Contacts of the helix formed by residues 39 - 49 (chain C) in PDB entry 5CTR
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 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ILE 3.1 3.2 + - - -
38C ASP* 1.3 74.9 + - - +
40C ARG* 1.3 59.6 + - - +
42C PHE* 3.7 0.2 - - - +
43C LYS* 2.7 50.6 + - - +
90C GLU 5.2 2.5 - - - -
91C LEU* 2.4 30.9 + - - -
92C ASP* 2.8 15.7 + - - -
93C TYR 3.5 17.3 - - - -
94C VAL* 3.8 13.5 - - - -
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Residues in contact with ARG 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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38C ASP* 3.1 26.9 + - - +
39C SER* 1.3 83.3 + - - +
41C TRP* 1.3 61.4 + - - +
43C LYS* 3.1 31.3 - - + +
44C GLN* 3.4 9.4 + - - +
92C ASP* 5.1 3.6 - - - +
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Residues in contact with TRP 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 ILE* 4.1 12.3 - - + -
38C ASP* 3.2 12.8 + - + +
40C ARG* 1.3 79.0 - - - +
42C PHE* 1.3 77.0 + + - +
44C GLN* 3.1 10.4 + - + +
45C TRP* 3.0 47.2 + + + -
66C PRO* 3.7 29.5 + - + -
67C GLY 3.5 12.3 + - - -
68C PRO 3.3 24.9 + - - -
69C ILE* 3.4 21.0 - - + +
70C ASP* 3.8 29.4 - - + +
71C ASN* 4.9 0.4 - - - +
104C LEU* 3.7 32.1 - - + -
108C TYR* 4.2 12.6 - + - -
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Residues in contact with PHE 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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20C LEU* 5.2 5.2 - - + -
23C LEU* 4.9 17.3 - - + -
37C ILE* 4.3 10.3 - - + -
38C ASP 3.1 7.5 + - - +
39C SER 3.2 1.5 + - - +
41C TRP* 1.3 99.5 - + + +
43C LYS* 1.3 53.6 + - - +
45C TRP* 3.0 29.9 + + - +
46C LYS* 2.7 72.5 + - + +
51C PHE* 6.4 2.0 - + - -
94C VAL* 3.5 48.2 - - + -
95C LEU 5.8 0.9 - - - -
96C VAL* 6.6 0.2 - - + -
104C LEU* 4.9 10.1 - - + -
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Residues in contact with LYS 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 SER* 2.7 42.7 + - - +
40C ARG* 3.1 27.6 - - + +
42C PHE* 1.3 72.2 - - - +
44C GLN* 1.3 57.0 + - - +
46C LYS* 3.2 18.9 - - + +
47C LYS* 2.9 55.0 + - - +
91C LEU* 4.5 12.5 + - - +
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Residues in contact with GLN 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 ARG 3.7 9.0 - - - +
41C TRP* 3.1 11.6 + - + +
43C LYS* 1.3 83.4 - - - +
45C TRP* 1.3 57.5 + - - +
47C LYS* 3.3 19.4 + - - +
48C TYR* 2.8 25.6 + - - +
63C ASN 4.2 4.2 + - - -
64C LEU* 2.7 40.4 + - + +
65C PHE 2.8 22.2 + - - -
66C PRO* 3.6 15.6 + - + +
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Residues in contact with TRP 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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16C GLN* 3.2 31.2 + - + -
20C LEU* 3.7 34.8 - - + -
23C LEU* 6.3 0.2 - - + -
41C TRP* 3.0 33.1 + + + +
42C PHE* 3.0 28.9 + + - +
44C GLN* 1.3 74.8 - - - +
46C LYS* 1.3 67.6 + - + +
48C TYR* 2.9 22.9 + - + +
49C VAL* 3.0 43.9 + - + +
51C PHE* 4.1 20.9 - + + -
66C PRO* 3.9 13.5 - - + -
104C LEU* 6.0 2.2 - - + -
107C TRP* 4.6 3.4 - + - -
108C TYR* 2.5 45.9 + + - -
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Residues in contact with LYS 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 PHE* 2.7 52.4 + - + +
43C LYS* 3.2 24.6 - - + +
45C TRP* 1.3 78.9 - - + +
47C LYS* 1.3 58.6 + - + +
50C GLY* 2.9 8.5 + - - -
51C PHE* 2.8 44.2 + - + -
52C ASP* 3.6 33.0 + - - +
55C ASP 4.6 0.6 - - - +
94C VAL* 5.2 5.7 - - - +
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Residues in contact with LYS 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 LYS* 2.9 49.3 + - - +
44C GLN* 3.5 12.3 + - - +
46C LYS* 1.3 75.8 - - + +
48C TYR* 1.3 62.1 + - - +
50C GLY* 3.2 12.2 + - - -
55C ASP* 3.9 32.3 - - - +
56C MET* 5.1 1.4 - - - -
58C ASN 5.4 0.5 + - - -
59C VAL 3.7 7.6 + - - +
64C LEU* 3.3 35.9 - - + +
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Residues in contact with TYR 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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13C ALA* 4.3 10.0 - - + +
16C GLN* 5.4 3.1 - - - -
44C GLN 2.8 14.8 + - - +
45C TRP* 2.9 14.5 + - - +
47C LYS* 1.3 77.8 - - - +
49C VAL* 1.3 68.4 + - + +
50C GLY 3.3 0.2 - - - -
59C VAL 2.7 26.6 - - - +
60C GLY* 3.2 24.4 + - - -
61C GLU 3.5 17.9 - - - -
62C HIS* 4.3 13.9 + - - -
64C LEU* 3.2 30.5 - - + +
65C PHE* 3.4 41.8 - + + -
66C PRO* 3.7 7.6 - - + -
108C TYR* 4.5 10.5 - - - -
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Residues in contact with VAL 49 (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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13C ALA* 3.2 41.5 - - + +
16C GLN* 3.7 22.2 - - + +
17C LYS* 3.2 27.1 + - + +
45C TRP* 3.0 51.1 + - + +
46C LYS 3.9 0.7 - - - +
48C TYR* 1.3 82.9 - - + +
50C GLY* 1.3 65.1 + - - +
51C PHE* 3.9 10.5 - - + +
56C MET* 4.6 1.8 - - - +
59C VAL* 5.5 4.5 - - - -
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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