Contacts of the helix formed by residues 27 - 37 (chain D) in PDB entry 1L0V
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 ILE 27 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ALA* 5.0 3.8 - - + -
123C ILE* 3.9 18.6 - - + -
23D TRP* 2.9 53.5 + - + +
26D ILE* 1.3 92.9 - - + +
28D ALA* 1.3 61.1 + - - +
29D PRO* 3.5 3.4 - - - -
30D VAL* 3.4 10.1 - - - +
31D MET* 3.2 19.4 - - + +
66D PHE* 3.9 29.6 - - + -
70D MET* 4.0 7.6 - - - -
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 5.7 1.8 - - + -
79C ALA* 4.9 4.9 - - + -
23D TRP 3.9 1.8 + - - -
24D SER* 2.9 38.3 + - - +
27D ILE* 1.3 74.4 - - - +
29D PRO* 1.3 72.8 - - + +
31D MET* 3.6 1.2 + - - +
32D ILE* 3.0 36.4 + - + +
70D MET* 4.2 17.9 - - + +
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Residues in contact with PRO 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU* 3.6 21.3 - - + +
79C ALA* 4.7 7.2 - - + +
80C LEU* 3.9 26.2 - - + -
83C THR* 3.8 19.1 - - - +
116C THR* 5.2 6.1 - - + -
120C THR* 5.3 6.3 - - + +
24D SER 3.9 1.6 - - - +
25D ALA 3.8 15.0 - - - +
26D ILE 3.9 6.3 - - - +
27D ILE 3.5 3.4 - - - -
28D ALA* 1.3 97.1 - - + +
30D VAL* 1.3 65.4 + - - +
32D ILE* 3.0 2.3 + - + -
33D LEU* 3.0 17.1 + - - +
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C THR* 3.6 46.9 + - + +
123C ILE* 3.4 42.6 - - + -
124C LEU* 3.6 22.0 - - + -
26D ILE 5.2 1.1 - - - +
27D ILE* 3.4 16.6 - - - +
29D PRO* 1.3 78.6 - - - +
31D MET* 1.3 69.2 + - + +
33D LEU* 2.9 30.7 + - + +
34D LEU* 3.0 9.5 + - + +
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Residues in contact with MET 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.9 13.5 - - + -
42C LEU* 5.5 2.5 - - + -
123C ILE* 4.6 7.9 - - - -
27D ILE* 3.2 22.4 - - + +
28D ALA 3.6 4.0 + - - +
29D PRO 3.2 0.6 - - - -
30D VAL* 1.3 77.7 - - + +
32D ILE* 1.3 65.7 + - - +
33D LEU 3.0 1.3 - - - -
34D LEU* 4.5 8.1 - - + +
35D VAL* 3.0 38.5 + - + +
66D PHE* 3.6 30.1 - - + -
70D MET* 3.8 24.5 - - + -
700D MQ7 2.1 49.4 - - + +
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Residues in contact with ILE 32 (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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35C ALA* 6.5 0.2 - - - -
38C PHE* 3.5 40.2 - - + -
72C ASN* 4.1 14.4 - - + +
75C THR* 3.7 25.4 - - + +
76C LEU* 4.0 23.8 - - + +
79C ALA* 3.7 25.4 - - + -
28D ALA* 3.0 21.6 + - + +
29D PRO 3.0 4.8 + - - +
31D MET* 1.3 76.5 - - - +
33D LEU* 1.3 57.8 + - - +
36D GLY* 2.8 29.6 + - - -
37D ILE* 3.5 4.8 + - + +
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Residues in contact with LEU 33 (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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76C LEU* 4.6 11.2 - - + +
120C THR* 5.8 2.9 - - + -
124C LEU* 4.3 27.1 - - + -
29D PRO 3.0 9.5 + - - +
30D VAL* 2.9 19.2 + - - +
32D ILE* 1.3 77.3 - - - +
34D LEU* 1.3 54.4 + - - +
37D ILE* 2.9 36.0 + - + +
38D LEU* 2.8 50.3 + - + +
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Residues in contact with LEU 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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123C ILE* 3.8 25.6 - - + -
124C LEU* 4.0 15.5 - - + -
127C ALA* 3.8 21.5 - - + -
128C LEU* 4.2 13.2 - - + -
30D VAL* 3.0 12.3 + - + +
31D MET* 3.9 9.4 - - - +
33D LEU* 1.3 79.5 - - - +
35D VAL* 1.3 63.1 + - + +
38D LEU* 3.6 22.2 - - + +
39D LEU* 2.8 34.0 + - - +
49D LEU* 3.9 14.0 - - + +
700D MQ7 3.5 28.3 - - + -
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Residues in contact with VAL 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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38C PHE* 4.4 9.6 - - + -
41C GLU* 5.9 2.5 - - + +
42C LEU* 4.2 17.3 - - + -
59C PHE* 4.5 11.4 - - + -
63C LEU* 3.8 23.5 - - + +
31D MET* 3.0 18.4 + - + +
34D LEU* 1.3 74.6 - - + +
36D GLY* 1.3 60.6 + - - +
39D LEU* 3.8 12.0 - - + +
40D PRO* 3.3 19.4 - - - +
700D MQ7 3.4 49.1 - - + +
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Residues in contact with GLY 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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38C PHE* 4.7 3.0 - - - -
41C GLU* 5.6 0.2 - - - -
63C LEU* 5.1 2.7 - - - +
69C VAL* 5.0 8.5 - - - +
72C ASN* 3.5 34.5 - - - +
32D ILE* 2.8 22.6 + - - +
35D VAL* 1.3 76.9 - - - +
37D ILE* 1.3 66.1 + - - +
40D PRO* 3.8 11.4 - - - +
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Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C VAL* 5.5 4.7 - - + -
72C ASN* 5.0 5.6 - - + +
73C LEU* 3.9 27.4 - - + -
76C LEU* 3.9 31.4 - - + -
32D ILE* 3.9 15.3 - - + +
33D LEU* 2.9 24.6 + - + +
35D VAL 3.5 1.0 - - - -
36D GLY* 1.3 84.9 - - - +
38D LEU* 1.3 70.7 + - + +
39D LEU 3.4 0.9 - - - -
40D PRO* 3.5 3.1 - - - +
41D LEU* 3.1 47.1 + - + +
43D LEU* 4.9 3.1 - - + -
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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