Contacts of the helix formed by residues 104 - 115 (chain C) in PDB entry 5FLZ
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 SER 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C ALA 3.1 21.9 + - - +
102C GLY* 4.5 4.2 + - - -
103C ASN* 1.4 75.8 + - - +
105C TRP* 1.4 63.4 + - - +
106C ALA* 4.7 3.6 - - - -
107C ASN* 3.9 15.4 + - - -
108C GLY* 3.5 10.9 + - - -
145C GLY* 4.4 6.0 - - - +
148C SER* 6.1 0.4 - - - -
182C VAL* 6.0 1.7 - - - +
186C ASN* 3.9 6.4 + - - +
406C ASN* 3.8 22.0 + - - +
407C TYR* 4.9 1.6 + - - -
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Residues in contact with TRP 105 (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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104C SER* 1.4 68.0 - - - +
106C ALA* 1.4 65.3 + - - +
108C GLY* 3.3 2.6 + - - -
109C TYR* 2.9 74.3 + + + +
148C SER* 3.4 32.8 + - - +
149C GLY* 3.8 7.3 - - - +
152C SER* 2.9 24.9 + - - -
186C ASN* 3.3 22.1 - - - +
189C LEU* 3.7 37.3 - - + +
190C ALA 4.2 2.0 - - - -
193C ARG* 3.2 33.7 - - - -
407C TYR* 4.5 8.1 - + + -
412C LEU* 5.9 2.2 - - + -
413C PHE* 3.7 32.3 - + - -
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Residues in contact with ALA 106 (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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104C SER* 3.5 2.8 - - - -
105C TRP* 1.4 88.0 - - - +
107C ASN* 1.4 52.4 + - - +
109C TYR* 3.3 4.2 - - - +
110C ASP* 2.7 45.0 + - - +
406C ASN 5.2 2.7 - - - +
407C TYR* 4.2 22.4 - - + +
410C GLY* 5.7 4.7 - - - -
412C LEU* 5.6 1.9 - - + +
413C PHE* 4.2 19.7 - - + -
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Residues in contact with ASN 107 (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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99C ALA* 3.7 24.9 + - - +
100C SER 3.1 29.4 + - - +
101C ALA* 3.4 11.7 - - - +
104C SER* 3.9 15.7 + - - -
105C TRP 3.5 0.6 - - - -
106C ALA* 1.4 62.4 - - - +
108C GLY* 1.4 63.8 + - - +
110C ASP* 3.8 8.0 - - - +
111C ILE* 3.1 31.3 + - - +
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Residues in contact with GLY 108 (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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101C ALA* 4.1 20.9 - - - -
104C SER 3.5 5.8 + - - -
105C TRP 3.3 6.7 + - - -
107C ASN* 1.4 77.0 - - - +
109C TYR* 1.4 54.8 + - - +
111C ILE* 3.6 6.9 - - - +
112C GLY* 3.0 23.6 + - - -
145C GLY 4.2 2.0 - - - -
146C THR* 5.7 0.4 - - - -
149C GLY* 3.8 15.0 - - - -
150C LEU* 3.8 13.0 + - - +
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Residues in contact with TYR 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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105C TRP* 2.9 59.1 + + + +
106C ALA 3.3 5.6 - - - +
108C GLY* 1.4 71.4 - - - +
110C ASP* 1.4 59.5 + - - +
111C ILE 3.3 0.2 - - - -
112C GLY 3.0 13.5 + - - -
113C THR* 3.1 28.1 + - - -
116C GLN* 4.7 3.5 + - - -
149C GLY* 3.8 7.9 - - - +
152C SER* 4.4 0.9 - - - -
153C ASN* 3.1 40.9 + - - +
156C GLU* 3.2 27.7 + - - -
193C ARG* 4.6 2.2 - - - -
412C LEU* 4.1 29.8 - - + -
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Residues in contact with ASP 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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106C ALA* 2.7 35.4 + - - +
107C ASN* 3.8 7.9 + - - +
109C TYR* 1.4 69.2 - - - +
111C ILE* 1.4 67.3 + - + +
113C THR* 3.4 14.7 + - - -
114C ARG* 3.5 11.1 + - - +
410C GLY* 4.9 9.7 - - - -
411C ASP* 3.9 9.2 + - - +
412C LEU* 3.4 26.4 - - - +
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Residues in contact with ILE 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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95C ALA* 5.4 6.5 - - + -
96C SER* 5.2 2.2 - - - +
97C ASP* 3.6 26.7 - - + +
99C ALA 3.6 22.4 - - - +
100C SER* 3.8 13.7 - - - -
101C ALA* 3.9 8.1 - - + +
107C ASN 3.1 16.5 + - - +
108C GLY* 3.6 6.5 - - - +
110C ASP* 1.4 78.7 - - + +
112C GLY* 1.4 62.9 + - - +
114C ARG* 3.0 29.9 + - - +
115C ASN* 3.0 36.6 + - - +
150C LEU* 4.5 9.6 - - + -
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Residues in contact with GLY 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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108C GLY 3.0 7.3 + - - -
109C TYR 3.0 9.1 + - - -
111C ILE* 1.4 76.3 - - - +
113C THR* 1.4 60.0 - - - +
115C ASN* 3.4 5.5 - - - +
116C GLN* 3.1 26.3 + - - +
119C ILE* 4.8 1.6 - - - +
150C LEU* 3.5 22.2 - - - -
153C ASN* 3.5 21.8 - - - -
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Residues in contact with THR 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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109C TYR* 3.1 25.5 + - - -
110C ASP* 3.7 9.3 - - - -
111C ILE 3.2 0.4 - - - -
112C GLY* 1.4 77.5 - - - +
114C ARG* 1.4 59.1 + - - +
116C GLN* 3.3 29.3 + - + +
153C ASN* 3.3 13.2 + - - -
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Residues in contact with ARG 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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95C ALA* 4.6 4.0 - - - +
96C SER 3.3 24.5 + - - -
97C ASP* 3.3 22.7 + - - -
110C ASP 3.5 8.3 + - - +
111C ILE* 3.0 21.8 + - - +
113C THR* 1.4 76.4 - - - +
115C ASN* 1.4 96.9 + - - +
116C GLN 3.3 2.3 + - - -
117C ASP* 4.8 7.1 + - - +
118C ASP* 4.2 3.6 - - - +
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Residues in contact with ASN 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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69C MET* 6.3 0.7 - - + -
93C TRP* 3.7 26.8 - - + +
95C ALA* 4.7 5.5 - - - +
111C ILE* 3.0 28.8 + - - +
112C GLY* 3.4 6.9 - - - +
114C ARG* 1.4 117.3 + - - +
116C GLN* 1.4 61.3 + - - -
117C ASP 3.3 1.8 - - - -
118C ASP* 3.3 27.2 + - + +
119C ILE* 3.3 28.8 + - + +
150C LEU* 5.3 3.9 - - + +
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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