Contacts of the helix formed by residues 39 - 48 (chain Q) in PDB entry 2D2I
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 ASP 39 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36Q ASN* 3.2 10.6 - - - +
38Q SER* 1.3 80.8 - - - +
40Q ALA* 1.3 61.9 + - - +
41Q ARG* 3.0 15.6 + - + +
42Q THR* 2.6 45.5 + - - -
43Q ALA* 3.5 7.6 + - - +
64Q GLU 5.7 2.0 - - - +
76Q ILE* 4.6 2.9 - - - -
78Q CYS* 6.3 0.9 - - - -
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Residues in contact with ALA 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Q ASP* 1.3 73.8 - - - +
41Q ARG* 1.3 66.3 + - - +
43Q ALA* 3.3 6.3 + - - +
44Q ALA* 3.0 23.4 + - - +
62Q TYR* 4.0 2.7 - - + +
63Q ASP 3.3 26.2 - - - +
64Q GLU* 4.0 13.4 + - - +
66Q SER 3.4 15.9 - - - +
67Q ILE* 3.6 4.0 - - - +
76Q ILE* 3.9 23.9 - - + +
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Residues in contact with ARG 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282O PRO* 4.7 15.4 - - - +
196P ARG 6.0 0.2 + - - -
198P LEU* 3.7 29.9 - - + +
39Q ASP* 3.0 13.8 + - + +
40Q ALA* 1.3 80.5 - - - +
42Q THR* 1.3 64.8 + - - +
44Q ALA* 3.2 2.4 + - - +
45Q HIS* 3.0 23.2 + - + +
62Q TYR* 3.0 48.9 + - + +
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Residues in contact with THR 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P SER* 4.1 21.3 - - - -
195P HIS 4.7 4.4 + - - +
198P LEU* 3.7 30.3 - - + +
201P ALA* 5.9 0.2 - - + -
38Q SER* 3.8 16.3 - - - +
39Q ASP* 2.6 27.5 + - - -
41Q ARG* 1.3 74.0 - - - +
43Q ALA* 1.3 57.3 + - - +
45Q HIS* 3.3 6.2 + - - +
46Q LEU* 3.0 48.9 + - + +
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Residues in contact with ALA 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q PHE* 3.5 25.7 - - + -
36Q ASN* 3.7 21.0 + - - +
39Q ASP 3.5 5.3 + - - +
40Q ALA 3.3 3.8 + - - +
41Q ARG 3.1 0.4 - - - -
42Q THR* 1.3 77.2 - - - +
44Q ALA* 1.3 65.4 + - - +
46Q LEU* 4.0 2.9 - - - +
47Q LEU* 3.1 24.3 + - - +
67Q ILE* 3.2 24.0 - - + -
76Q ILE* 4.2 6.3 - - + -
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Residues in contact with ALA 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Q ALA 3.0 15.6 + - - +
41Q ARG 3.9 2.5 - - - +
43Q ALA* 1.3 75.9 - - - +
45Q HIS* 1.3 63.4 + - - +
47Q LEU* 3.2 8.2 + - - +
48Q GLU* 3.0 25.4 + - - +
60Q ILE* 3.9 23.0 - - + +
61Q SER 4.6 0.9 - - - +
62Q TYR* 3.8 27.6 - - + -
67Q ILE* 3.6 10.0 - - + +
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Residues in contact with HIS 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281O LEU* 5.6 1.8 - - + +
282O PRO* 3.5 42.6 + - + +
283O LEU* 4.1 6.3 - - + -
198P LEU* 3.6 39.0 + - + +
202P ARG* 4.7 8.5 + - - -
41Q ARG* 3.0 18.6 + - + +
42Q THR 3.5 4.7 - - - +
43Q ALA 3.2 0.2 - - - -
44Q ALA* 1.3 79.2 - - - +
46Q LEU* 1.3 72.3 + - + +
48Q GLU* 5.0 1.3 - - - -
49Q TYR* 3.0 57.1 + + + +
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Residues in contact with LEU 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192P ASP* 4.6 9.8 - - + +
193P ALA* 4.0 4.3 - - - +
194P SER* 3.8 28.7 - - - +
198P LEU* 5.9 0.4 - - + -
201P ALA* 4.5 10.8 - - + -
202P ARG* 3.9 28.7 - - - +
15Q ARG* 3.2 37.7 + - - +
42Q THR* 3.0 35.1 + - + +
43Q ALA* 4.4 2.5 - - - +
45Q HIS* 1.3 84.4 - - + +
47Q LEU* 1.3 64.7 + - - +
49Q TYR 3.5 17.0 - - - +
50Q ASP* 4.4 7.1 - - - +
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Residues in contact with LEU 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q PHE* 4.0 13.7 - - + -
15Q ARG* 4.0 12.5 - - + +
18Q LEU* 3.9 30.1 - - + -
19Q ARG* 3.5 24.3 + - + -
43Q ALA 3.1 18.6 + - - +
44Q ALA* 3.4 5.2 - - - +
45Q HIS 3.2 0.2 - - - -
46Q LEU* 1.3 80.4 - - - +
48Q GLU* 1.3 58.7 + - - +
56Q PHE* 3.3 34.7 - - + +
60Q ILE* 4.4 9.2 - - + -
67Q ILE* 4.7 8.1 - - + -
69Q VAL* 3.6 31.2 - - + -
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Residues in contact with GLU 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q ALA 3.0 13.6 + - - +
45Q HIS* 4.0 0.7 - - - +
47Q LEU* 1.3 80.4 - - - +
49Q TYR* 1.3 90.4 + - + +
50Q ASP 3.9 0.2 - - - -
54Q GLY 3.7 1.6 - - - +
55Q ARG* 3.1 43.2 + - + +
56Q PHE* 2.7 32.0 + - - +
58Q ALA 4.8 4.9 - - - +
60Q ILE* 3.6 37.1 - - + +
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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