Contacts of the helix formed by residues 47 - 63 (chain T) in PDB entry 6CP3
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 VAL 47 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ILE* 4.8 11.4 - - + -
37K VAL* 3.7 30.5 - - + -
38K SER* 5.0 2.0 - - - +
44K LYS* 5.7 1.3 - - + +
33T LEU* 3.7 23.6 - - + -
36T GLY* 5.9 1.1 - - - -
37T VAL* 5.8 1.3 - - + +
43T ILE* 3.4 40.8 - - + +
44T LYS* 5.1 1.6 - - - +
46T THR* 1.3 77.5 - - + +
48T PHE* 1.3 63.2 + - + +
49T PRO 3.4 0.4 - - - -
50T MET* 3.2 21.6 - - + +
51T ALA* 3.0 27.6 + - - +
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Residues in contact with PHE 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S MET* 3.6 31.2 - - + -
53S LEU* 5.4 8.7 - - + -
30T PHE* 4.8 11.9 - + - -
33T LEU* 4.0 16.8 - - + -
44T LYS 3.2 22.4 + - - +
45T ASP* 4.9 4.5 - - - -
46T THR 3.4 0.2 - - - -
47T VAL* 1.3 81.1 - - + +
49T PRO* 1.3 70.8 - - + +
51T ALA* 4.2 5.2 - - + -
52T ILE* 3.2 40.6 + - + +
76X GLN* 3.4 39.0 - - - -
236X ILE* 4.6 15.0 - - + -
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Residues in contact with PRO 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T ASP* 4.2 13.5 - - - +
46T THR 3.4 20.6 - - - +
48T PHE* 1.3 93.5 - - + +
50T MET* 1.3 60.3 + - - +
52T ILE* 3.4 10.8 - - + +
53T LEU* 3.2 18.5 + - - +
243X LYS* 3.8 26.9 - - - +
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Residues in contact with MET 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K PHE* 4.3 9.6 - - + -
33K LEU* 3.7 32.3 - - + -
34K ILE* 3.8 26.5 - - + -
37K VAL* 3.7 29.2 - - + -
44K LYS* 3.1 31.2 - - - +
48K PHE* 4.4 15.5 - - + -
46T THR 4.6 0.8 + - - -
47T VAL* 3.2 23.3 + - + +
49T PRO* 1.3 77.6 - - - +
51T ALA* 1.3 54.0 + - - +
53T LEU* 2.8 12.4 - - + +
54T GLY* 2.5 33.1 + - - -
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Residues in contact with ALA 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PHE* 5.6 1.8 - - - -
34K ILE* 4.1 21.3 - - + -
29T VAL* 4.4 13.7 - - + +
30T PHE* 5.6 6.9 - - + -
33T LEU* 4.8 15.7 - - + -
47T VAL 3.0 18.2 + - - +
48T PHE* 4.0 9.6 - - + +
49T PRO 3.3 0.4 - - - -
50T MET* 1.3 78.5 - - - +
52T ILE* 1.3 51.6 + - - +
54T GLY* 2.9 2.9 + - - +
55T PHE* 2.5 36.4 + - - +
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Residues in contact with ILE 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53S LEU* 5.3 4.3 - - + -
57S LEU* 5.0 3.1 - - + -
30T PHE* 4.8 11.6 - - + -
48T PHE* 3.2 35.5 + - + +
49T PRO* 3.4 15.7 - - + +
51T ALA* 1.3 73.9 - - - +
53T LEU* 1.3 66.5 + - - +
55T PHE* 3.8 24.7 - - + +
56T ALA* 3.7 16.8 + - - +
76X GLN* 5.6 2.5 - - - +
236X ILE* 5.4 7.0 - - + +
237X LEU* 4.4 21.1 - - + -
240X SER* 3.6 33.3 + - - +
241X TYR* 6.2 0.2 - - - -
243X LYS* 5.9 2.0 - - - +
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Residues in contact with LEU 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PHE* 4.1 18.2 - - + -
48K PHE* 6.0 8.5 - - + -
52K ILE* 5.9 7.2 - - + -
49T PRO 3.2 14.8 + - - +
50T MET* 2.8 17.4 + - + +
52T ILE* 1.3 77.3 - - - +
54T GLY* 1.3 58.6 + - - +
56T ALA* 3.0 21.0 + - + +
57T LEU* 3.2 40.6 + - + +
147X PRO* 6.6 0.2 - - + -
162X GLU* 5.3 7.9 - - - +
169X ARG* 5.4 7.4 - - - +
244X ASP* 5.6 6.1 - - - +
249X HIS* 6.5 0.9 - - + -
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Residues in contact with GLY 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PHE* 3.6 37.8 - - - -
29T VAL* 4.5 7.2 - - - +
50T MET 2.5 17.3 + - - -
51T ALA* 2.9 4.6 + - - -
53T LEU* 1.3 69.2 - - - +
55T PHE* 1.3 59.3 + - - +
57T LEU* 4.7 0.9 - - - -
58T SER* 2.5 33.6 + - - -
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Residues in contact with PHE 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57S LEU* 3.6 49.6 - - + -
26T ILE* 3.6 32.8 - - + +
29T VAL* 4.9 3.3 - - + +
30T PHE* 4.2 10.5 - + + -
51T ALA 2.5 20.1 + - - +
52T ILE* 3.8 25.1 - - + +
