Contacts of the helix formed by residues 115 - 139 (chain C) in PDB entry 2FBW
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 LYS 115 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ASN* 4.5 5.6 - - - +
114C PHE* 1.3 77.7 - - - +
116C LEU* 1.3 58.3 + - - +
117C SER* 4.0 11.7 - - - +
118C GLN* 2.7 56.5 + - + +
119C VAL* 2.8 11.1 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 4.9 5.6 - - + +
222B THR* 3.8 23.1 - - + +
223B ARG* 3.7 59.5 - - + +
230B ASN* 5.2 0.2 - - - +
114C PHE 3.4 3.4 + - - -
115C LYS* 1.3 69.8 - - - +
117C SER* 1.3 58.0 + - - +
119C VAL* 3.2 17.1 + - + +
120C GLU* 2.9 36.7 + - + +
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LYS* 4.0 14.6 - - - +
116C LEU* 1.3 78.0 - - - +
118C GLN* 1.3 63.7 + - - +
120C GLU* 3.4 6.0 + - - +
121C GLN* 2.9 49.5 + - - +
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLY* 3.2 30.7 + - - +
114C PHE 3.2 1.2 + - - -
115C LYS* 2.7 57.4 + - + +
117C SER* 1.3 79.5 + - - +
119C VAL* 1.3 59.0 + - - +
121C GLN* 4.3 11.0 - - - +
122C SER* 2.8 35.0 + - - -
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 4.1 25.8 - - + -
35C PRO* 3.8 28.5 - - + +
104C ARG* 3.2 27.2 + - - +
108C TRP* 4.1 16.8 - - + +
113C GLY 3.6 14.8 - - - +
114C PHE 4.0 11.0 - - - +
115C LYS 2.8 19.9 + - - +
116C LEU* 3.5 15.0 - - + +
118C GLN* 1.3 71.7 - - - +
120C GLU* 1.3 61.8 + - - +
122C SER* 3.3 5.3 + - - -
123C GLY* 3.3 7.6 + - - -
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ARG* 2.5 40.3 + - - +
33C SER* 5.2 0.2 - - - -
34C LEU* 4.1 13.8 + - - +
35C PRO* 3.5 18.4 - - + +
116C LEU* 2.9 23.7 + - + +
117C SER* 3.8 6.3 - - - +
119C VAL* 1.3 76.0 - - + +
121C GLN* 1.3 65.0 + - + +
123C GLY* 3.4 1.2 + - - -
124C VAL* 3.2 28.2 + - + +
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Residues in contact with GLN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER* 2.9 38.0 + - - +
118C GLN* 4.0 9.9 + - - +
120C GLU* 1.3 78.8 - - + +
122C SER* 1.3 64.0 + - - +
124C VAL* 3.2 7.6 + - - +
125C VAL* 3.0 28.6 + - + +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ARG* 2.9 33.6 + - - +
108C TRP* 4.6 4.0 + - - -
113C GLY 5.3 0.7 + - - -
118C GLN 2.8 23.6 + - - -
119C VAL* 3.3 7.1 + - - -
121C GLN* 1.3 72.9 - - - +
123C GLY* 1.3 56.5 + - - +
125C VAL* 3.3 9.3 + - - +
126C VAL* 2.9 33.5 + - - +
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Residues in contact with GLY 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.9 1.1 - - - -
38C MET* 3.3 35.0 - - - +
104C ARG* 3.4 15.9 - - - +
119C VAL 3.3 6.8 + - - -
120C GLU 3.9 2.9 - - - -
121C GLN 3.2 0.8 - - - -
122C SER* 1.3 82.6 + - - +
124C VAL* 1.3 61.7 + - - +
126C VAL 3.2 1.6 + - - -
127C LEU* 3.1 20.4 + - - +
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Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.9 19.5 - - + +
120C GLU* 3.2 16.0 + - - +
121C GLN* 3.7 8.7 - - - +
123C GLY* 1.3 74.2 - - - +
125C VAL* 1.3 63.6 + - + +
127C LEU* 3.1 11.6 + - + +
128C ILE* 3.0 40.1 + - + +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLN* 3.0 21.4 + - + +
122C SER* 3.3 11.0 + - - +
124C VAL* 1.3 79.2 - - + +
126C VAL* 1.3 58.3 + - + +
128C ILE* 3.2 10.7 + - + +
129C LEU* 2.9 50.6 + - + +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 3.8 17.9 - - + -
97C TYR* 4.3 6.5 - - + +
100C TRP* 3.9 24.4 - - + +
101C ASN* 3.7 25.1 - - + +
104C ARG* 3.6 22.7 - - + -
122C SER 2.9 17.8 + - - +
123C GLY 3.2 8.3 + - - +
125C VAL* 1.3 77.3 - - + +
127C LEU* 1.3 54.0 + - - +
129C LEU* 4.0 7.8 - - + +
130C THR* 2.6 43.3 + - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.3 31.2 - - + -
38C MET* 4.0 9.9 - - + -
93C PHE* 6.3 1.8 - - + -
97C TYR* 3.7 30.3 - - + -
123C GLY 3.1 18.1 + - - +
124C VAL* 3.1 11.4 + - + +
126C VAL* 1.3 73.7 - - - +
