Contacts of the helix formed by residues 37 - 47 (chain B) in PDB entry 2EZT
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 ILE 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE 4.2 4.0 - - - +
33B PRO* 4.1 9.4 - - + -
34B GLY 3.0 26.4 + - - +
36B SER* 1.3 80.9 + - - +
38B ASN* 1.3 57.9 + - - +
39B SER 3.3 3.5 + - - -
40B ILE* 3.4 26.4 + - + +
41B MET* 3.1 24.3 + - + +
80B PHE* 3.8 38.4 - - + -
81B GLY 4.0 1.8 - - - +
82B SER* 4.1 14.8 - - - -
107B LEU* 4.1 10.5 - - + +
108B ILE 4.3 2.2 - - - -
109B GLY* 3.8 24.2 - - - +
168B ILE* 5.9 2.9 - - + -
170B VAL* 4.3 1.8 - - - -
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Residues in contact with ASN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 4.1 7.4 - - - +
34B GLY 3.0 22.2 + - - +
35B GLY* 3.5 22.6 + - - +
36B SER 3.8 0.2 - - - -
37B ILE* 1.3 74.8 - - - +
39B SER* 1.3 60.0 + - - +
40B ILE 3.4 0.2 - - - -
41B MET* 3.5 18.7 - - - +
42B ASP* 2.8 27.0 + - - +
174B TRP* 3.8 17.7 - - + -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 5.0 0.3 - - - -
38B ASN* 1.3 75.7 - - - +
40B ILE* 1.3 63.7 + - - +
42B ASP* 3.5 2.8 + - - +
43B ALA* 3.3 20.8 + - - +
170B VAL* 2.6 31.1 + - - +
173B PRO* 3.2 28.6 - - - +
174B TRP* 3.3 44.5 + - - +
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY* 4.6 5.8 - - - +
17B VAL* 4.1 30.3 - - + -
18B ILE* 4.6 6.9 - - + +
29B LEU* 6.0 1.1 - - + -
37B ILE* 3.4 29.2 + - + +
39B SER* 1.3 76.7 + - - +
41B MET* 1.3 64.6 + - - +
43B ALA* 3.2 4.7 + - - +
44B LEU* 3.0 38.8 + - + +
80B PHE* 5.4 4.0 - - + -
107B LEU* 4.6 15.0 - - + -
168B ILE* 4.4 22.4 - - + -
173B PRO* 4.1 26.0 - - + -
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Residues in contact with MET 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 3.6 28.7 - - + -
37B ILE* 3.1 21.8 + - - +
38B ASN* 3.5 18.6 - - - +
40B ILE* 1.3 78.0 - - - +
42B ASP* 1.3 56.5 + - - +
44B LEU* 3.3 13.9 + - + +
45B SER* 3.0 29.2 + - - -
53B TYR* 3.7 39.3 - - + +
80B PHE* 3.4 33.0 - - + -
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 5.9 1.0 - - - +
38B ASN 2.8 20.6 + - - +
39B SER 3.6 7.2 - - - +
40B ILE 3.2 0.2 - - - -
41B MET* 1.3 72.4 - - - +
43B ALA* 1.3 62.9 + - - +
45B SER* 3.4 19.8 + - - -
46B ALA* 3.5 8.3 + - - +
174B TRP* 2.9 31.5 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLY* 3.4 37.0 - - - +
15B ALA* 3.7 8.2 - - + +
18B ILE* 3.6 12.1 - - + -
39B SER 3.3 9.8 + - - +
40B ILE* 3.2 7.8 + - - +
42B ASP* 1.3 75.5 - - - +
44B LEU* 1.3 65.1 + - - +
46B ALA* 3.3 14.0 + - - +
47B GLU* 3.5 18.2 + - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.7 23.8 - - + +
29B LEU* 3.8 33.4 - - + -
40B ILE* 3.0 28.1 + - + +
41B MET* 3.3 22.2 + - + +
43B ALA* 1.3 76.8 - - - +
45B SER* 1.3 57.9 + - - +
47B GLU* 3.0 20.6 + - - +
48B ARG* 3.4 13.7 + - - +
51B ILE* 4.1 20.6 - - + +
53B TYR* 4.5 15.1 - - + +
80B PHE* 4.0 26.2 - - + -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B MET 3.0 12.9 + - - -
42B ASP* 3.5 17.3 - - - -
43B ALA 3.2 0.4 - - - -
44B LEU* 1.3 76.7 - - - +
46B ALA* 1.3 58.5 + - - +
47B GLU 3.5 0.3 + - - -
48B ARG* 2.8 54.6 + - - +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP 3.5 7.6 + - - +
43B ALA* 3.3 11.2 + - - +
45B SER* 1.3 77.7 - - - +
47B GLU* 1.3 69.7 + - + +
48B ARG 3.6 1.4 + - - -
49B ASP 5.5 0.2 + - - -
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA* 5.6 3.1 - - + +
18B ILE* 3.8 19.7 - - + -
19B LYS* 3.0 34.2 + - - -
22B GLU* 2.6 30.1 - - - +
43B ALA 3.5 15.9 + - - +
44B LEU 3.0 9.4 + - - +
46B ALA* 1.3 90.0 - - + +
48B ARG* 1.3 63.7 + - - +
49B ASP 3.1 3.8 - - - +
50B ARG* 3.1 13.5 + - - +
51B ILE* 3.1 23.5 + - + +
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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