Contacts of the helix formed by residues 39 - 50 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ILE 3.2 3.5 + - - -
38D ASP* 1.3 74.0 + - - +
40D ARG* 1.3 64.2 + - - +
41D TRP 3.2 0.2 - - - -
42D PHE* 3.6 9.4 - - - -
43D LYS* 3.0 48.1 + - - +
90D GLU 5.3 0.2 - - - -
91D LEU* 2.2 33.1 + - - -
92D ASP* 3.1 14.6 + - - -
93D TYR* 3.9 9.6 - - - -
94D VAL* 4.0 10.3 - - - -
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Residues in contact with ARG 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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38D ASP* 3.1 29.6 - - - +
39D SER* 1.3 84.4 + - - +
41D TRP* 1.3 60.4 + - - +
43D LYS* 4.6 3.5 - - - +
44D GLN* 3.3 25.1 + - - +
73D GLY* 6.1 2.2 - - - -
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Residues in contact with TRP 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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37D ILE* 3.8 18.6 - - + -
38D ASP* 3.3 9.6 + - + +
39D SER 3.2 0.2 - - - -
40D ARG* 1.3 80.1 - - - +
42D PHE* 1.3 77.5 + + - +
44D GLN* 3.4 6.9 + - - +
45D TRP* 2.9 41.8 + + + -
66D PRO* 3.3 32.5 + - + +
67D GLY 4.2 0.2 + - - -
68D PRO 3.1 28.8 + - - -
69D ILE* 4.2 20.9 - - + -
70D ASP* 4.2 23.3 - - + +
104D LEU* 3.7 34.8 - - + -
108D TYR* 3.5 28.5 - + - -
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Residues in contact with PHE 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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20D LEU* 4.7 1.6 - - + -
23D LEU* 4.6 12.6 - - + -
37D ILE* 4.5 7.6 - - + -
38D ASP 3.2 13.3 + - - +
39D SER* 3.3 10.1 + - - +
41D TRP* 1.3 95.4 - + + +
43D LYS* 1.3 60.5 + - + +
45D TRP* 2.8 27.4 + + - +
46D LYS* 2.8 61.0 + - + +
51D PHE* 5.5 3.6 - + - -
90D GLU* 5.9 0.9 - - - -
94D VAL* 3.8 40.4 - - + -
96D VAL* 4.2 16.2 - - + -
104D LEU* 4.5 11.0 - - + -
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D SER* 3.0 38.3 + - - +
40D ARG* 4.6 3.6 - - - +
42D PHE* 1.3 75.7 - - + +
44D GLN* 1.3 61.8 + - + +
46D LYS* 3.4 29.8 + - - +
47D LYS* 3.1 41.5 + - - +
90D GLU* 4.7 15.7 + - - -
91D LEU* 4.8 7.0 - - - +
94D VAL* 6.0 2.6 - - + +
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Residues in contact with GLN 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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40D ARG 3.3 16.7 + - - +
41D TRP* 3.4 10.3 + - - +
42D PHE 3.1 0.4 - - - -
43D LYS* 1.3 76.9 - - - +
45D TRP* 1.3 65.1 + - - +
47D LYS* 3.2 29.8 + - - +
48D TYR* 3.0 21.7 + - - +
63D ASN 5.4 0.5 - - - +
64D LEU* 3.8 30.6 - - - +
66D PRO* 4.2 15.2 - - + +
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Residues in contact with TRP 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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16D GLN* 3.2 29.7 + - + -
20D LEU* 3.4 41.7 - - + -
41D TRP* 2.9 42.9 + + + +
42D PHE* 2.8 26.5 + + - +
44D GLN* 1.3 77.2 - - - +
46D LYS* 1.3 89.1 + - + +
48D TYR* 3.0 7.4 + - - +
49D VAL* 2.9 54.4 + - + +
51D PHE* 4.0 23.6 - + + -
66D PRO* 4.3 5.5 - - + +
104D LEU* 4.0 14.6 - - + +
108D TYR* 3.9 21.0 - + - -
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Residues in contact with LYS 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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42D PHE* 2.8 42.5 + - + +
43D LYS* 3.6 34.7 - - - +
45D TRP* 1.3 94.3 - - + +
47D LYS* 1.3 53.0 + - + +
49D VAL 4.5 0.2 - - - +
50D GLY* 2.5 31.7 + - - -
51D PHE* 2.9 38.5 + - + +
52D ASP* 3.5 28.4 + - + +
55D ASP* 5.8 0.6 - - - +
90D GLU* 4.9 9.5 + - - -
94D VAL* 5.8 0.6 - - - +
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Residues in contact with LYS 47 (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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43D LYS* 3.1 28.6 + - - +
44D GLN* 3.6 31.9 - - - +
45D TRP 3.2 0.2 - - - -
46D LYS* 1.3 75.1 - - + +
48D TYR* 1.3 65.2 + - - +
50D GLY* 3.5 8.4 + - - +
55D ASP* 4.3 35.7 - - + +
58D ASN* 3.2 23.4 - - - +
59D VAL* 4.1 0.3 - - - -
64D LEU* 3.7 18.1 - - + +
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Residues in contact with TYR 48 (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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10D ARG* 5.8 2.0 - - - -
13D ALA* 3.9 14.0 - - + +
16D GLN* 4.7 8.1 - - - -
44D GLN 3.0 12.9 + - - +
45D TRP* 3.0 11.4 + - - +
47D LYS* 1.3 76.4 - - - +
49D VAL* 1.3 69.0 + - + +
59D VAL* 3.5 3.5 - - - +
60D GLY* 3.1 39.9 + - - +
61D GLU 3.1 33.4 - - - -
62D HIS* 4.2 7.2 + - - -
64D LEU* 3.5 14.5 - - - +
65D PHE* 3.2 49.8 - + + -
66D PRO* 4.6 0.9 - - + -
108D TYR* 3.3 25.6 - - - -
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Residues in contact with VAL 49 (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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13D ALA* 3.0 36.5 - - + +
14D GLU* 4.7 5.0 + - - +
16D GLN* 3.7 10.1 - - + +
17D LYS* 3.5 32.2 - - + +
45D TRP* 2.9 52.8 + - + +
46D LYS 4.2 1.8 - - - +
48D TYR* 1.3 87.3 - - + +
50D GLY* 1.3 62.8 + - - +
51D PHE 4.4 3.1 - - - +
56D MET* 5.7 0.7 - - - +
59D VAL* 4.0 11.7 - - - +
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Residues in contact with GLY 50 (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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17D LYS* 3.4 20.0 + - - +
46D LYS 2.5 16.1 + - - -
47D LYS 3.5 8.5 + - - -
49D VAL* 1.3 74.1 - - - +
51D PHE* 1.3 64.6 + - - +
52D ASP 3.4 10.6 + - - +
53D SER 4.5 0.2 + - - -
55D ASP* 4.5 2.0 - - - -
56D MET* 3.9 33.0 - - - +
59D VAL* 4.9 1.3 - - - -
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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