128C ILE* 1.3 66.8 + - + +
130C THR* 3.3 4.8 + - - -
131C LEU* 3.1 33.8 + - + +
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Residues in contact with ILE 128 (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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124C VAL* 3.0 32.0 + - + +
125C VAL* 3.8 10.8 - - + +
127C LEU* 1.3 75.8 - - + +
129C LEU* 1.3 61.2 + - + +
131C LEU* 3.2 8.7 + - + +
132C LEU* 2.9 50.9 + - + +
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C TRP* 3.3 51.3 + - + -
125C VAL* 2.9 40.2 + - + +
126C VAL* 4.0 5.6 - - + +
128C ILE* 1.3 77.2 - - + +
130C THR* 1.3 53.9 + - - +
132C LEU* 4.6 13.9 - - + -
133C SER* 2.7 36.4 + - - -
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Residues in contact with THR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C PHE* 3.6 30.1 - - + +
96C SER* 3.5 9.5 + - - +
97C TYR* 3.5 49.0 - - + +
100C TRP* 3.8 6.4 - - - -
126C VAL* 2.6 24.7 + - - +
127C LEU* 3.6 7.6 - - - -
128C ILE 3.1 0.2 - - - -
129C LEU* 1.3 75.2 - - - +
131C LEU* 1.3 64.1 + - - +
134C SER* 2.9 31.9 + - - -
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PHE* 4.2 15.6 - - + -
93C PHE* 3.5 28.5 - - + -
127C LEU* 3.1 21.2 + - + +
128C ILE* 3.8 5.6 - - - +
130C THR* 1.3 75.0 - - - +
132C LEU* 1.3 67.3 + - + +
134C SER* 3.9 1.4 - - - -
135C ALA* 2.9 27.6 + - - +
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ILE* 2.9 39.8 + - + +
129C LEU* 4.2 15.3 - - + +
131C LEU* 1.3 77.8 - - + +
133C SER* 1.3 57.9 + - - +
135C ALA* 3.3 4.4 + - - +
136C ALA* 2.9 30.4 + - - +
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Residues in contact with SER 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C SER* 2.7 24.6 + - - -
100C TRP* 3.0 18.3 + - - -
129C LEU 2.7 21.9 + - - -
132C LEU* 1.3 79.5 - - - +
134C SER* 1.3 52.8 + - - +
136C ALA* 3.3 5.5 + - - +
137C ILE* 2.8 52.6 + - - +
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Residues in contact with SER 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PHE* 3.8 23.6 - - - -
92C VAL* 3.8 20.6 - - - +
93C PHE* 3.4 17.3 - - - -
96C SER* 3.3 20.3 + - - -
130C THR 2.9 22.5 + - - -
131C LEU 4.0 0.4 - - - -
133C SER* 1.3 77.4 + - - +
135C ALA* 1.3 56.8 + - - +
137C ILE* 3.9 0.6 - - - -
138C ALA* 2.9 32.6 + - - +
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Residues in contact with ALA 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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85C TYR* 3.6 21.5 + - - +
89C PHE* 3.8 13.8 - - + -
131C LEU 2.9 19.7 + - - +
132C LEU* 3.7 4.7 - - - +
134C SER* 1.3 77.1 - - - +
136C ALA* 1.3 63.4 + - - +
138C ALA* 3.6 0.6 + - - +
139C ALA* 3.4 17.2 + - - +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 2.9 17.6 + - - +
133C SER* 3.7 6.7 - - - +
135C ALA* 1.3 78.0 - - - +
137C ILE* 1.3 64.4 + - + +
139C ALA* 3.2 14.8 + - - +
140C MET* 3.6 14.9 + - - +
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C VAL* 3.8 31.6 - - + -
96C SER* 5.7 2.0 - - - +
133C SER* 2.8 36.9 + - - +
134C SER 4.1 2.2 - - - +
136C ALA* 1.3 74.2 - - + +
138C ALA* 1.3 63.8 + - - +
140C MET* 3.1 27.6 + - - +
101D TRP* 3.0 37.2 + - + +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.3 33.6 - - + +
88C LYS* 3.2 33.1 + - - +
89C PHE* 3.7 30.7 - - + +
92C VAL* 4.8 0.6 - - + +
134C SER 2.9 19.2 + - - +
135C ALA 3.9 1.8 - - - +
137C ILE* 1.3 76.2 - - - +
139C ALA* 1.3 59.3 + - - +
140C MET* 3.6 0.9 - - - +
101D TRP* 4.7 0.7 - - - -
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.5 17.9 - - + -
135C ALA 3.4 7.5 + - - +
136C ALA* 3.2 10.2 + - - +
137C ILE 3.1 1.4 - - - -
138C ALA* 1.3 76.3 - - - +
140C MET* 1.3 64.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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