Contacts of the helix formed by residues 108 - 117 (chain C) in PDB entry 5U07
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 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C THR* 5.6 2.3 - - - +
106C ARG* 3.7 4.2 + - - -
107C LEU* 1.3 77.8 - - - +
109C PRO* 1.3 70.4 - - + +
110C GLU* 3.8 14.7 - - - +
111C ALA* 3.1 34.2 + - - +
112C VAL* 3.7 9.3 + - - +
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Residues in contact with PRO 109 (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 ILE* 3.5 41.3 - - + -
106C ARG* 4.4 5.6 - - + +
107C LEU 3.6 7.9 - - - +
108C ASP* 1.3 82.9 - - - +
110C GLU* 1.3 69.3 + - - +
112C VAL* 2.9 24.8 + - + +
113C ASP* 2.9 20.4 + - - +
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Residues in contact with GLU 110 (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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108C ASP* 3.2 14.1 - - - +
109C PRO* 1.3 92.4 - - - +
111C ALA* 1.3 57.3 + - - +
113C ASP* 3.8 7.5 - - - +
114C ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 111 (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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79C ILE* 3.6 21.3 - - + +
80C THR* 5.4 4.0 - - + -
107C LEU* 5.8 0.7 - - + -
108C ASP* 3.1 31.9 + - - +
109C PRO 3.1 0.8 - - - -
110C GLU* 1.3 77.1 - - - +
112C VAL* 1.3 60.9 + - + +
114C ALA* 3.8 7.1 - - - +
115C TYR* 2.9 27.5 + - - +
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Residues in contact with VAL 112 (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 ARG* 4.9 9.0 - - + +
48C LEU* 4.2 31.0 - - + +
49C ILE* 5.4 6.3 - - + +
79C ILE* 3.9 21.8 - - + -
106C ARG* 6.4 0.2 - - - +
107C LEU* 5.2 12.6 - - + +
108C ASP 4.2 8.5 - - - +
109C PRO* 2.9 15.4 + - + +
111C ALA* 1.3 76.1 - - - +
113C ASP* 1.3 65.4 + - - +
115C TYR* 3.2 1.9 + - - +
116C PHE* 2.9 53.3 + - + +
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Residues in contact with ASP 113 (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 ARG* 2.6 50.8 + - - +
49C ILE* 6.3 0.4 - - - -
109C PRO* 2.9 22.4 + - - +
110C GLU* 4.2 6.4 - - - +
112C VAL* 1.3 76.8 - - - +
114C ALA* 1.3 57.2 + - - +
116C PHE* 3.8 5.8 - - - +
117C ALA* 2.9 27.7 + - - +
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Residues in contact with ALA 114 (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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110C GLU 2.9 20.2 + - - +
111C ALA* 3.8 7.9 - - - +
112C VAL 3.1 0.2 - - - -
113C ASP* 1.3 77.2 - - - +
115C TYR* 1.3 62.9 + - - +
117C ALA* 3.4 18.4 + - - +
118C ASP* 4.0 5.5 + - - +
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Residues in contact with TYR 115 (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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75C ILE* 3.7 21.0 - - + -
78C ARG* 3.3 35.8 - - + +
79C ILE* 3.2 33.2 - - + -
111C ALA 2.9 18.3 + - - +
112C VAL 3.2 3.8 + - - +
114C ALA* 1.3 78.8 - - - +
116C PHE* 1.3 73.8 + + - +
118C ASP* 2.5 40.2 - - - +
119C TYR* 5.6 1.6 - + - -
249C TRP* 3.9 17.1 - + - -
250C GLU* 2.3 31.0 + - + -
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Residues in contact with PHE 116 (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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23C THR* 4.3 13.5 - - + -
44C LEU* 5.2 4.9 - - + -
45C ARG* 4.3 32.8 - - + -
48C LEU* 4.1 19.7 - - + -
75C ILE* 4.1 11.0 - - + -
112C VAL* 2.9 35.1 + - + +
113C ASP* 3.8 6.3 - - - +
115C TYR* 1.3 96.8 - + - +
117C ALA* 1.3 60.8 + - - +
118C ASP* 3.0 7.7 + - - -
119C TYR* 3.1 6.0 + - - +
120C SER* 3.1 26.3 + - - -
123C PHE* 3.5 36.1 - + + -
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Residues in contact with ALA 117 (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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113C ASP 2.9 19.6 + - - +
114C ALA* 3.4 14.6 - - - +
115C TYR 3.2 0.8 - - - -
116C PHE* 1.3 77.4 - - - +
118C ASP* 1.3 57.9 + - - +
120C SER* 3.3 17.1 + - - -
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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