Contacts of the helix formed by residues 116 - 129 (chain C) in PDB entry 5YWB
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 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLU* 6.0 2.0 - - - -
91C TRP* 4.0 8.8 - - - +
100C LEU* 4.6 2.9 - - - +
114C ILE* 4.6 2.6 - - - +
115C HIS* 1.3 83.3 + - - +
117C PHE* 1.3 75.1 + - - +
118C SER* 3.2 12.9 + - - -
119C SER* 3.5 6.6 + - - -
120C ALA* 3.1 21.1 + - - +
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 4.8 20.0 - - + -
87C ALA* 4.3 9.2 - - + -
88C MET* 4.0 36.8 - - + -
91C TRP* 3.4 45.7 - + + +
116C SER* 1.3 83.7 + - - +
118C SER* 1.3 57.9 + - - +
120C ALA* 3.3 1.5 + - + +
121C PHE* 2.9 33.9 + + + +
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 4.0 26.0 + - - -
143A PRO* 5.7 5.7 - - - +
146A ILE* 5.2 11.6 - - - +
116C SER* 3.2 7.9 + - - -
117C PHE* 1.3 80.8 - - - +
119C SER* 1.3 57.8 + - - +
121C PHE* 3.3 7.3 + - - +
122C LEU* 2.9 27.4 + - - +
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 3.5 21.7 - - - +
113C SER 3.8 6.4 + - - -
114C ILE* 3.4 19.7 - - - +
115C HIS* 4.2 13.9 - - - -
116C SER 3.5 8.9 + - - -
117C PHE 3.4 0.2 - - - -
118C SER* 1.3 80.3 - - - +
120C ALA* 1.3 58.2 + - - +
122C LEU* 3.3 6.1 + - - +
123C PHE* 2.9 24.6 + - - +
136C ARG* 3.1 26.9 + - - -
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Residues in contact with ALA 120 (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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87C ALA* 4.5 6.2 - - - +
90C TRP* 4.9 5.6 - - + +
91C TRP* 3.9 37.2 - - + +
114C ILE* 3.5 16.3 - - + +
116C SER 3.1 14.7 + - - +
117C PHE* 3.5 8.3 - - + +
118C SER 3.2 0.2 - - - -
119C SER* 1.3 78.1 - - - +
121C PHE* 1.3 56.4 + - - +
123C PHE* 3.2 5.3 + - - +
124C SER* 2.9 27.0 + - - -
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Residues in contact with PHE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 4.2 23.6 - - + -
150A ILE* 3.8 33.4 - - + -
80C LEU* 6.5 1.1 - - + -
83C TRP* 4.4 12.6 - + + -
84C LEU* 3.6 40.2 - - + -
87C ALA* 3.5 27.5 - - + +
117C PHE* 2.9 26.1 + + + +
118C SER* 3.7 5.6 - - - +
120C ALA* 1.3 76.3 - - - +
122C LEU* 1.3 59.2 + - - +
124C SER* 3.2 1.8 + - - -
125C ILE* 2.9 31.7 + - + +
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Residues in contact with LEU 122 (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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138A VAL* 3.6 42.0 - - + +
139A THR 3.9 11.4 - - - +
140A GLU* 4.5 3.4 - - - +
146A ILE* 3.5 31.4 - - + +
149A LEU* 4.9 6.3 - - + -
118C SER 2.9 13.3 + - - +
119C SER* 3.5 9.6 - - - +
120C ALA 3.2 0.2 - - - -
121C PHE* 1.3 79.4 - - - +
123C PHE* 1.3 56.2 + - - +
125C ILE* 3.2 16.8 - - + +
126C GLU* 2.9 31.0 + - + +
131C ILE* 6.1 0.4 - - + -
133C PHE* 4.6 9.2 - - + -
136C ARG* 3.4 24.0 - - - +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TRP* 3.4 51.8 - + - -
