Contacts of the helix formed by residues 41 - 48 (chain C) in PDB entry 5W4A
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 ASN 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C TYR* 2.9 36.1 + - + -
40C ALA* 1.3 73.7 - - - +
42C SER* 1.3 60.4 + - - +
43C PHE* 2.9 29.9 + - - +
44C ALA* 3.0 12.5 + - + +
45C ALA* 2.9 26.5 + - - +
59C ASP* 4.6 8.3 + - - +
62C GLN* 5.8 2.6 - - - +
63C ILE* 3.5 31.4 - - - +
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA 3.3 5.1 + - - -
41C ASN* 1.3 73.7 - - - +
43C PHE* 1.3 66.2 + - - +
45C ALA* 3.9 5.9 - - - +
46C TYR* 3.1 24.9 + - - +
51C SER* 5.7 0.2 - - - -
53C LYS* 3.5 35.5 - - - +
55C PRO* 3.7 8.0 - - - +
59C ASP* 2.6 35.6 + - - +
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Residues in contact with PHE 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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19C PHE* 3.9 24.2 - + - -
22C LEU* 3.9 15.3 - - + -
41C ASN* 2.9 9.7 + - - +
42C SER* 1.3 79.8 + - - +
44C ALA* 1.3 64.7 + - - +
46C TYR* 3.8 1.2 - - - +
47C VAL* 3.0 37.2 + - + +
55C PRO* 3.7 16.8 - - + -
59C ASP 4.4 8.7 - - - +
60C ILE* 3.9 22.2 - - + -
63C ILE* 3.8 26.9 - - + -
64C LEU* 3.9 24.0 - - + -
84C LEU* 6.3 0.2 - - + -
174C VAL* 4.0 1.6 - - + -
178C ILE* 3.5 34.8 - - + -
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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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22C LEU* 3.7 21.7 - - + +
25C TYR* 3.6 37.7 - - + -
26C ALA* 5.5 0.2 - - + -
33C LEU* 4.1 11.0 - - + -
41C ASN* 3.0 11.6 + - - +
43C PHE* 1.3 76.3 - - - +
45C ALA* 1.3 63.2 + - - +
47C VAL* 3.4 1.0 + - - -
48C PHE* 3.1 35.1 + - + +
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Residues in contact with ALA 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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33C LEU* 3.7 15.5 - - + +
37C PRO* 4.0 17.9 - - + +
41C ASN 2.9 18.4 + - - +
42C SER* 3.9 7.6 - - - +
43C PHE 3.3 0.2 - - - -
44C ALA* 1.3 76.6 - - - +
46C TYR* 1.3 61.4 + - - +
49C GLY 3.3 2.3 + - - -
50C ALA* 2.8 36.3 + - + -
51C SER* 3.2 21.6 + - - -
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Residues in contact with TYR 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 SER 3.1 17.7 + - - +
43C PHE 3.8 2.0 - - - +
45C ALA* 1.3 74.8 - - - +
47C VAL* 1.3 67.9 + - - +
49C GLY* 3.2 10.7 + - - -
51C SER* 3.5 17.3 - - - +
52C ASP* 3.7 22.0 - - - -
53C LYS 3.3 20.9 - - - +
54C LYS* 3.9 27.0 - - + +
55C PRO* 3.6 20.0 - - + -
177C LYS* 3.6 59.8 + - + -
178C ILE* 4.1 13.7 - - + -
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Residues in contact with VAL 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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22C LEU* 4.2 6.5 - - + -
43C PHE* 3.0 46.6 + - + +
44C ALA 3.4 3.6 + - - +
46C TYR* 1.3 76.3 - - - +
48C PHE* 1.3 79.4 + - + +
49C GLY 3.5 1.0 + - - -
170C PHE* 4.7 3.1 - - + -
173C TYR* 3.6 30.2 + - + -
174C VAL* 3.9 33.7 - - + -
177C LYS* 4.0 14.8 - - + +
178C ILE* 4.4 10.1 - - + -
197C PHE* 6.2 0.4 - - + -
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Residues in contact with PHE 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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14C ILE* 4.2 9.2 - - + -
22C LEU* 4.7 9.0 - - + -
26C ALA* 3.5 34.8 - - + -
33C LEU* 4.8 13.2 - - + -
44C ALA* 3.1 25.6 + - + +
45C ALA* 4.6 1.1 - - - +
47C VAL* 1.3 88.8 - - + +
49C GLY* 1.3 61.6 + - - +
50C ALA* 3.3 5.0 + - + +
170C PHE* 3.8 25.4 - + - -
197C PHE* 4.1 22.4 - + - -
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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