Contacts of the helix formed by residues 45 - 53 (chain D) in PDB entry 1L3I
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 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.6 6.5 - - - -
42D CYS 2.8 15.1 + - - -
43D GLY 3.3 0.2 - - - -
44D THR* 1.3 78.6 - - - +
46D GLY* 1.3 66.9 + - - +
47D VAL 3.2 2.6 + - - -
48D THR* 3.8 5.4 - - - -
49D LEU* 2.9 32.9 + - - +
71D THR* 3.5 19.7 - - - -
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Residues in contact with GLY 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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7D PHE* 3.5 22.2 - - - -
16D PRO* 4.0 4.0 - - - -
22D ARG* 3.3 20.3 + - - -
44D THR 3.6 0.2 - - - -
45D GLY* 1.3 78.5 - - - +
47D VAL* 1.3 59.4 + - - +
50D GLU* 3.3 24.4 + - - +
804D SAH 3.2 20.4 + - - -
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Residues in contact with VAL 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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17D THR* 4.7 2.2 - - - +
22D ARG* 4.5 10.1 - - + +
25D ILE* 4.0 30.5 - - + -
26D MSE 5.6 2.9 - - - -
39D ASP* 3.7 15.2 + - - +
46D GLY* 1.3 76.4 - - - +
48D THR* 1.3 66.6 + - - +
50D GLU* 3.3 6.5 + - - +
51D LEU* 3.0 40.7 + - + +
105D VAL* 3.8 28.5 - - + -
107D GLY* 6.2 1.1 - - - -
133D THR* 5.7 0.9 - - - +
804D SAH 3.7 20.9 + - - +
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Residues in contact with THR 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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39D ASP* 2.6 28.9 + - - +
42D CYS* 3.4 13.0 - - - +
45D GLY* 3.2 8.6 + - - -
47D VAL* 1.3 77.6 - - - +
49D LEU* 1.3 57.6 + - - +
51D LEU* 3.4 6.0 + - - +
52D ALA* 2.8 28.8 + - - +
58D VAL* 4.5 6.4 - - + +
60D ALA* 3.5 8.8 - - + +
71D THR* 4.0 23.8 - - + -
75D LEU* 4.4 6.1 - - + -
84D VAL* 4.0 29.4 - - + -
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Residues in contact with LEU 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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2D ILE* 3.6 28.7 - - + +
7D PHE* 3.9 17.5 - - + -
45D GLY* 2.9 35.2 + - - +
46D GLY 4.5 0.2 - - - +
48D THR* 1.3 72.9 - - + +
50D GLU* 1.3 63.0 + - - +
52D ALA* 3.3 19.4 + - - +
53D GLY* 3.4 6.1 + - - -
71D THR 4.2 3.1 - - - +
74D ASN* 3.6 28.5 - - + +
75D LEU* 3.7 37.0 - - + +
78D HIS* 3.7 16.2 - - + -
80D LEU* 3.9 11.4 - - + +
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Residues in contact with GLU 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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1D MSE 3.8 26.8 - - + +
2D ILE* 3.0 38.6 + - - +
7D PHE* 4.8 0.3 - - - -
22D ARG* 2.7 28.4 + - + +
26D MSE 3.2 33.8 - - + +
46D GLY 3.3 16.8 - - - +
47D VAL* 3.3 7.7 + - - +
49D LEU* 1.3 77.0 - - - +
51D LEU* 1.3 62.6 + - - +
53D GLY* 3.6 4.0 + - - -
54D ARG* 3.5 22.9 + - - +
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Residues in contact with LEU 51 (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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26D MSE 3.9 22.9 - - + -
29D ALA* 5.1 2.5 - - + -
31D PRO* 4.5 10.3 - - + -
37D ALA* 4.1 26.5 - - + -
38D VAL 4.9 2.0 - - - +
39D ASP* 4.5 10.8 - - + -
47D VAL* 3.0 38.5 + - + +
48D THR 3.8 3.6 - - - +
50D GLU* 1.3 73.6 - - - +
52D ALA* 1.3 66.0 + - - +
54D ARG* 2.9 13.0 + - - -
55D VAL* 3.0 25.4 + - + +
58D VAL* 3.8 22.2 - - + -
103D ILE* 4.6 11.2 - - + -
105D VAL* 4.5 10.8 - - + -
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Residues in contact with ALA 52 (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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48D THR 2.8 19.4 + - - +
49D LEU 3.3 7.9 - - - +
50D GLU 3.3 0.2 - - - -
51D LEU* 1.3 75.5 - - - +
53D GLY* 1.3 60.9 + - - +
54D ARG 3.3 1.4 + - - -
55D VAL 3.9 2.4 - - - +
58D VAL* 3.7 11.4 - - - +
75D LEU* 4.0 12.6 - - + -
80D LEU* 4.4 10.9 - - + +
83D ASN* 3.0 28.1 + - - +
84D VAL* 3.8 21.5 - - + -
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Residues in contact with GLY 53 (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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33D LYS* 6.1 1.0 - - - -
49D LEU 3.4 9.1 + - - -
50D GLU 3.6 2.4 + - - -
51D LEU 3.2 0.8 - - - -
52D ALA* 1.3 77.0 - - - +
54D ARG* 1.3 65.0 + - - +
55D VAL 5.2 0.7 - - - -
80D LEU* 4.5 15.1 - - - +
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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