111C VAL* 3.6 26.9 - - + -
114C ILE* 4.6 4.5 - - + -
119C SER 2.9 16.9 + - - +
120C ALA* 3.2 7.4 + - - +
122C LEU* 1.3 76.7 - - - +
124C SER* 1.3 57.9 + - - +
126C GLU* 3.2 6.5 + - + +
127C VAL* 2.9 30.5 + - + +
136C ARG* 3.3 49.2 - - + +
138C VAL* 4.2 10.1 - - + -
149C LEU* 5.3 0.4 - - + -
133E PHE* 3.8 28.0 - + - -
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TRP* 3.3 24.5 + - - +
86C PHE* 3.9 5.0 - - - +
87C ALA* 3.4 25.4 + - - -
90C TRP* 4.8 3.8 - - - -
120C ALA 2.9 14.5 + - - -
121C PHE* 3.2 8.9 + - - -
123C PHE* 1.3 79.8 - - - +
125C ILE* 1.3 57.4 + - - +
127C VAL* 3.5 8.2 - - - +
128C GLN* 2.9 33.8 + - - +
152C GLN* 4.0 9.1 + - - +
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Residues in contact with ILE 125 (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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146A ILE* 6.3 1.1 - - + -
149A LEU* 4.1 25.6 - - + -
150A ILE* 3.7 17.5 - - + -
153A ASN* 4.5 6.7 - - + +
83C TRP* 3.5 54.7 - - + +
121C PHE* 2.9 24.0 + - + +
122C LEU* 3.2 26.0 - - + +
124C SER* 1.3 77.2 - - - +
126C GLU* 1.3 60.6 + - - +
128C GLN* 4.1 1.3 - - + -
129C VAL* 3.3 32.1 + - + +
131C ILE* 3.7 3.2 - - + +
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 2.9 23.8 + - + +
123C PHE* 3.2 11.8 + - + +
125C ILE* 1.3 79.0 - - - +
127C VAL* 1.3 59.2 + - - +
130C THR* 4.0 0.7 + - - -
131C ILE* 3.3 26.8 + - + -
132C GLY* 2.9 25.7 + - - -
133C PHE* 4.3 21.5 - - + +
134C GLY 5.8 0.4 - - - +
136C ARG* 5.2 3.4 - - + +
131E ILE* 5.3 0.3 - - - +
133E PHE* 5.6 4.3 - - + -
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TRP* 3.7 29.6 - - + -
123C PHE* 2.9 23.0 + - + +
124C SER 3.5 5.6 - - - +
126C GLU* 1.3 76.4 - - - +
128C GLN* 1.3 68.3 + - - +
130C THR 3.8 4.8 + - - -
149C LEU* 4.1 31.4 - - + -
152C GLN* 3.8 9.7 - - + +
153C ASN* 4.0 11.1 - - - +
131E ILE* 3.9 25.7 - - + +
133E PHE* 4.3 20.2 - - + -
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Residues in contact with GLN 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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79C PHE* 5.8 1.9 - - - -
82C SER* 4.9 5.4 + - - -
83C TRP* 3.3 39.5 + - + +
86C PHE* 5.0 1.4 - - - -
124C SER* 2.9 22.0 + - - +
125C ILE* 4.6 2.5 - - + -
127C VAL* 1.3 79.1 - - - +
129C VAL* 1.3 62.2 + - + +
130C THR* 3.0 18.1 + - - +
152C GLN* 2.5 53.0 + - - +
153C ASN* 4.5 4.9 - - - +
155C VAL* 5.1 0.6 - - - +
156C GLY* 3.3 26.4 - - - +
159C ILE* 4.7 5.2 - - - +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 4.4 10.1 - - + +
153A ASN* 3.4 39.5 - - + +
157A LEU* 4.3 25.1 - - + -
83C TRP* 4.8 11.2 - - + +
125C ILE* 3.3 29.2 + - + +
128C GLN* 1.3 79.6 - - + +
130C THR* 1.3 74.2 + - - +
131C ILE* 3.9 11.9 - - + -
160C ASN* 5.9 1.3 - - - +
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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