 1.3 60.0 + - - +
25I SER* 2.3 29.1 + - - +
26I MET* 3.9 4.3 + - - +
44M PHE* 4.7 28.9 - - + +
47M VAL* 5.8 2.2 - - + -
48M THR* 4.2 24.4 - - + +
51M LEU* 4.8 3.7 - - + +
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Residues in contact with ALA 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I MET 2.8 18.7 + - - +
20I LYS* 3.6 5.4 - - - +
21I VAL 3.2 0.2 - - - -
22I VAL* 1.3 77.9 - - - +
24I GLU* 1.3 57.6 + - - +
26I MET* 2.9 29.1 + - - +
28I ILE* 3.3 26.2 - - + +
31I ILE* 3.7 17.5 - - + -
36I CYS* 5.5 2.5 - - - -
51M LEU* 3.7 25.3 - - + +
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I LYS* 2.8 30.2 + - - +
21I VAL* 3.7 3.3 - - - +
23I ALA* 1.3 67.8 - - - +
25I SER* 1.3 60.0 + - - +
27I GLY* 2.9 24.1 + - - +
28I ILE 3.9 6.1 - - - +
29I ALA 2.8 28.1 - - - +
30I GLN* 4.1 2.7 - - - -
31I ILE* 3.5 27.8 + - + +
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Residues in contact with SER 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 2.9 17.4 + - - -
22I VAL* 2.3 30.3 + - - +
24I GLU* 1.3 77.9 - - - +
26I MET* 1.3 65.1 + - - +
27I GLY 3.6 0.5 + - - -
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Residues in contact with MET 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I VAL 4.5 2.7 - - - +
23I ALA 2.9 14.4 + - - +
25I SER* 1.3 85.5 + - - +
27I GLY* 1.3 63.2 + - - +
28I ILE* 4.4 2.2 - - + -
48M THR* 5.5 13.9 - - + +
51M LEU* 6.0 3.6 - - + -
52M ASP* 4.8 12.8 - - - +
55M LYS* 3.4 36.0 + - - +
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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