Contacts of the helix formed by residues 47 - 66 (chain A) in PDB entry 2E1O
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 SER 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.0 3.1 - - - -
46A LEU* 1.3 76.9 + - - +
48A GLU* 1.3 58.8 + - - +
49A ARG* 4.3 5.6 - - - -
50A GLN* 2.7 49.4 + - - -
51A VAL* 2.8 13.0 + - - +
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Residues in contact with GLU 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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37A ARG* 2.7 43.3 + - - +
38A LYS* 3.9 30.8 - - - +
41A ALA* 4.0 10.6 - - + +
47A SER* 1.3 72.1 - - - +
49A ARG* 1.3 57.5 + - - +
51A VAL* 3.2 2.7 + - - -
52A LYS* 2.8 33.6 + - - +
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Residues in contact with ARG 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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13A ARG* 5.8 4.2 - - - +
47A SER* 3.1 5.8 - - - -
48A GLU* 1.3 78.9 - - - +
50A GLN* 1.3 65.3 + - + +
52A LYS* 3.6 18.2 - - - +
53A THR* 2.8 46.6 + - - +
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Residues in contact with GLN 50 (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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13A ARG* 3.1 33.5 + - - +
14A PHE* 3.5 25.8 - - + -
45A GLN 5.2 0.3 - - - +
46A LEU* 4.1 10.9 - - + +
47A SER* 2.7 48.8 + - - +
49A ARG* 1.3 84.5 - - + +
51A VAL* 1.3 54.8 + - - -
53A THR* 4.8 2.0 - - - -
54A TRP* 3.2 29.8 + - - +
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Residues in contact with VAL 51 (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 LEU* 4.6 3.4 - - + -
32A LEU* 4.5 2.6 - - + +
37A ARG* 3.4 27.5 - - + +
40A LEU* 3.6 27.8 - - + -
41A ALA* 4.1 18.4 - - + +
46A LEU* 3.8 31.4 - - + -
47A SER 2.8 17.3 + - - +
48A GLU 3.9 0.7 - - - +
50A GLN* 1.3 76.7 - - - +
52A LYS* 1.3 61.1 + - - +
54A TRP* 4.4 1.1 - - - -
55A PHE* 2.9 35.9 - - + +
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Residues in contact with LYS 52 (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 ARG* 3.1 34.8 - - - +
48A GLU 2.8 9.4 + - - +
49A ARG* 3.4 24.6 - - - +
51A VAL* 1.3 79.5 - - - +
53A THR* 1.3 85.2 + - - +
55A PHE* 4.5 1.4 - - - +
56A GLN* 3.0 58.1 + - - +
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Residues in contact with THR 53 (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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49A ARG* 2.8 28.4 + - - +
50A GLN* 4.5 2.0 - - - -
52A LYS* 1.3 100.7 + - - +
54A TRP* 1.3 67.5 + - - +
56A GLN* 3.3 5.1 + - - +
57A ASN* 2.9 45.3 + - - +
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Residues in contact with TRP 54 (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 VAL* 4.8 13.4 - - + +
14A PHE* 3.6 35.1 - + + -
19A THR* 5.0 8.4 - - + +
22A LEU* 3.2 33.6 - - + +
23A GLU* 3.5 42.4 - - + -
26A PHE* 3.7 18.2 - - + -
50A GLN 3.2 20.2 + - - +
51A VAL* 4.8 0.4 - - - -
53A THR* 1.3 82.2 - - - +
55A PHE* 1.3 86.0 + + + +
57A ASN* 3.6 4.9 - - - +
58A ARG* 2.7 66.2 + - + +
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Residues in contact with PHE 55 (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 LEU* 3.5 31.6 - - + -
25A LYS* 3.7 10.5 - - + -
26A PHE* 3.4 32.5 - - + -
29A GLN 3.8 4.3 - - - -
30A LYS 3.4 27.4 - - - +
31A TYR* 4.7 3.8 - - + -
32A LEU* 3.1 36.3 - - + +
40A LEU* 4.4 2.5 - - + -
51A VAL* 2.9 39.0 + - + +
52A LYS* 4.5 1.3 - - - +
53A THR 3.4 0.6 - - - -
54A TRP* 1.3 89.1 - + + +
56A GLN* 1.3 67.6 + - - +
58A ARG* 2.7 20.8 + - - +
59A ARG* 3.0 8.2 + - - +
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Residues in contact with GLN 56 (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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31A TYR* 4.2 34.4 + - + +
52A LYS* 3.0 47.6 + - - +
53A THR* 3.5 6.2 - - - +
55A PHE* 1.3 79.1 - - + +
57A ASN* 1.3 69.0 + - - +
59A ARG* 3.5 3.5 + - - +
