Contacts of the helix formed by residues 34 - 48 (chain C) in PDB entry 3BFT
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 GLY 34 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO 3.3 9.0 - - - -
16C TYR 3.1 11.4 - - - -
18C MET* 4.3 0.9 - - - -
33C GLU* 1.3 78.1 - - - +
35C TYR* 1.3 67.7 + - - -
37C VAL* 3.0 3.0 + - - +
38C ASP* 2.9 24.4 + - - -
254C TRP* 3.4 27.1 - - - -
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO 2.9 16.2 + - - +
16C TYR* 4.0 17.3 - + + -
34C GLY* 1.3 71.5 - - - +
36C CYS* 1.3 62.5 + - - +
38C ASP* 3.2 3.9 + - - +
39C LEU* 2.9 33.8 + - + +
106C PHE* 3.6 39.6 + + - -
107C MET* 3.5 28.9 - - + +
247C LEU* 3.7 22.6 + - + +
250C LEU* 3.6 37.9 - - + +
251C LYS 3.6 8.1 - - - -
254C TRP* 3.4 17.2 - - + +
255C TRP* 3.6 24.5 - + + -
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Residues in contact with CYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 3.0 36.5 + - - +
17C VAL* 3.9 11.2 - - + -
35C TYR* 1.3 84.6 - - - +
37C VAL* 1.3 61.2 + - - +
39C LEU* 3.7 7.0 - - - +
40C ALA* 2.8 30.5 + - - +
53C LEU* 5.5 0.8 - - - +
87C ILE* 3.8 20.9 - - + +
88C ALA* 3.4 34.3 - - - -
106C PHE* 4.8 5.6 - - - -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR 3.6 5.6 + - - +
17C VAL* 4.3 11.2 - - + -
29C ASN* 4.8 4.5 - - + +
32C TYR* 3.7 30.3 - - + +
33C GLU* 3.6 29.6 - - - +
34C GLY 3.0 11.1 + - - +
36C CYS* 1.3 78.8 - - - +
38C ASP* 1.3 67.3 + - - +
40C ALA* 3.6 6.0 - - - +
41C ALA* 3.2 21.5 + - + +
51C TYR* 4.6 2.7 + - - +
53C LEU* 4.3 20.0 - - + -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU* 5.9 0.2 - - - -
34C GLY 2.9 13.6 + - - +
35C TYR 3.6 6.7 - - - +
37C VAL* 1.3 82.5 - - - +
39C LEU* 1.3 63.2 + - - +
41C ALA* 3.3 8.0 + - - +
42C GLU* 3.1 25.3 + - + +
250C LEU* 3.5 23.4 - - + +
253C LYS* 3.0 22.5 + - - -
254C TRP* 2.9 26.9 + - - -
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 2.9 25.3 + - + +
36C CYS* 3.7 7.6 - - - +
37C VAL 3.3 0.2 - - - -
38C ASP* 1.3 77.1 - - - +
40C ALA* 1.3 57.3 + - - +
42C GLU* 3.0 5.0 + - - +
43C ILE* 2.8 60.4 + - + +
87C ILE* 4.4 11.0 - - + -
106C PHE* 3.9 43.3 - - + -
222C ILE* 4.5 2.7 - - + -
238C VAL* 6.0 1.3 - - + -
241C LEU* 4.2 14.6 - - + -
246C LEU* 4.5 4.5 - - + -
247C LEU* 3.9 22.4 - - + -
250C LEU* 4.2 8.7 - - + +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C CYS 2.8 18.7 + - - +
37C VAL 3.6 5.2 - - - +
39C LEU* 1.3 75.6 - - - +
41C ALA* 1.3 63.3 + - - +
43C ILE* 3.4 1.3 + - - +
44C ALA* 3.0 26.7 + - - +
49C PHE* 5.5 0.3 - - - -
51C TYR* 4.1 21.6 - - + -
53C LEU* 4.1 14.4 - - + -
87C ILE* 3.7 30.8 - - + +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 3.2 10.3 + - + +
38C ASP* 3.6 10.3 - - - +
39C LEU 3.2 0.4 - - - -
40C ALA* 1.3 79.2 - - - +
42C GLU* 1.3 58.4 + - + +
44C ALA* 3.9 1.6 - - - +
45C LYS* 3.0 30.7 + - - +
51C TYR* 3.3 23.4 + - - +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP* 3.1 15.3 + - + +
39C LEU 3.0 8.4 + - - +
41C ALA* 1.3 76.2 - - + +
43C ILE* 1.3 66.2 + - - +
45C LYS* 3.1 15.1 + - - +
46C HIS* 2.9 57.1 + - - -
241C LEU* 3.9 10.4 - - + +
246C LEU* 3.6 39.5 - - + +
250C LEU* 5.5 0.2 - - + -
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 2.8 54.1 + - + +
40C ALA* 4.0 6.3 - - - +
42C GLU* 1.3 73.3 - - - +
44C ALA* 1.3 59.8 + - - +
46C HIS* 3.7 2.4 - - - -
47C CYS* 2.8 46.0 + - - -
49C PHE* 4.2 10.5 - - + -
85C ILE* 5.0 0.9 - - + -
87C ILE* 4.6 10.1 - - + -
222C ILE* 3.2 32.8 - - + -
234C VAL* 4.0 21.5 - - + -
237C ALA* 4.7 9.2 - - + -
238C VAL* 5.0 4.0 - - + -
241C LEU* 4.3 11.9 - - + -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA 3.0 18.0 + - - +
41C ALA 3.9 1.6 - - - +
43C ILE* 1.3 78.5 - - - +
45C LYS* 1.3 58.4 + - - +
48C GLY* 2.8 24.1 + - - -
49C PHE* 3.0 41.6 + - + +
51C TYR* 3.4 33.0 - - + -
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Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA 3.0 18.9 + - - +
42C GLU* 3.5 22.7 - - - +
44C ALA* 1.3 76.3 - - - +
46C HIS* 1.3 67.4 + - + +
48C GLY* 3.5 10.2 + - - -
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Residues in contact with HIS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU* 2.9 48.0 + - - +
43C ILE 4.0 2.5 - - - +
45C LYS* 1.3 85.6 - - + +
47C CYS* 1.3 60.6 + - - +
237C ALA* 4.5 16.9 - - + +
240C LYS* 4.5 25.9 - - - +
241C LEU* 3.8 22.9 - - + +
244C GLN* 4.8 5.2 - - - -
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Residues in contact with CYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 2.8 36.5 + - - +
46C HIS* 1.3 80.7 - - - +
48C GLY* 1.3 64.2 + - - +
49C PHE* 3.6 21.7 - - + +
230C LEU* 5.3 2.2 - - + -
233C ALA* 4.1 14.9 - - + +
234C VAL* 4.0 21.8 - - - -
237C ALA* 4.0 17.9 - - - -
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Residues in contact with GLY 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA 2.8 11.1 + - - -
45C LYS* 3.5 7.4 + - - -
46C HIS 3.4 2.8 - - - -
47C CYS* 1.3 80.6 - - - +
49C PHE* 1.3 59.5 + - - +
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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