Contacts of the helix formed by residues 52 - 57 (chain C) in PDB entry 5LSW
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 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.0 26.2 - - + -
26C ILE* 4.2 5.6 - - + -
42C LEU* 4.1 24.5 - - + +
45C LYS* 4.6 3.6 - - + +
46C ARG* 4.0 27.8 - - + +
49C VAL* 3.2 25.8 + - + +
50C PRO 3.3 1.4 - - - -
51C ASP* 1.3 77.5 - - - +
53C ALA* 1.3 58.9 + - - +
55C MET* 3.2 9.3 + - + +
56C LEU* 2.9 49.6 + - + +
96C LEU* 4.1 14.6 - - + -
99C CYS* 4.0 15.7 - - - -
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Residues in contact with ALA 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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50C PRO 4.9 0.2 + - - -
51C ASP* 4.4 0.2 - - - +
52C LEU* 1.3 78.5 - - - +
54C PRO* 1.3 64.7 - - + +
56C LEU* 3.1 4.3 + - - +
57C TRP* 2.8 28.1 + - - +
99C CYS* 3.4 38.7 - - - +
100C VAL* 3.7 17.9 - - - +
103C HIS* 3.5 19.4 - - + -
106C THR* 3.8 5.5 - - - +
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Residues in contact with PRO 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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51C ASP* 3.1 31.9 - - + +
53C ALA* 1.3 89.9 - - + +
55C MET* 1.3 59.8 + - + +
57C TRP 4.3 0.2 - - - +
58C HIS* 3.0 38.3 + - + +
103C HIS* 3.8 20.9 - - + +
105C GLU* 3.5 36.8 - - - +
106C THR* 3.7 12.8 - - + -
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Residues in contact with MET 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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19C ARG* 4.2 14.4 - - + -
22C ILE* 3.8 25.4 - - + -
23C TYR* 3.5 57.2 - - + +
26C ILE* 3.8 16.3 - - + +
49C VAL* 4.2 9.0 - - - -
51C ASP* 3.1 42.0 - - + +
52C LEU* 3.2 12.9 + - - +
54C PRO* 1.3 78.4 - - + +
56C LEU* 1.3 62.5 + - - +
58C HIS* 4.3 1.1 - - - -
59C SER* 3.4 21.3 + - - -
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Residues in contact with LEU 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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26C ILE* 3.8 26.5 - - + -
29C LEU* 4.2 10.8 - - + -
42C LEU* 4.6 2.0 - - + -
52C LEU* 2.9 37.6 + - + +
53C ALA 3.5 4.5 - - - +
55C MET* 1.3 75.5 - - - +
57C TRP* 1.3 67.2 + - - +
59C SER 3.2 10.4 + - - +
62C THR* 3.5 37.3 - - + -
63C ILE* 4.1 6.9 - - + +
66C LEU* 5.0 2.7 - - + -
96C LEU* 4.0 42.4 - - + +
99C CYS* 4.4 3.8 - - - -
100C VAL* 4.1 11.9 - - + -
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Residues in contact with TRP 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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53C ALA 2.8 20.3 + - - +
54C PRO* 4.1 1.6 - - + +
56C LEU* 1.3 74.3 - - - +
58C HIS* 1.3 78.3 + + + +
59C SER 3.3 8.0 + - - +
63C ILE* 3.5 37.5 - - + +
97C LEU* 6.3 0.2 - - + -
100C VAL* 3.5 28.0 - - + +
105C GLU 6.0 0.4 - - - -
106C THR* 3.6 21.1 - - + -
109C ALA* 3.5 46.1 - - + +
110C PHE* 3.8 4.3 - - - -
113C ALA* 4.4 8.5 - - + -
115C ILE* 3.6 31.6 - - + -
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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