Contacts of the helix formed by residues 37 - 47 (chain C) in PDB entry 3LRQ
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 PHE 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C ARG 3.5 2.2 + - - -
24C ASP* 3.0 44.1 + - + +
26C ARG* 3.0 50.0 - - + -
36C CYS* 1.3 71.0 - - - +
38C SER* 1.3 63.7 + - - +
40C ILE* 3.1 6.3 - - + +
41C ARG* 3.0 27.4 + - + +
60C LEU* 4.1 30.3 - - + -
63C LEU* 4.3 5.2 - - + -
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Residues in contact with SER 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ARG* 5.0 9.0 + - - -
24C ASP* 5.6 0.2 - - - +
36C CYS* 3.2 3.7 - - - +
37C PHE* 1.3 80.0 - - - +
39C CYS* 1.3 65.2 + - - +
41C ARG* 3.2 6.5 + - - +
42C ARG* 2.9 27.0 + - - +
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Residues in contact with CYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 3.8 18.4 - - + +
18C CYS* 3.8 13.0 - - - -
35C CYS* 3.8 14.1 - - - -
36C CYS* 3.3 8.4 + - - +
38C SER* 1.3 82.8 - - - +
40C ILE* 1.3 59.1 + - - +
42C ARG* 3.3 5.5 + - - +
43C TRP* 2.9 29.3 + - - +
100C ZN 2.4 37.5 - - - -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE* 5.1 3.4 - - + -
17C ILE* 3.9 6.3 - - + -
26C ARG* 4.6 5.8 - - + -
35C CYS* 3.6 15.0 - - + -
36C CYS 3.2 10.1 + - - +
37C PHE* 3.1 20.6 - - + +
39C CYS* 1.3 78.4 - - - +
41C ARG* 1.3 64.8 + - - +
43C TRP* 4.1 5.8 - - + -
44C LEU* 3.0 47.7 + - + +
52C PRO* 4.0 27.4 - - + -
58C LEU* 4.2 8.5 - - + -
63C LEU* 3.4 46.0 - - + -
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PHE* 3.0 26.7 + - + +
38C SER* 3.3 8.7 - - - +
40C ILE* 1.3 79.4 - - - +
42C ARG* 1.3 65.1 + - - +
44C LEU* 3.2 3.6 + - - +
45C THR* 2.8 60.0 + - - +
60C LEU* 3.9 38.2 - - + +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C SER* 2.9 16.8 + - - +
39C CYS* 3.8 4.9 - - - +
41C ARG* 1.3 78.1 - - - +
43C TRP* 1.3 54.6 + - - +
45C THR* 3.1 8.4 + - - -
46C GLU* 2.7 68.9 + - + +
47C GLN* 6.0 1.6 - - - +
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Residues in contact with TRP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 3.9 24.9 - - + -
39C CYS 2.9 17.8 + - - +
40C ILE* 3.5 7.4 - - + +
41C ARG 3.1 0.2 - - - -
42C ARG* 1.3 76.2 - - - +
44C LEU* 1.3 66.8 + - - +
47C GLN* 2.8 64.9 + - + +
48C ARG* 3.3 22.3 + - + +
50C GLN* 3.5 25.4 + - - +
52C PRO* 3.5 33.3 - - + +
41D ARG* 3.6 47.3 - - - -
45D THR* 5.9 3.6 - - - -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 3.0 23.8 + - + +
41C ARG 3.8 3.4 - - - +
43C TRP* 1.3 76.3 - - - +
45C THR* 1.3 60.4 + - - +
46C GLU 3.6 0.6 + - - -
47C GLN 4.6 1.4 + - - -
48C ARG 3.6 12.2 - - - +
49C ALA* 4.1 7.0 + - + +
50C GLN 3.8 28.5 - - - +
58C LEU* 3.4 39.3 - - + +
59C GLN* 4.1 0.9 - - - -
60C LEU* 3.6 49.4 - - + +
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Residues in contact with THR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ARG* 2.8 46.0 + - - +
42C ARG* 3.1 5.8 + - - +
43C TRP 3.0 0.8 - - - -
44C LEU* 1.3 80.3 - - - +
46C GLU* 1.3 73.6 + - + +
47C GLN 3.8 0.2 - - - -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ARG* 2.7 51.0 + - + +
45C THR* 1.3 88.9 - - + +
47C GLN* 1.3 68.3 + - - +
42D ARG* 2.9 24.5 + - - +
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Residues in contact with GLN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ARG* 6.0 1.4 - - - +
43C TRP* 2.8 66.7 + - + +
44C LEU 4.5 1.9 + - - -
45C THR 3.8 0.6 - - - -
46C GLU* 1.3 94.6 + - - +
48C ARG* 1.3 75.0 + - + +
38D SER* 5.2 4.1 + - - +
41D ARG* 5.4 5.4 - - - +
42D ARG* 3.0 43.9 + - - +
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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