60A ALA* 3.3 19.1 + - - +
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Residues in contact with ASN 57 (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 VAL* 6.3 1.6 - - - +
53A THR* 2.9 37.9 + - - +
54A TRP* 3.6 4.4 - - - +
56A GLN* 1.3 78.1 - - - +
58A ARG* 1.3 69.0 + - - +
60A ALA* 3.2 17.8 + - - +
61A LYS* 3.2 11.3 + - - +
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Residues in contact with ARG 58 (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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23A GLU* 4.3 22.3 + - - +
26A PHE* 3.2 55.2 - - + +
27A GLU* 4.3 10.9 + - - -
54A TRP* 2.7 47.7 + - + +
55A PHE* 2.7 17.7 + - - +
57A ASN* 1.3 69.7 - - - +
59A ARG* 1.3 64.4 + - - +
61A LYS* 2.8 20.8 + - - +
62A TRP* 2.8 18.3 + - - +
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Residues in contact with ARG 59 (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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26A PHE* 3.3 16.0 - - + -
30A LYS* 3.7 20.8 - - + +
31A TYR* 3.5 38.6 + - + -
55A PHE 3.0 5.7 + - - +
56A GLN 3.9 6.7 - - - +
58A ARG* 1.3 78.4 - - - +
60A ALA* 1.3 66.4 + - - +
61A LYS 2.7 2.4 + - - -
62A TRP* 2.8 40.1 + - + -
63A ARG* 2.8 52.5 + - + +
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Residues in contact with ALA 60 (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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56A GLN 3.3 10.2 + - - +
57A ASN* 3.2 15.8 + - - +
59A ARG* 1.3 77.5 - - - +
61A LYS* 1.3 58.9 + - - +
63A ARG* 4.1 10.4 - - - +
64A ARG* 3.9 17.2 + - - +
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Residues in contact with LYS 61 (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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57A ASN 3.2 7.6 + - - +
58A ARG* 2.8 14.5 + - - +
59A ARG 2.7 3.2 + - - -
60A ALA* 1.3 73.6 - - - +
62A TRP* 1.3 66.3 + - - +
63A ARG 3.1 2.0 - - - -
64A ARG* 3.0 29.4 + - - +
65A SER* 3.2 10.8 + - - -
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Residues in contact with TRP 62 (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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26A PHE* 3.5 27.6 - + + -
27A GLU* 5.9 1.1 - - - -
30A LYS* 3.5 29.0 - - + +
58A ARG* 2.8 20.0 + - + +
59A ARG* 2.8 37.0 + - + +
61A LYS* 1.3 72.0 - - - +
63A ARG* 1.3 98.8 + - + +
65A SER* 2.7 23.8 + - - -
66A GLY* 2.7 23.3 + - - -
68A SER* 4.6 17.5 - - - -
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Residues in contact with ARG 63 (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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59A ARG* 2.8 56.8 + - + +
60A ALA* 4.1 10.3 - - - +
61A LYS 3.1 0.2 + - - -
62A TRP* 1.3 99.8 - - + +
64A ARG* 1.3 59.7 + - + +
66A GLY* 2.8 25.2 + - - +
68A SER* 4.5 9.9 + - - +
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Residues in contact with ARG 64 (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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60A ALA 3.9 17.2 + - - +
61A LYS* 3.0 18.5 + - + +
63A ARG* 1.3 77.1 - - + +
65A SER* 1.3 63.2 + - - +
66A GLY 3.6 4.5 - - - +
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Residues in contact with SER 65 (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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61A LYS* 3.2 6.2 + - - -
62A TRP* 2.7 30.5 + - - -
64A ARG* 1.3 76.0 - - - +
66A GLY* 1.3 55.7 + - - -
67A PRO* 3.9 2.9 - - - +
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Residues in contact with GLY 66 (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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62A TRP* 2.7 27.9 + - - -
63A ARG* 2.8 17.3 - - - +
64A ARG* 3.6 5.6 - - - +
65A SER* 1.3 76.8 - - - +
67A PRO* 1.3 73.2 - - - +
68A SER* 3.2 9.3 + - - +
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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