Contacts of the helix formed by residues 40 - 50 (chain S) in PDB entry 3L73
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 ASP 40 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38S TYR* 2.9 34.1 + - + +
39S GLU* 1.3 72.3 - - - +
41S ASP* 1.3 68.4 + - - +
42S ASP* 2.8 23.4 + - - +
43S VAL* 3.1 18.9 + - - +
44S LYS* 2.8 28.5 + - - +
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Residues in contact with ASP 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40S ASP* 1.3 78.9 + - - +
42S ASP* 1.3 66.4 + - - +
44S LYS* 3.3 19.2 + - - +
45S GLU* 3.1 21.5 + - - +
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Residues in contact with ASP 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40S ASP* 2.8 16.1 + - - +
41S ASP* 1.3 72.4 - - - +
43S VAL* 1.3 61.8 + - - +
45S GLU* 3.0 5.1 + - - +
46S ALA* 2.9 28.6 + - - +
94S LEU* 3.8 19.3 - - + -
97S VAL* 3.8 19.6 - - + +
98S ILE* 3.8 15.4 - - + +
101S ARG* 2.4 47.2 + - - -
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Residues in contact with VAL 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37S LEU* 4.5 15.3 - - + -
38S TYR 3.6 16.8 - - - +
39S GLU* 4.0 14.6 - - + -
40S ASP* 3.1 21.9 + - - +
42S ASP* 1.3 76.4 - - - +
44S LYS* 1.3 57.6 + - - +
46S ALA* 3.5 2.9 - - - +
47S LEU* 3.0 43.1 + - + +
58S ARG* 5.7 1.6 - - - +
90S LEU* 4.1 15.3 - - + -
94S LEU* 4.0 27.1 - - + -
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Residues in contact with LYS 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39S GLU* 3.6 37.1 + - + +
40S ASP* 2.8 26.2 + - - +
41S ASP* 3.5 24.3 + - - +
42S ASP 3.1 0.2 - - - -
43S VAL* 1.3 74.9 - - - +
45S GLU* 1.3 65.2 + - - +
47S LEU* 3.5 10.8 + - - +
48S LYS* 3.5 32.8 + - - +
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Residues in contact with GLU 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LYS* 6.0 0.5 + - - -
135B TRP* 5.5 2.4 - - - -
41S ASP 3.1 12.0 + - - +
42S ASP* 3.0 7.9 + - - +
44S LYS* 1.3 74.4 - - - +
46S ALA* 1.3 67.3 + - - +
48S LYS* 2.9 48.7 + - - +
49S ARG* 3.5 32.3 + - - +
97S VAL* 3.9 23.8 - - + -
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Residues in contact with ALA 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S ASP 2.9 15.7 + - - +
43S VAL* 3.5 7.4 - - - +
44S LYS 3.3 0.2 - - - -
45S GLU* 1.3 75.9 - - - +
47S LEU* 1.3 63.4 + - - +
49S ARG* 2.9 20.4 + - - +
50S LEU 3.5 4.5 + - - -
90S LEU* 3.7 23.7 - - + +
93S TYR* 4.3 6.8 - - + +
94S LEU* 3.8 29.6 - - + +
97S VAL* 4.0 10.3 - - + +
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Residues in contact with LEU 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39S GLU* 3.8 17.9 - - + +
43S VAL* 3.0 35.3 + - + +
44S LYS* 3.8 8.3 - - - +
45S GLU 3.2 0.2 - - - -
46S ALA* 1.3 75.8 - - - +
48S LYS* 1.3 60.8 + - + +
49S ARG 3.3 0.3 + - - -
50S LEU* 3.4 24.8 + - + +
55S TYR* 3.9 24.5 - - + -
58S ARG* 3.5 54.5 - - - +
89S TYR* 4.9 0.2 - - + -
90S LEU* 3.9 23.8 - - + -
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Residues in contact with LYS 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TRP* 5.0 5.0 - - - +
44S LYS* 3.5 22.3 + - - +
45S GLU* 2.9 39.1 + - - +
47S LEU* 1.3 78.0 - - - +
49S ARG* 1.3 60.9 + - + +
50S LEU 4.2 3.9 - - - +
55S TYR* 6.0 0.2 - - - -
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Residues in contact with ARG 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PRO* 5.9 0.7 - - - +
135B TRP* 3.5 64.8 - - + +
45S GLU* 3.6 35.5 + - - +
46S ALA* 2.9 8.0 + - - +
48S LYS* 1.3 78.6 - - + +
50S LEU* 1.3 66.5 + - - +
51S PRO* 3.4 4.0 - - - +
93S TYR* 3.5 31.9 + - + +
96S GLU* 4.1 11.1 - - - +
97S VAL* 3.1 33.2 - - - +
100S GLU* 2.8 37.2 + - - -
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Residues in contact with LEU 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S ALA 3.5 1.4 + - - -
47S LEU* 3.4 31.2 + - + +
48S LYS 4.2 4.5 - - - +
49S ARG* 1.3 80.9 - - - +
51S PRO* 1.3 78.3 - - + +
52S GLU* 3.6 1.4 + - - -
54S LEU* 4.4 11.2 - - + +
55S TYR* 4.3 26.2 - - + +
58S ARG* 4.5 2.9 - - - -
89S TYR* 3.8 49.6 - - + +
90S LEU* 3.8 20.6 - - + -
93S TYR* 4.0 14.1 - - + -
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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