Contacts of the helix formed by residues 34 - 47 (chain C) in PDB entry 3I5D
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 LEU 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C ASN* 1.3 63.9 + - - +
36C ARG* 3.1 4.4 - - - +
37C PHE* 2.9 31.9 + - + +
38C THR* 2.9 27.0 + - + +
356C CYS* 5.0 12.1 - - + -
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Residues in contact with ASN 35 (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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34C LEU* 1.3 78.4 - - - +
36C ARG* 1.3 59.5 + - - +
38C THR* 3.6 7.9 + - - -
39C GLN* 3.4 21.5 + - - +
353C ASN* 5.5 11.7 - - + +
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Residues in contact with ARG 36 (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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34C LEU* 3.1 1.4 - - - +
35C ASN* 1.3 77.6 - - - +
37C PHE* 1.3 61.7 + - - +
39C GLN* 4.0 7.4 + - - +
40C ALA* 3.4 20.3 + - - +
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Residues in contact with PHE 37 (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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34C LEU* 2.9 21.3 + - + +
36C ARG* 1.3 76.0 - - - +
38C THR* 1.3 77.5 + - + +
39C GLN 3.2 1.6 - - - -
40C ALA* 3.3 9.0 + - + +
41C LEU* 3.1 36.8 + - + +
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Residues in contact with THR 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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34C LEU* 2.9 17.1 + - + +
35C ASN* 3.6 12.2 + - - -
37C PHE* 1.3 86.0 - - + +
39C GLN* 1.3 59.3 + - - +
41C LEU* 3.0 14.7 + - + +
42C VAL* 2.9 34.4 + - - +
349C LEU* 4.9 4.3 + - - +
352C VAL* 4.5 21.3 - - + +
353C ASN* 4.6 13.5 + - - +
356C CYS* 4.5 20.0 - - + -
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Residues in contact with GLN 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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35C ASN 3.4 17.6 + - - +
36C ARG* 4.1 7.2 - - - +
37C PHE 3.2 0.4 - - - -
38C THR* 1.3 82.8 + - - +
40C ALA* 1.3 56.6 + - - +
42C VAL* 3.5 11.8 - - - +
43C ILE* 3.3 25.3 + - - +
349C LEU* 4.7 17.0 - - + +
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Residues in contact with ALA 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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36C ARG 3.4 15.2 + - - +
37C PHE* 3.3 9.7 + - + +
38C THR 3.2 0.2 - - - -
39C GLN* 1.3 77.9 - - - +
41C LEU* 1.3 59.7 + - - +
43C ILE* 3.2 22.1 - - + +
44C ALA* 3.4 13.5 - - - +
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Residues in contact with LEU 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* 3.1 29.4 + - + +
38C THR* 3.0 17.0 + - + +
40C ALA* 1.3 77.0 - - - +
42C VAL* 1.3 66.2 + - + +
44C ALA* 3.3 5.9 + - + +
45C TYR* 2.8 30.3 + - + +
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Residues in contact with VAL 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 THR 2.9 18.7 + - - +
39C GLN* 3.5 15.5 - - - +
41C LEU* 1.3 77.4 - - + +
43C ILE* 1.3 64.9 + - + +
45C TYR* 3.4 12.6 - - + +
46C VAL* 2.9 36.3 + - + +
345C GLY* 4.4 11.4 - - - +
348C LEU* 4.9 4.7 - - + +
349C LEU* 3.8 42.8 - - + +
352C VAL* 4.6 11.9 - - + -
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Residues in contact with ILE 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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39C GLN 3.3 15.0 - - - +
40C ALA* 3.2 22.9 - - + +
42C VAL* 1.3 83.3 - - + +
44C ALA* 1.3 62.0 + - + +
45C TYR 3.2 0.2 - - - -
46C VAL* 4.0 5.4 - - + -
47C ILE* 3.2 50.1 + - + +
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Residues in contact with ALA 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 ALA 3.4 15.3 - - - +
41C LEU* 3.3 8.6 + - + +
43C ILE* 1.3 81.2 - - + +
45C TYR* 1.3 58.4 + - - +
48C GLY* 3.2 26.7 - - - +
49C TYR* 3.4 4.3 + - - +
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Residues in contact with TYR 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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335A ILE* 4.3 6.2 + - + +
336A ILE* 4.4 10.4 + - - -
339A LEU* 3.0 40.7 - - + +
41C LEU* 2.8 20.3 + - + +
42C VAL* 3.1 14.3 + - + +
44C ALA* 1.3 78.6 - - - +
46C VAL* 1.3 80.0 + - + +
49C TYR* 2.8 50.9 - + + +
50C VAL* 3.1 12.6 + - + +
341C ASN* 6.2 0.2 - - - -
348C LEU* 6.4 1.6 - - + -
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Residues in contact with VAL 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 VAL* 2.9 20.3 + - + +
43C ILE* 3.7 11.4 - - + +
45C TYR* 1.3 96.5 - - + +
47C ILE* 1.3 83.7 + - + +
50C VAL* 3.0 33.5 + - + +
51C CYS* 3.0 15.0 + - - -
341C ASN* 4.7 13.5 - - - +
342C ILE* 5.6 13.0 - - + -
345C GLY* 4.2 24.9 - - - -
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Residues in contact with ILE 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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43C ILE* 3.2 34.6 + - + +
46C VAL* 1.3 86.8 - - + +
48C GLY* 1.3 62.5 + - - +
51C CYS* 3.5 15.5 - - + +
52C VAL* 3.5 19.6 - - + +
342C ILE* 6.2 6.1 - - + -
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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