Contacts of the helix formed by residues 44 - 49 (chain A) in PDB entry 3L8N
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 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.8 14.6 - - + +
32A GLN* 3.7 25.1 - - - +
37A LEU* 4.4 7.9 - - + -
38A GLY 4.1 2.0 - - - +
39A THR 4.0 3.1 - - - +
40A SER 3.5 22.4 - - - +
41A VAL* 3.7 6.4 + - + +
43A ASP* 1.3 72.8 - - - +
45A ALA* 1.3 62.9 + - - +
47A PHE* 3.2 13.3 + - + +
48A LEU* 3.1 26.1 + - + +
62A PHE* 4.1 29.4 - - + -
69A PHE* 3.6 28.0 - - + -
73A VAL* 5.7 5.8 - - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL 3.0 19.2 + - - -
44A ILE* 1.3 72.9 - - - +
46A GLN* 1.3 58.6 + - - +
47A PHE 3.0 8.2 + - - -
48A LEU* 4.6 4.5 - - - -
49A HIS* 3.4 22.0 + - - +
73A VAL 4.4 15.4 + - - -
76A ALA* 4.7 1.6 - - - -
77A TYR* 4.0 15.2 - - - +
80A GLN* 3.3 13.7 - - - +
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU 3.1 16.2 + - - -
43A ASP* 3.2 8.9 + - - +
44A ILE 3.2 0.8 - - - -
45A ALA* 1.3 75.5 - - - +
47A PHE* 1.3 56.9 + - - +
50A GLN* 3.1 24.7 - - - +
80A GLN* 3.4 18.4 - - - +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.7 27.1 - - + -
20A PHE* 4.7 14.1 - + - -
28A ILE* 5.6 0.9 - - + -
31A LEU* 3.8 24.0 - - + -
37A LEU* 3.8 28.0 - - + -
43A ASP 3.4 10.5 - - - +
44A ILE* 3.4 10.5 - - + +
45A ALA 3.0 0.2 - - - -
46A GLN* 1.3 79.5 - - - +
48A LEU* 1.3 79.3 + - + +
49A HIS 3.1 1.6 - - - -
50A GLN* 3.7 2.5 - - + +
51A GLU* 3.1 47.6 + - + +
54A LEU* 3.7 20.8 - - + +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.8 31.9 - - + -
44A ILE* 3.1 19.9 + - + +
45A ALA* 4.7 0.7 - - - -
47A PHE* 1.3 89.6 - - + +
49A HIS* 1.3 61.6 + - - +
51A GLU 4.7 6.8 - - - +
52A GLU* 5.5 2.4 - - - +
54A LEU* 4.8 6.1 - - + +
59A VAL* 3.9 21.1 - - + +
62A PHE* 3.6 33.7 - - + -
63A LEU* 4.4 9.0 - - + -
73A VAL 4.4 9.6 - - - +
77A TYR* 3.4 34.5 + - + -
98A GLY* 5.2 2.9 - - - +
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Residues in contact with HIS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA 3.4 17.4 + - - +
46A GLN* 4.9 0.2 - - - -
47A PHE 3.1 0.2 - - - -
48A LEU* 1.3 81.9 - - - +
50A GLN* 1.3 61.4 + - - +
52A GLU* 5.1 5.4 - - - +
77A TYR* 3.0 46.2 + + + -
80A GLN* 3.7 28.7 - - + +
81A LEU* 3.4 49.1 + - + +
94A THR 5.5 6.7 - - - -
95A PHE* 5.6 2.5 - + - -
98A GLY* 5.7 4.0 - - - -
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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