Contacts of the helix formed by residues 33 - 46 (chain D) in PDB entry 3BID
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 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D TYR* 3.3 10.3 - - - -
31D TYR* 4.0 6.4 - - - +
32D THR* 1.3 82.7 - - - +
34D LYS* 1.3 63.7 + - - +
35D GLN* 3.3 11.2 + - - +
36D ASN* 3.0 40.0 + - - +
37D CYS* 3.5 8.0 + - - +
39H HIS* 6.1 5.4 - - - -
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLU* 3.7 20.2 + - + +
57C LEU* 3.6 37.8 - - + +
5D ILE* 4.8 12.8 - - + -
13D TYR* 3.2 42.1 - - + +
33D SER* 1.3 74.4 - - - +
35D GLN* 1.3 63.4 + - - +
37D CYS* 3.3 3.0 + - - +
38D GLN* 3.1 33.0 + - + +
21G ASN* 5.1 12.1 - - - +
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Residues in contact with GLN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D SER* 3.1 10.3 - - - +
34D LYS* 1.3 81.0 - - - +
36D ASN* 1.3 66.9 + - - +
38D GLN* 3.2 17.1 + - - +
39D HIS* 3.2 22.5 + - + +
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TYR* 3.8 23.6 - - + -
32D THR* 3.7 22.4 - - - +
33D SER* 3.0 23.7 + - - +
35D GLN* 1.3 81.4 - - - +
37D CYS* 1.3 61.3 + - - +
39D HIS* 3.4 8.4 + - - +
40D ALA* 3.2 21.5 + - - +
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Residues in contact with CYS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.0 28.9 - - + -
13D TYR* 4.0 18.6 - - + -
14D ARG 4.1 13.9 - - - -
15D TRP* 4.3 10.1 - - - -
31D TYR* 3.9 29.3 - - + -
33D SER 3.5 9.4 + - - +
34D LYS* 3.3 9.1 + - - +
35D GLN 3.2 0.4 - - - -
36D ASN* 1.3 78.4 - - - +
38D GLN* 1.3 63.3 + - - +
40D ALA* 3.4 4.2 + - - +
41D VAL* 3.3 21.7 + - - +
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 6.0 2.0 - - + -
55C GLU* 3.7 19.5 - - - +
5D ILE* 4.1 20.5 - - + +
34D LYS* 3.1 25.2 + - + +
35D GLN* 3.2 16.1 + - - +
37D CYS* 1.3 81.0 - - - +
39D HIS* 1.3 61.1 + - - +
41D VAL* 3.4 3.9 + - + +
42D ASP* 3.0 38.8 + - - +
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Residues in contact with HIS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 6.0 0.2 - - + -
35D GLN* 3.2 15.9 + - + +
36D ASN* 3.7 12.8 - - - +
37D CYS 3.2 0.4 - - - -
38D GLN* 1.3 73.7 - - - +
40D ALA* 1.3 64.8 + - - +
42D ASP* 3.3 10.9 + - + +
43D LEU* 3.1 53.2 + - + +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.9 22.6 - - + +
26C ALA* 4.8 4.9 - - + -
15D TRP* 5.2 4.0 - - - +
31D TYR* 3.1 34.8 - - + +
36D ASN 3.2 5.1 + - - +
37D CYS 3.6 9.0 - - - +
38D GLN 3.3 0.2 - - - -
39D HIS* 1.3 80.0 - - - +
41D VAL* 1.3 62.4 + - + +
43D LEU* 3.3 4.8 + - - +
44D LEU* 3.0 27.6 + - - +
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 4.2 16.6 - - + -
3D PHE* 3.8 39.7 - - + -
5D ILE* 4.2 14.8 - - + -
15D TRP* 4.1 32.1 - - + -
37D CYS* 3.3 15.3 + - - +
38D GLN* 3.7 8.7 - - + +
39D HIS 3.3 0.2 - - - -
40D ALA* 1.3 77.4 - - - +
42D ASP* 1.3 63.4 + - - +
44D LEU* 3.3 9.3 + - - +
45D LYS* 3.0 27.5 + - + +
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 5.6 1.2 - - - +
38D GLN* 3.0 32.2 + - - +
39D HIS* 3.3 13.6 + - + +
41D VAL* 1.3 77.6 - - - +
43D LEU* 1.3 62.5 - - + +
45D LYS* 3.2 24.7 + - - +
46D SER* 3.1 23.7 + - - -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 4.2 19.1 - - - +
17C LEU* 5.5 2.2 - - + -
25C ILE* 3.5 40.8 - - + -
39D HIS* 3.1 49.0 + - + +
40D ALA 3.6 6.7 - - - +
41D VAL 3.2 0.2 - - - -
42D ASP* 1.3 75.6 - - + +
44D LEU* 1.3 65.9 + - - +
46D SER* 2.8 27.4 + - - +
47D THR* 3.4 7.4 + - - -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 4.8 9.2 - - + -
15C TRP* 4.5 8.5 - - + -
17C LEU* 4.5 22.0 - - + +
25C ILE* 6.1 0.2 - - + -
26C ALA* 4.4 11.2 - - + -
44C LEU* 4.3 33.2 - - + +
3D PHE* 4.5 15.7 - - + -
15D TRP* 3.5 44.2 - - + +
40D ALA 3.0 16.9 + - - +
41D VAL* 3.3 11.2 + - - +
43D LEU* 1.3 75.7 - - + +
45D LYS* 1.3 58.7 + - - +
47D THR* 2.9 30.7 + - - +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C THR* 3.5 32.5 - - + +
48C THR* 3.6 24.7 - - - +
49C ALA* 3.4 32.0 + - + +
51C THR* 3.1 27.4 + - - -
53C VAL* 3.5 15.4 - - + +
3D PHE* 4.3 4.7 - - + -
41D VAL* 3.0 29.9 + - + +
42D ASP* 3.2 29.2 + - + +
44D LEU* 1.3 71.8 - - - +
46D SER* 1.3 57.9 + - - +
47D THR 3.1 6.1 + - - +
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Residues in contact with SER 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 4.8 6.1 - - - +
49C ALA* 5.6 4.5 - - - -
42D ASP 3.1 14.1 + - - -
43D LEU* 2.8 26.1 + - - +
45D LYS* 1.3 76.9 - - - +
47D THR* 1.3 62.7 + - - +
48D THR* 3.5 5.5 + - - +
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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