Contacts of the helix formed by residues 50 - 59 (chain C) in PDB entry 5W1F
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 GLY 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.8 0.9 - - - -
47C ARG 3.0 14.7 + - - -
48C LYS 3.3 1.3 - - - -
49C LYS* 1.3 79.0 - - - +
51C ALA* 1.3 60.2 + - - -
52C ASP 3.3 2.9 - - - -
53C VAL* 3.4 5.3 + - - -
54C TRP* 2.9 35.0 + - - -
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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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31C ARG* 5.3 4.4 - - + +
34C LEU* 4.2 3.2 - - + +
35C LYS* 4.0 43.5 - - + +
38C LEU* 3.7 17.0 - - + +
47C ARG 4.8 0.6 + - - -
50C GLY* 1.3 72.1 - - - -
52C ASP* 1.3 63.1 + - - +
54C TRP* 3.4 1.9 + - - +
55C PHE* 2.9 30.1 + - - +
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Residues in contact with ASP 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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31C ARG* 3.6 19.8 + - - +
50C GLY* 3.3 1.0 - - - -
51C ALA* 1.3 77.2 - - - +
53C VAL* 1.3 68.0 + - + +
55C PHE* 3.9 4.7 - - - +
56C LYS* 3.1 25.3 + - - +
31G ARG* 3.4 31.1 + - - +
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Residues in contact with VAL 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 LYS* 3.4 41.5 - - + +
50C GLY* 3.4 3.7 + - - +
51C ALA 3.3 0.2 - - - -
52C ASP* 1.3 80.7 - - + +
54C TRP* 1.3 61.1 + - - +
56C LYS* 4.1 4.0 - - - +
57C GLU* 3.3 39.0 + - + +
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Residues in contact with TRP 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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34C LEU* 4.2 4.5 - - + -
38C LEU* 3.8 27.1 - - + -
46C ILE* 2.8 57.0 + - + +
47C ARG* 5.3 0.4 - - - -
49C LYS* 3.2 43.2 - - + +
50C GLY 2.9 25.9 + - - +
51C ALA 3.7 3.6 - - - +
53C VAL* 1.3 77.9 - - - +
55C PHE* 1.3 57.0 + - - +
57C GLU* 3.2 9.8 + - + +
58C LEU* 2.8 49.8 + - + +
74C LEU* 3.6 26.0 - - + -
77C LYS* 3.9 33.7 - - + -
78C MET* 5.6 0.2 - - + -
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Residues in contact with PHE 55 (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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29C VAL 3.7 10.5 - - - -
30C TYR 3.6 7.0 - - - -
31C ARG* 3.4 77.8 - - + -
34C LEU* 3.6 21.3 - - + +
51C ALA 2.9 18.1 + - - +
52C ASP 3.9 3.4 - - - +
53C VAL 3.3 0.2 - - - -
54C TRP* 1.3 78.1 - - - +
56C LYS* 1.3 58.8 + - - +
58C LEU* 4.4 1.1 - - - +
59C ASP* 2.8 53.8 + - + +
64C GLY* 3.3 31.9 - - - -
65C ALA* 3.6 5.4 - - - -
66C VAL* 3.9 9.4 - - + -
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Residues in contact with LYS 56 (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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77A LYS* 5.5 3.6 + - - -
31C ARG* 5.6 4.5 - - - +
52C ASP 3.1 16.6 + - - +
53C VAL* 4.1 5.6 - - - +
55C PHE* 1.3 81.3 - - - +
57C GLU* 1.3 62.9 + - + +
59C ASP* 3.8 15.8 - - - +
62C THR* 5.8 0.7 - - - +
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Residues in contact with GLU 57 (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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77A LYS* 5.0 5.8 + - - +
49C LYS* 3.4 26.7 + - - +
53C VAL* 3.3 32.8 + - + +
54C TRP* 3.2 12.6 + - + +
56C LYS* 1.3 80.8 - - + +
58C LEU* 1.3 65.6 + - + +
60C ILE* 3.4 19.1 - - - +
73C ILE* 5.4 2.0 - - - +
77C LYS* 5.3 6.1 - - - -
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Residues in contact with LEU 58 (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* 3.9 32.3 - - + -
54C TRP* 2.8 37.7 + - + +
55C PHE 4.0 0.7 - - - +
57C GLU* 1.3 74.0 - - + +
59C ASP* 1.3 58.7 + - - +
60C ILE* 2.8 14.5 + - - +
66C VAL* 3.8 25.4 - - + -
70C GLU* 3.2 40.7 - - - +
71C PHE* 5.4 0.4 - - - -
73C ILE* 3.9 22.2 - - + -
74C LEU* 3.9 29.6 - - + +
77C LYS* 5.8 0.2 - - + -
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Residues in contact with ASP 59 (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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77A LYS* 5.2 2.1 - - - -
55C PHE* 2.8 37.7 + - + +
56C LYS* 3.8 12.5 - - - +
57C GLU 3.5 0.6 - - - -
58C LEU* 1.3 69.6 - - - +
60C ILE* 1.3 64.8 + - - +
62C THR* 3.2 31.3 + - + +
63C ASP* 2.9 6.3 - - - +
64C GLY* 3.1 22.7 + - - -
65C ALA 3.6 12.3 - - - +
66C VAL* 4.5 0.8 - - - +
70C GLU* 3.7 4.3 - - - -
103C CA 2.5 28.1 - - - -
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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