54T GLY* 1.3 72.6 - - - +
56T ALA* 1.3 65.1 + - + +
58T SER* 2.9 9.5 + - - -
59T GLU* 2.9 45.4 + - + +
176X ARG* 4.0 10.3 - - - -
237X LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T ILE 3.7 8.9 + - - +
53T LEU* 3.0 10.6 + - + +
55T PHE* 1.3 89.4 - - + +
57T LEU* 1.3 62.2 + - + +
59T GLU* 2.9 13.3 + - - +
60T ALA* 2.9 23.4 + - - +
165X SER* 5.0 8.5 + - - +
169X ARG* 6.1 4.0 - - - +
241X TYR* 4.8 17.7 - - + +
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Residues in contact with LEU 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K ILE* 4.0 4.1 - - - +
30K PHE* 4.7 3.8 - - + -
55K PHE* 3.6 40.8 - - + -
59K GLU* 5.2 1.2 - - - +
53T LEU* 3.2 47.6 + - + +
54T GLY 4.5 3.1 - - - +
56T ALA* 1.3 82.5 - - + +
58T SER* 1.3 57.7 + - - +
60T ALA* 2.9 30.8 + - + +
61T THR* 3.2 11.3 + - - +
158X LEU* 6.4 0.7 - - + -
161X ILE* 4.4 21.8 - - + +
162X GLU* 4.5 17.9 - - - +
165X SER* 4.6 9.2 - - - +
169X ARG* 6.2 0.7 - - - +
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Residues in contact with SER 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLY 5.4 2.2 - - - +
26K ILE* 3.3 22.6 - - - +
27K ALA* 4.1 13.3 - - - -
30K PHE* 4.7 0.3 - - - -
22T ALA* 3.9 10.6 - - - +
25T GLY* 4.7 2.7 - - - -
26T ILE* 3.6 26.0 - - - +
29T VAL* 4.2 2.8 - - - +
54T GLY 2.5 21.9 + - - -
55T PHE* 2.9 8.6 + - - -
57T LEU* 1.3 75.2 - - - +
59T GLU* 1.3 59.8 + - - +
61T THR* 2.5 24.5 + - - -
62T GLY 3.8 1.0 + - - -
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Residues in contact with GLU 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S THR* 3.3 30.5 - - - +
64S PHE* 4.4 10.4 - - - -
22T ALA* 5.3 4.2 - - - +
26T ILE* 3.4 20.7 - - - +
55T PHE* 2.9 38.1 + - + +
56T ALA* 2.9 12.7 + - - +
58T SER* 1.3 77.5 - - - +
60T ALA* 1.3 56.1 + - - +
61T THR 3.1 0.2 - - - -
62T GLY 2.9 6.9 + - - +
63T LEU* 2.9 49.4 + - + +
172X SER* 4.8 6.0 + - - +
176X ARG* 4.9 9.4 + - - +
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Residues in contact with ALA 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K GLU* 4.5 6.4 - - - +
63K LEU* 5.5 3.8 - - - +
56T ALA 2.9 10.1 + - - +
57T LEU* 2.9 30.4 + - + +
59T GLU* 1.3 75.1 - - - +
61T THR* 1.3 57.8 + - - +
63T LEU* 4.9 2.5 - - - -
64T PHE* 3.1 40.6 - - + -
161X ILE 5.5 1.3 - - - +
165X SER* 4.7 13.9 - - - +
168X ALA* 5.8 3.4 - - + -
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Residues in contact with THR 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LEU* 3.2 30.9 - - - +
22K ALA 3.4 18.8 - - - +
23K GLY* 3.5 24.3 - - - -
26K ILE* 3.9 7.4 - - + -
59K GLU* 3.3 35.4 - - - +
22T ALA* 3.8 1.4 - - - +
57T LEU 3.2 9.8 + - - +
58T SER* 2.5 22.5 + - - +
60T ALA* 1.3 81.8 - - - +
62T GLY* 1.3 61.8 + - - -
63T LEU 3.3 5.2 + - - -
64T PHE* 4.0 4.2 + - - -
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Residues in contact with GLY 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LEU* 4.0 2.0 - - - -
23K GLY* 5.8 0.2 - - - -
64S PHE* 5.6 2.3 - - - -
18T GLY 3.8 16.6 - - - -
19T LEU* 3.4 23.5 + - - +
22T ALA* 3.8 18.6 - - - +
58T SER 3.8 0.4 + - - -
59T GLU* 2.9 12.1 + - - +
61T THR* 1.3 82.5 + - - +
63T LEU* 1.3 58.7 + - - +
65T CYS 4.8 2.2 - - - -
66T LEU* 4.3 7.4 + - - +
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Residues in contact with LEU 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64S PHE* 4.5 11.9 - - + -
59T GLU* 2.9 26.2 + - + +
60T ALA* 4.9 2.9 - - - -
61T THR 3.3 0.4 + - - -
62T GLY* 1.3 78.3 - - - +
64T PHE* 1.3 68.7 + - + +
65T CYS 3.3 1.6 - - - -
66T LEU* 2.9 41.6 + - + +
67T MET* 2.9 13.4 + - + +
168X ALA* 4.4 16.8 - - + +
171X ILE* 3.8 20.9 - - + -
172X SER* 3.7 37.5 - - - +
175X LEU* 5.1 5.4 - - + -
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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
------------------------------------------------------------
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