Contacts of the helix formed by residues 42 - 51 (chain N) in PDB entry 5L4K
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 VAL 42 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38N ILE* 3.4 9.4 - - + +
39N SER* 3.4 21.3 - - - +
40N GLU 3.6 1.6 + - - +
41N SER* 1.3 75.7 - - - +
43N ASP* 1.3 76.4 + - - +
44N LYS 3.3 1.1 - - - -
45N ILE* 3.0 22.2 + - + +
46N GLU* 3.1 36.0 + - + +
67N VAL* 3.7 34.1 - - + -
68N PHE* 5.3 9.0 - - + -
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Residues in contact with ASP 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N GLU 4.0 15.4 - - - +
41N SER* 3.3 1.7 - - - -
42N VAL* 1.3 87.0 + - - +
44N LYS* 1.3 63.3 + - - +
46N GLU* 3.3 9.7 + - - +
47N VAL* 3.0 35.9 + - + +
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Residues in contact with LYS 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N ILE* 4.2 7.1 + - - +
9N ILE* 3.3 32.9 + - + +
11N LEU* 2.8 33.2 + - - +
12N LEU* 3.9 31.4 - - + +
19N LEU* 5.9 0.2 - - - +
23N ALA* 4.9 12.3 - - - +
24N LEU* 5.9 5.6 - - - +
41N SER* 4.3 10.8 + - - +
42N VAL 3.3 0.2 - - - -
43N ASP* 1.3 78.8 - - - +
45N ILE* 1.3 66.0 + - + +
47N VAL* 4.3 4.4 - - - +
48N LEU* 3.2 32.0 + - - +
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Residues in contact with ILE 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N ILE* 5.3 3.8 - - + -
24N LEU* 4.8 9.4 - - + -
27N LEU* 4.2 13.7 - - + -
38N ILE* 4.4 12.6 - - + -
41N SER 4.2 15.3 - - - +
42N VAL* 3.0 11.6 + - - +
44N LYS* 1.3 87.6 - - + +
46N GLU* 1.3 60.9 + - + +
47N VAL 3.4 0.2 - - - -
48N LEU* 3.4 7.3 + - + +
49N TYR* 2.9 26.6 + - - +
60N ALA* 3.4 36.4 - - + +
63N VAL* 3.6 27.4 - - + -
64N ALA* 4.3 12.8 - - + +
67N VAL* 5.2 2.0 - - + -
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Residues in contact with GLU 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N VAL* 3.1 37.5 + - + +
43N ASP* 4.1 9.1 - - - +
45N ILE* 1.3 76.1 - - + +
47N VAL* 1.3 67.0 + - + +
49N TYR* 3.1 7.4 + - - +
50N GLU* 3.0 29.4 + - + +
64N ALA* 5.5 3.6 - - + -
68N PHE* 4.4 13.7 - - + -
80N TYR* 3.1 33.9 + - + +
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Residues in contact with VAL 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N ASP* 3.0 22.6 + - + +
44N LYS* 4.5 4.7 - - - +
46N GLU* 1.3 78.9 - - + +
48N LEU* 1.3 67.0 + - + +
50N GLU* 3.3 12.9 + - - +
51N ASP* 3.3 15.2 + - + +
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Residues in contact with LEU 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LEU* 4.0 24.2 - - + -
20N LYS* 3.8 31.2 - - + -
24N LEU* 4.2 24.0 - - + -
44N LYS* 3.2 28.1 + - - +
45N ILE* 3.4 7.5 + - - +
46N GLU 3.2 0.6 - - - -
47N VAL* 1.3 81.1 - - + +
49N TYR* 1.3 63.3 + - - +
51N ASP* 3.3 18.9 + - - +
54N PHE* 3.9 27.5 - - + +
56N SER* 5.2 4.9 - - - +
57N ARG* 4.1 7.4 - - - +
60N ALA* 4.4 8.5 - - + -
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Residues in contact with TYR 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N ILE 2.9 17.6 + - - +
46N GLU 3.1 5.8 + - - +
48N LEU* 1.3 76.7 - - - +
50N GLU* 1.3 84.3 + - + +
52N GLU* 4.0 0.2 - - - +
57N ARG* 3.6 51.3 + - - -
60N ALA* 4.1 13.2 - - + +
61N ALA* 3.6 33.9 - - + +
79N ASN 3.9 8.7 + - - -
80N TYR* 3.4 33.4 - + + -
83N GLY* 3.6 22.8 - - - -
129N ARG* 4.4 6.8 + - - -
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Residues in contact with GLU 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N GLU* 3.0 20.7 + - + +
47N VAL* 3.3 6.7 + - - +
48N LEU 3.2 0.2 - - - -
49N TYR* 1.3 95.0 - - + +
51N ASP* 1.3 63.5 + - - +
52N GLU* 3.3 22.0 + - - +
80N TYR* 5.6 1.8 + - - +
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Residues in contact with ASP 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N VAL* 3.3 14.3 + - + +
48N LEU 3.3 12.3 - - - +
49N TYR 3.4 2.6 - - - +
50N GLU* 1.3 77.6 - - - +
52N GLU* 1.3 64.8 + - - +
53N GLY* 3.4 13.3 + - - -
54N PHE* 3.3 40.4 + - + +
57N ARG* 4.1 6.6 - - - -
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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