Contacts of the helix formed by residues 46 - 54 (chain C) in PDB entry 6I3N
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 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LEU* 3.6 15.5 - - - +
39C VAL 3.3 23.1 - - - +
40C ARG* 3.4 21.0 + - - +
41C THR* 3.3 29.5 + - + +
44C ALA 3.5 1.4 + - - -
45C ALA* 1.3 77.2 - - - +
47C TRP* 1.3 66.6 + - + +
48C THR* 2.7 15.7 + - - +
49C ALA* 3.3 8.5 + - - +
50C LEU* 3.5 6.9 + - - +
96C LEU* 4.7 0.9 - - - +
98C ARG* 4.1 5.2 - - - +
31F ARG* 2.5 30.6 + - - -
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Residues in contact with TRP 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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37C LEU* 2.8 40.4 + - + +
38C ASN* 3.5 20.8 + - + +
40C ARG* 3.9 15.4 - - + +
46C ASP* 1.3 80.2 + - + +
48C THR* 1.3 69.0 + - + +
49C ALA 3.4 0.2 - - - -
50C LEU* 3.4 4.7 + - + +
51C ALA* 2.9 24.8 + - + +
61C ILE* 3.5 37.2 - - + -
64C LEU* 3.9 19.5 - - + -
65C GLU* 3.5 31.4 - - + -
70C PRO* 3.5 32.3 - - + +
71C THR* 3.6 17.3 - - + +
74C LEU* 3.6 21.9 - - + +
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Residues in contact with THR 48 (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 ARG* 3.4 30.2 + - - +
46C ASP* 2.7 6.8 + - - +
47C TRP* 1.3 96.7 - - + +
49C ALA* 1.3 60.0 + - - +
51C ALA* 3.6 5.3 - - - +
52C GLU* 2.9 27.9 + - - +
61C ILE* 3.8 19.6 - - + +
65C GLU* 4.3 2.7 - - - +
27F MET* 4.1 19.0 - - + +
31F ARG* 2.6 34.0 + - - -
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Residues in contact with ALA 49 (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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45C ALA* 3.8 27.1 - - + -
46C ASP* 3.3 9.9 + - - +
48C THR* 1.3 80.3 + - - +
50C LEU* 1.3 58.3 + - - +
52C GLU* 3.3 11.6 + - - +
53C GLU* 3.0 31.7 + - - +
96C LEU* 3.9 11.8 - - + +
27F MET* 5.8 0.4 - - - -
31F ARG* 4.3 12.0 - - - +
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Residues in contact with LEU 50 (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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33C LEU* 6.5 0.4 - - + -
37C LEU* 4.5 13.9 - - + -
46C ASP 3.5 4.8 + - - +
47C TRP* 3.4 11.6 + - - +
48C THR 3.3 0.4 - - - -
49C ALA* 1.3 80.0 - - - +
51C ALA* 1.3 60.6 + - - +
53C GLU* 3.2 6.0 + - + +
54C MET* 3.1 49.4 + - + +
71C THR* 5.6 4.3 - - + -
74C LEU* 4.5 8.7 - - + -
75C LEU* 5.5 4.3 - - + -
89C LEU* 4.4 14.6 - - + -
92C LEU* 4.1 25.4 - - + -
93C LEU* 4.1 24.9 - - + -
96C LEU* 3.7 24.5 - - + +
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Residues in contact with ALA 51 (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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47C TRP* 2.9 23.5 + - + +
48C THR* 3.6 8.1 - - - +
49C ALA 3.3 0.2 - - - -
50C LEU* 1.3 76.3 - - - +
52C GLU* 1.3 61.9 + - - +
54C MET* 3.4 12.4 + - - +
56C PHE* 3.2 31.3 + - + +
61C ILE* 3.7 23.1 - - + -
64C LEU* 5.4 0.2 - - + -
74C LEU* 3.7 21.1 - - + -
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Residues in contact with GLU 52 (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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48C THR 2.9 16.6 + - - +
49C ALA* 3.6 8.5 - - - +
51C ALA* 1.3 76.4 - - - +
53C GLU* 1.3 66.2 + - + +
55C ASP* 3.2 17.2 + - - +
56C PHE 4.4 5.9 + - - +
61C ILE* 4.0 11.1 - - + +
26F ASN* 2.5 41.3 + - + +
27F MET* 3.6 7.7 - - + +
28F ARG* 3.0 41.4 + - - +
112F ASP* 5.0 0.2 - - - +
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Residues in contact with GLU 53 (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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49C ALA 3.0 18.5 + - - +
50C LEU* 3.2 12.3 + - + +
52C GLU* 1.3 79.7 - - - +
54C MET* 1.3 57.3 + - - +
55C ASP* 3.3 8.0 + - - +
88C ARG* 4.6 7.6 + - - -
92C LEU* 4.0 28.1 - - + +
95C LYS* 3.4 30.2 + - + +
96C LEU* 3.7 23.3 - - + +
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Residues in contact with MET 54 (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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50C LEU* 3.1 34.2 + - + +
51C ALA* 3.4 0.4 + - - -
52C GLU 3.1 1.2 - - - -
53C GLU* 1.3 76.5 - - - +
55C ASP* 1.3 68.9 + - - +
56C PHE* 3.3 21.0 + - + -
74C LEU* 3.6 42.0 - - + -
75C LEU* 5.5 2.7 - - + -
78C TRP* 3.4 53.7 + - + +
81C ARG* 3.8 10.2 + - - -
88C ARG* 6.0 1.1 - - - +
89C LEU* 4.9 4.0 - - - -
92C LEU* 3.7 22.0 - - + -
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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