Contacts of the helix formed by residues 38 - 44 (chain A) in PDB entry 2DB9
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 PHE 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A TRP* 5.3 6.9 - + + -
36A MET* 3.1 43.1 - - + -
37A PRO* 1.3 89.3 - - + +
39A PHE* 1.3 58.3 + - - +
40A ALA 3.9 0.2 - - - -
41A LYS* 4.2 13.2 - - + -
42A THR* 2.4 47.4 + - - +
143A ALA* 3.4 38.6 - - + -
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Residues in contact with PHE 39 (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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30A LEU* 3.5 34.3 - - + -
33A TRP* 2.8 42.4 - - + +
34A CYS* 3.5 7.4 - - + -
36A MET 3.4 10.5 + - - +
37A PRO 2.9 6.5 + - - +
38A PHE* 1.3 73.6 - - - +
40A ALA* 1.3 69.8 + - + +
41A LYS 3.1 0.7 - - - -
42A THR 2.9 2.6 + - - -
43A VAL* 2.6 56.0 + - + +
69A VAL* 3.9 23.6 - - + -
85A LYS* 3.5 33.0 - - + -
87A LEU* 4.7 6.5 - - + -
100A LEU* 4.2 15.3 - - + -
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Residues in contact with ALA 40 (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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37A PRO 4.6 1.4 + - - -
39A PHE* 1.3 81.0 - - + +
41A LYS* 1.3 52.3 + - - +
44A THR* 2.4 45.0 + - - +
69A VAL* 3.2 46.2 - - + +
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Residues in contact with LYS 41 (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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37A PRO 5.2 1.3 + - - +
38A PHE* 4.3 17.5 - - + -
39A PHE 3.1 0.8 - - - +
40A ALA* 1.3 80.9 - - - +
42A THR* 1.3 65.1 + - - +
44A THR* 3.2 17.0 - - - +
136A LYS* 4.0 2.9 + - - -
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Residues in contact with THR 42 (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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33A TRP* 3.4 32.8 - - + -
38A PHE* 2.4 37.2 + - - +
39A PHE 2.9 2.3 + - - -
41A LYS* 1.3 73.6 - - - +
43A VAL* 1.3 54.6 + - - -
44A THR 2.5 28.8 + - - +
46A CYS* 3.4 3.4 - - - -
136A LYS* 2.9 19.8 + - - +
139A SER* 4.6 12.7 + - - +
140A ILE* 4.6 8.5 - - + -
143A ALA* 4.1 14.4 - - + +
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Residues in contact with VAL 43 (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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25A LEU* 3.3 22.0 - - + -
30A LEU* 3.5 25.4 - - + -
33A TRP* 4.1 7.6 - - + -
39A PHE* 2.6 44.1 + - + +
40A ALA* 3.2 17.5 - - - +
42A THR* 1.3 72.6 - - - +
44A THR* 1.3 59.0 + - - +
45A GLY 3.0 0.7 + - - -
46A CYS* 3.0 21.1 + - - +
66A ILE* 3.1 28.8 - - + +
69A VAL* 3.3 18.6 - - + -
87A LEU* 4.0 2.5 - - + -
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Residues in contact with THR 44 (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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40A ALA* 2.4 25.7 + - - +
41A LYS* 3.2 11.4 - - - +
42A THR 2.5 15.1 + - - +
43A VAL* 1.3 70.2 - - - +
45A GLY* 1.3 59.2 + - - +
66A ILE* 3.7 6.9 - - - +
67A THR* 3.5 22.2 - - - +
68A GLY* 3.1 25.6 - - - -
136A LYS* 3.2 10.6 + - - -
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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