Contacts of the strand formed by residues 128 - 137 (chain C) in PDB entry 3F5O
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 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 4.0 41.5 - - + +
108B LYS* 5.6 2.8 - - + +
91C MET* 3.8 34.4 - - + +
92C SER* 2.9 25.0 + - - -
119C ASP* 3.7 28.9 - - + +
120C LEU 3.6 15.0 - - - +
121C THR* 4.0 7.8 - - + +
126C GLY 3.5 2.8 + - - -
127C LYS* 1.3 74.2 - - - +
129C ILE* 1.3 55.2 + - - +
130C ALA 3.7 11.7 - - - +
131C GLN* 4.8 5.4 - - + +
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Residues in contact with ILE 129 (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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55C LEU* 4.8 4.3 - - + -
60C THR* 5.5 1.6 - - - +
90C TYR* 3.7 3.3 - - + -
91C MET* 2.8 26.8 + - - -
92C SER* 3.2 31.4 + - - +
93C PRO 4.8 1.8 - - - +
94C ALA* 3.8 18.4 - - + +
98C GLU* 3.5 24.5 - - - +
100C ILE* 3.5 26.0 - - + -
120C LEU* 2.8 26.2 + - + +
121C THR* 3.6 16.8 - - - +
122C ASN* 3.9 8.7 - - + +
127C LYS 4.1 0.9 - - - +
128C LEU* 1.3 73.0 - - - +
130C ALA* 1.3 66.2 + - + +
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Residues in contact with ALA 130 (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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60C THR* 3.9 28.0 - - + -
88C ILE* 4.3 6.3 - - + -
89C THR 3.1 15.9 - - - +
90C TYR* 4.4 5.6 - - + -
91C MET* 3.8 6.3 - - - -
118C VAL 4.1 0.2 - - - +
119C ASP* 3.6 2.3 - - - -
120C LEU* 2.9 33.2 + - + +
128C LEU* 3.7 3.5 - - - +
129C ILE* 1.3 89.0 - - + +
131C GLN* 1.3 60.7 - - - +
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Residues in contact with GLN 131 (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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105B HIS* 5.6 1.2 + - - -
107B LEU* 3.9 23.0 - - - +
117B SER* 4.2 10.3 + - - -
131B GLN* 5.2 7.2 - - - +
133B ARG* 2.8 43.3 - - - +
64C VAL* 5.3 0.9 - - - -
88C ILE* 3.4 4.2 - - - -
89C THR 2.8 32.3 + - - -
91C MET* 3.6 14.3 - - + +
117C SER* 4.4 9.4 + - - +
118C VAL 3.3 5.6 - - - +
119C ASP* 3.0 29.5 - - - +
128C LEU* 4.8 3.2 - - + +
130C ALA* 1.3 74.8 - - - +
132C GLY* 1.3 64.7 + - - +
133C ARG* 5.4 0.6 - - - +
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Residues in contact with GLY 132 (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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133B ARG* 3.4 7.6 + - - -
64C VAL* 4.2 19.9 - - - +
87C ASN 3.0 13.7 - - - -
88C ILE* 4.1 2.5 - - - -
117C SER* 3.4 9.5 + - - -
118C VAL 2.8 32.9 + - - -
131C GLN* 1.3 73.7 - - - +
133C ARG* 1.3 58.3 + - - +
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Residues in contact with ARG 133 (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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87B ASN* 2.8 29.7 + - - -
88B ILE 4.1 1.2 - - - +
89B THR* 2.8 51.2 + - + +
131B GLN* 2.8 44.0 + - - +
132B GLY* 3.3 9.1 + - - +
133B ARG* 3.3 32.7 - - - +
64C VAL* 4.7 0.2 - - - +
85C ASP 4.6 0.2 - - - -
86C MET* 3.3 4.4 - - - +
87C ASN* 3.0 53.1 + - - +
107C LEU* 4.0 11.9 - - + -
115C PHE* 5.9 0.7 - - + -
116C THR 3.2 19.7 - - - +
117C SER* 4.5 0.4 - - - -
131C GLN* 5.4 0.4 - - - +
132C GLY* 1.3 73.6 - - - +
134C HIS* 1.3 64.0 + - - +
135C THR* 5.9 0.7 - - - +
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Residues in contact with HIS 134 (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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64C VAL* 4.5 6.1 - - + -
65C ASP* 3.2 30.1 + - - -
68C SER* 2.7 26.1 + - - +
83C SER* 2.7 27.9 + - - -
85C ASP 3.4 13.2 - - - -
86C MET* 4.1 20.1 - - + -
114C ALA 3.9 0.7 - - - +
115C PHE* 3.7 1.2 - - - -
116C THR* 2.9 45.9 + - - +
118C VAL* 5.8 0.4 - - + -
133C ARG* 1.3 78.6 - - - +
135C THR* 1.3 68.3 + - - +
136C LYS* 3.5 26.5 + - + +
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Residues in contact with THR 135 (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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84A VAL* 4.0 9.9 - - + -
85A ASP* 2.7 33.7 + - - +
89B THR* 4.0 2.3 + - - +
84C VAL* 2.9 31.1 + - + -
85C ASP 2.8 18.2 + - - +
113C LEU* 4.1 15.9 - - + -
114C ALA 3.4 6.7 - - - +
115C PHE* 3.3 32.4 - - + +
133C ARG* 5.7 1.0 - - - +
134C HIS* 1.3 77.2 - - - +
136C LYS* 1.3 65.8 + - - +
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Residues in contact with LYS 136 (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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65C ASP* 4.7 0.6 + - - -
69C THR* 2.8 27.1 + - - +
72C LEU* 3.6 21.8 - - + -
80C PRO 2.8 28.6 + - - +
81C GLY* 3.2 3.9 + - - -
82C VAL 3.2 10.5 - - - +
83C SER* 3.6 14.6 + - - +
84C VAL* 4.1 3.8 - - - +
113C LEU* 3.3 8.6 - - - +
114C ALA* 2.9 34.4 + - + +
116C THR* 5.6 0.7 - - + +
134C HIS* 3.5 34.3 - - + +
135C THR* 1.3 77.9 - - - +
137C HIS* 1.3 59.9 + - - +
138C LEU* 4.7 3.1 - - + -
149C UOC 2.9 29.1 + - - +
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Residues in contact with HIS 137 (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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112A THR* 3.7 14.3 + - + -
113A LEU* 4.1 8.7 - - + +
81C GLY* 3.1 3.1 - - - -
82C VAL* 2.8 39.5 + - + +
84C VAL* 3.5 22.1 - - + +
112C THR* 3.3 22.8 + - + -
113C LEU* 4.2 2.3 - - - +
136C LYS* 1.3 72.3 - - - +
138C LEU* 1.3 76.2 + - - +
139C GLY 4.0 1.9 + - - -
150C COA 2.5 76.1 + - + -
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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