Contacts of the helix formed by residues 16 - 26 (chain A) in PDB entry 1MAQ
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 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PRO 3.5 4.9 - - - +
15A ASP* 1.3 99.2 - - - +
17A ILE* 1.3 63.5 + - + +
20A VAL* 3.5 10.2 - - - +
141A GLY* 6.2 4.5 - - - -
382A THR* 3.4 19.5 - - - +
383A LYS 5.3 0.9 + - - -
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Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 3.1 8.2 + - - +
16A PRO* 1.3 88.0 - - + +
18A LEU* 1.3 67.3 + - + +
19A GLY 3.1 1.3 - - - -
20A VAL* 3.0 22.9 + - - +
21A THR 4.1 0.9 + - - -
37A VAL* 4.3 14.7 + - - +
140A TRP* 3.7 33.4 - - + +
141A GLY* 4.6 13.2 - - - +
142A ASN* 5.1 1.8 - - + +
382A THR* 4.0 13.5 - - + -
386A ARG* 3.5 29.4 - - - +
412A PGU 3.7 25.6 - - + +
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 3.2 20.0 + - + +
17A ILE* 1.3 79.9 - - + +
19A GLY* 1.3 63.0 + - - +
20A VAL 3.1 1.2 + - - -
21A THR* 3.2 18.4 + - - +
22A GLU* 3.6 14.4 + - - +
37A VAL* 4.8 8.5 - - + -
412A PGU 3.7 39.9 - - + +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PRO* 4.4 8.1 - - - +
15A ASP* 2.9 31.3 + - - +
18A LEU* 1.3 77.6 - - - +
20A VAL* 1.3 61.4 + - - +
21A THR 3.3 0.2 - - - -
22A GLU* 3.3 20.0 + - - +
23A ALA* 3.2 20.4 + - - +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP 5.1 0.2 - - - +
16A PRO 3.5 18.2 - - - +
17A ILE 3.0 15.8 + - - +
19A GLY* 1.3 75.2 - - - +
21A THR* 1.3 55.2 + - - +
23A ALA* 3.2 7.1 + - - +
24A PHE* 2.7 33.1 + - - +
34A ASN* 4.1 2.9 - - - +
36A GLY* 4.0 20.6 - - - -
37A VAL 5.3 0.2 - - - +
380A TYR* 3.7 29.2 - - + -
381A MET 4.2 14.8 - - - +
382A THR* 4.2 13.7 - - + -
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE 4.1 0.2 + - - -
18A LEU* 3.2 10.4 + - - -
20A VAL* 1.3 75.3 - - - +
22A GLU* 1.3 68.5 + - + +
24A PHE* 3.8 3.4 - - + +
25A LYS* 3.0 49.0 + - + +
34A ASN* 3.1 20.0 + - - +
37A VAL* 3.0 30.7 - - - +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PRO* 4.8 10.9 - - - +
15A ASP* 5.6 2.1 + - - +
18A LEU* 3.6 12.1 + - - +
19A GLY* 3.3 19.5 + - - +
20A VAL 3.2 0.4 - - - -
21A THR* 1.3 82.0 - - + +
23A ALA* 1.3 61.3 + - - +
25A LYS* 3.3 17.9 + - - +
26A ARG* 3.7 25.8 + - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 3.2 10.0 + - - +
20A VAL* 3.5 8.3 - - - +
22A GLU* 1.3 78.1 - - - +
24A PHE* 1.3 65.5 + - - +
25A LYS 3.2 0.7 + - - -
26A ARG* 3.3 34.2 + - - +
27A ASP* 3.7 6.8 + - - +
380A TYR* 4.0 22.0 + - + -
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL 2.7 20.9 + - - +
21A THR* 3.3 9.4 + - - +
23A ALA* 1.3 73.9 - - - +
25A LYS* 1.3 79.4 + - + +
26A ARG 3.3 0.5 + - - -
27A ASP* 3.4 7.6 + - - +
32A LYS* 2.7 65.6 + - + -
33A MET* 3.6 9.2 - - - -
34A ASN* 3.5 50.9 - - + -
380A TYR* 3.9 26.8 - + + -
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 3.0 38.7 + - + +
22A GLU* 3.6 9.4 - - - +
23A ALA 3.1 0.4 - - - -
24A PHE* 1.3 92.5 - - + +
26A ARG* 1.3 61.2 + - + +
27A ASP 4.1 1.0 - - - +
32A LYS* 3.6 13.0 + - - +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 3.9 29.0 + - - +
23A ALA* 3.3 23.7 + - - +
24A PHE 3.2 1.0 - - - -
25A LYS* 1.3 81.2 - - + +
27A ASP* 1.3 63.8 + - - +
28A THR* 3.6 11.4 + - - +
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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