Contacts of the helix formed by residues 34 - 49 (chain A) in PDB entry 2E34
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.6 38.1 - - + +
21A PRO* 4.9 3.1 - - + -
24A GLY* 3.8 35.7 - - - +
27A LEU* 5.3 0.7 - - + -
28A GLY* 5.0 7.9 - - - +
33A ASN* 1.3 77.2 - - - +
35A MET* 1.3 63.3 + - - +
36A GLU 3.1 1.6 - - - -
37A PHE* 2.4 48.7 + - + +
38A VAL* 2.9 14.1 + - + -
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Residues in contact with MET 35 (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 PRO* 5.0 18.2 - - + -
34A ILE* 1.3 81.0 - - - +
36A GLU* 1.3 58.0 + - - +
38A VAL* 4.4 12.6 - - + +
39A LYS* 2.2 89.7 + - + +
42A ASN* 5.7 5.8 - - + +
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Residues in contact with GLU 36 (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 HIS* 4.6 8.2 - - + -
33A ASN* 3.4 36.1 + - + +
34A ILE 3.1 1.2 - - - +
35A MET* 1.3 76.5 - - - +
37A PHE* 1.3 67.0 + - - +
39A LYS* 3.6 8.5 - - + +
40A ALA* 2.9 22.5 + - - +
65A PHE* 5.5 10.9 - - + -
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Residues in contact with PHE 37 (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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12A LEU* 3.5 40.8 - - + -
21A PRO* 4.3 21.5 - - + -
23A VAL* 4.7 3.8 - - + -
27A LEU* 2.9 40.4 - - + -
30A HIS* 5.3 3.9 - - - +
33A ASN 3.9 9.9 + - - +
34A ILE* 2.4 40.6 + - + +
36A GLU* 1.3 76.4 - - - +
38A VAL* 1.3 67.8 + - + +
40A ALA* 3.3 4.0 + - - +
41A PHE* 3.0 22.7 + + + +
57A ILE* 4.4 5.6 - - + -
65A PHE* 6.3 3.1 - - - -
67A PHE* 4.3 22.9 - + - -
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Residues in contact with VAL 38 (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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12A LEU* 5.5 0.4 - - + -
17A ALA* 3.6 21.8 - - + +
18A THR* 3.6 46.4 - - - +
19A PRO* 4.8 0.4 - - + -
21A PRO* 4.5 6.3 - - + -
34A ILE* 2.9 20.2 + - + +
35A MET* 4.1 13.7 - - + +
37A PHE* 1.3 84.0 - - + +
39A LYS* 1.3 62.2 + - - +
41A PHE* 2.6 6.7 + - - -
42A ASN* 2.4 44.4 + - + +
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Residues in contact with LYS 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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35A MET* 2.2 72.0 + - + +
36A GLU* 3.6 7.6 - - - +
38A VAL* 1.3 65.5 - - - +
40A ALA* 1.3 50.8 + - - +
42A ASN* 4.2 3.3 - - + +
43A ALA* 2.5 48.0 + - + +
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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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36A GLU 2.9 17.6 + - - +
37A PHE* 3.7 3.1 - - - +
39A LYS* 1.3 77.5 - - - +
41A PHE* 1.3 63.6 + - - +
43A ALA* 3.6 5.6 - - - +
44A ALA* 3.0 20.8 + - - +
65A PHE* 6.5 1.1 - - + -
68A VAL* 6.3 3.4 - - + -
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Residues in contact with PHE 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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12A LEU* 3.2 38.6 - - + -
13A PRO 3.4 20.4 - - - -
14A ALA* 4.2 0.7 - - - -
17A ALA* 3.5 19.1 - - + -
37A PHE* 3.0 21.6 + + + +
38A VAL* 2.6 18.6 + - + +
40A ALA* 1.3 66.9 - - - +
42A ASN* 1.3 56.3 + - - +
43A ALA 2.8 2.9 - - - -
44A ALA* 2.4 30.9 + - + -
45A THR* 2.7 38.2 + - + -
53A VAL* 4.1 26.7 - - + -
55A VAL* 4.1 14.6 - - + -
67A PHE* 5.4 4.9 - + - -
69A THR* 5.0 9.4 - - + -
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Residues in contact with ASN 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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15A GLY* 4.7 7.6 - - - -
16A LYS 5.1 0.9 + - - +
17A ALA* 3.5 25.5 + - - -
18A THR* 4.7 6.1 - - - +
35A MET* 5.7 5.4 - - + +
38A VAL* 2.4 37.0 + - + +
39A LYS* 4.2 3.4 - - + +
41A PHE* 1.3 72.6 - - - +
43A ALA* 1.3 49.8 + - - +
45A THR* 3.4 13.8 + - - +
46A ALA* 2.5 49.4 + - - +
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Residues in contact with ALA 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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39A LYS* 2.5 33.5 + - + +
40A ALA* 3.6 7.2 - - - +
41A PHE 2.6 4.2 + - - -
42A ASN* 1.3 74.5 - - - +
44A ALA* 1.3 55.5 + - - +
46A ALA* 4.2 3.4 - - - +
47A ASN* 3.0 26.0 + - - +
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Residues in contact with ALA 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 3.0 15.3 + - - +
41A PHE* 2.4 21.8 + - + +
43A ALA* 1.3 67.8 - - - +
45A THR* 1.3 53.9 + - + +
46A ALA 3.0 1.1 - - - -
47A ASN* 2.9 7.1 + - - +
48A MET* 2.6 41.6 + - + +
68A VAL* 6.4 2.2 - - + -
70A LYS* 4.0 24.9 + - + +
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Residues in contact with THR 45 (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 ALA* 3.4 9.9 - - + -
15A GLY* 2.8 29.9 + - - -
17A ALA 5.6 0.3 + - - -
41A PHE* 2.7 56.1 + - + +
42A ASN* 3.4 13.7 + - - -
44A ALA* 1.3 73.7 - - + +
46A ALA* 1.3 56.1 + - - +
48A MET* 3.2 16.1 - - + +
49A GLY 2.3 39.6 + - - +
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Residues in contact with ALA 46 (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 GLY* 5.8 1.1 - - - -
42A ASN* 2.5 34.5 + - - +
43A ALA* 4.2 4.3 - - - +
45A THR* 1.3 74.1 + - - +
47A ASN* 1.3 63.2 + - - +
48A MET 2.9 10.9 + - - +
49A GLY* 3.9 2.6 + - - -
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Residues in contact with ASN 47 (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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43A ALA 3.0 21.9 + - - +
44A ALA* 2.9 9.5 + - - +
46A ALA* 1.3 76.6 - - - +
48A MET* 1.3 59.6 + - - +
70A LYS* 4.8 12.1 - - - +
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Residues in contact with MET 48 (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 ALA* 4.0 16.4 - - + -
44A ALA 2.6 25.1 + - - +
45A THR* 3.1 23.1 - - + +
46A ALA 2.9 3.6 + - - +
47A ASN* 1.3 81.3 - - - +
49A GLY* 1.3 77.9 + - - +
50A ASP 4.4 0.7 - - - -
51A ALA* 4.9 5.8 - - + -
53A VAL* 4.8 3.4 - - + -
70A LYS* 4.0 38.4 - - + +
71A THR* 4.1 24.2 - - + +
84A LEU* 6.3 2.7 - - + -
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Residues in contact with GLY 49 (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 GLY* 3.6 10.4 + - - -
45A THR 2.3 34.4 + - - +
46A ALA* 4.4 3.3 - - - -
48A MET* 1.3 84.8 - - - +
50A ASP* 1.3 61.0 + - - +
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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