Contacts of the helix formed by residues 117 - 129 (chain C) in PDB entry 4R0C
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 ALA 117 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C SER* 3.3 9.0 - - - +
114C SER* 3.1 14.2 + - - +
116C GLY* 1.3 75.8 - - - +
118C LEU* 1.3 53.0 + - - +
119C VAL 3.6 1.1 - - - -
120C PHE* 3.2 15.3 + - + +
121C THR* 2.6 49.7 + - - +
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Residues in contact with LEU 118 (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 VAL* 3.6 33.4 - - + +
113C SER* 3.2 12.3 - - - +
114C SER 3.1 8.4 + - - +
115C GLY* 3.3 8.0 + - - +
116C GLY 3.3 0.4 - - - -
117C ALA* 1.3 73.8 - - - +
119C VAL* 1.3 67.4 + - - +
121C THR* 3.8 0.2 - - - -
122C VAL* 3.0 27.5 + - + +
147C VAL* 3.7 23.6 - - + +
148C PHE* 3.4 33.9 - - + -
151C ALA* 5.0 4.3 - - + -
153C ARG* 3.3 32.5 - - - +
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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
----------------------------------------------------------
115C GLY 4.8 1.0 + - - -
116C GLY 5.0 2.3 + - - +
117C ALA 3.6 0.2 - - - -
118C LEU* 1.3 76.0 - - - +
120C PHE* 1.3 65.6 + - - +
122C VAL 3.5 0.3 + - - -
123C ALA* 3.2 16.8 + - - +
148C PHE* 3.8 18.6 - - + -
153C ARG* 4.3 4.5 - - - +
161C THR* 3.7 13.1 - - + +
221C THR* 3.7 35.9 - - + +
224C THR* 3.6 35.0 - - + -
225C ARG* 4.8 4.9 - - + +
229C GLU* 3.6 17.9 - - - +
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Residues in contact with PHE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLY 5.4 1.7 + - - +
117C ALA* 3.2 18.9 + - + +
119C VAL* 1.3 79.0 - - - +
121C THR* 1.3 72.5 + - - +
123C ALA* 3.0 6.1 + - - +
124C PHE* 2.9 36.1 + + + +
214C PHE* 5.7 10.8 - + - -
217C THR* 3.3 31.0 - - + +
218C GLY* 5.1 4.0 - - - -
221C THR* 3.3 24.8 + - + +
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Residues in contact with THR 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 3.4 45.3 - - + +
110C VAL* 3.9 4.0 - - - +
113C SER* 3.4 18.8 + - - -
117C ALA* 2.6 34.3 + - - +
118C LEU 3.9 2.2 - - - -
120C PHE* 1.3 79.9 - - - +
122C VAL* 1.3 57.4 + - - +
124C PHE* 3.5 5.9 + - + +
125C ALA* 3.0 26.9 + - - +
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C VAL* 3.5 39.3 - - + -
118C LEU* 3.0 27.1 + - + +
119C VAL* 4.0 3.8 - - - +
121C THR* 1.3 76.1 - - - +
123C ALA* 1.3 53.9 + - - +
125C ALA* 3.4 2.8 + - - +
126C GLY* 2.8 30.7 + - - -
140C LEU* 4.8 4.2 - - + +
144C ALA* 3.9 25.8 - - + -
148C PHE* 4.4 9.0 - - + -
158C GLY 4.3 0.4 - - - +
161C THR* 3.6 20.4 - - + -
162C ALA* 3.9 15.4 - - + +
165C ALA* 4.7 0.3 - - - +
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Residues in contact with ALA 123 (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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119C VAL 3.2 10.7 + - - +
120C PHE 3.0 8.1 + - - +
122C VAL* 1.3 76.4 - - - +
124C PHE* 1.3 65.2 + - - +
127C VAL* 3.1 24.3 + - - +
161C THR* 4.1 3.4 - - + -
165C ALA* 3.1 18.4 - - + +
217C THR* 3.9 20.6 - - - +
220C VAL* 3.8 28.7 - - + -
221C THR* 4.4 1.8 - - - +
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Residues in contact with PHE 124 (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 LEU* 4.2 11.9 - - + -
120C PHE* 2.9 27.6 + + + +
121C THR* 3.8 8.7 - - + +
123C ALA* 1.3 73.8 - - - +
125C ALA* 1.3 64.2 + - - +
126C GLY 2.9 5.1 + - - -
127C VAL* 3.0 13.3 + - - +
128C LEU* 3.0 45.0 + - + +
174C LEU* 3.8 27.1 - - + -
213C THR* 4.1 15.7 - - + -
214C PHE* 5.0 11.7 - + - -
217C THR* 3.6 24.3 + - + +
802C BOG 4.1 24.0 - - + -
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Residues in contact with ALA 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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106C LEU* 3.8 19.6 - - + +
109C LEU* 4.0 22.9 - - + -
110C VAL* 4.3 9.0 - - + -
121C THR 3.0 15.9 + - - +
122C VAL 3.7 4.0 - - - +
124C PHE* 1.3 79.2 - - - +
126C GLY* 1.3 60.3 + - - +
128C LEU* 3.4 7.8 + - - +
129C SER* 3.2 16.5 + - - -
140C LEU* 3.2 23.9 - - + +
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Residues in contact with GLY 126 (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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122C VAL 2.8 17.4 + - - -
123C ALA 3.6 2.9 - - - -
124C PHE 2.9 0.8 - - - -
125C ALA* 1.3 75.3 - - - +
127C VAL* 1.3 61.4 + - - +
129C SER* 2.7 21.7 + - - -
130C SER* 4.5 0.7 + - - -
140C LEU* 3.7 2.9 - - - +
162C ALA* 4.9 1.3 - - - -
165C ALA* 3.1 18.7 - - - +
166C VAL* 3.3 24.7 - - - +
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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
----------------------------------------------------------
123C ALA 3.1 14.1 + - - +
124C PHE 3.0 10.7 + - - +
126C GLY* 1.3 74.2 - - - +
128C LEU* 1.3 68.8 + - + +
129C SER 3.2 0.2 + - - -
130C SER* 2.8 27.0 + - - -
165C ALA* 3.4 12.3 - - + +
169C GLY 4.1 10.1 - - - +
172C ALA* 3.4 10.2 - - + +
173C ASN* 3.2 5.1 + - - -
213C THR* 3.5 35.7 - - + +
216C VAL* 3.5 34.3 - - + -
217C THR* 3.9 9.0 - - - +
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.2 8.1 - - + -
109C LEU* 4.6 7.4 - - + -
124C PHE* 3.0 52.3 + - + +
125C ALA* 3.8 8.7 - - - +
126C GLY 3.2 0.2 - - - -
127C VAL* 1.3 86.0 - - + +
129C SER* 1.3 58.4 + - - +
130C SER 3.0 6.2 + - - -
131C LEU* 3.3 16.8 + - + +
173C ASN* 3.2 26.6 + - - +
174C LEU* 4.2 28.9 - - + +
213C THR* 5.0 0.7 - - + -
802C BOG 4.2 19.1 - - + -
803C LMT 4.3 16.5 - - + +
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.5 30.1 - - - -
125C ALA 3.2 8.8 + - - -
126C GLY 2.7 20.1 + - - -
127C VAL 3.1 0.4 - - - -
128C LEU* 1.3 73.5 - - - +
130C SER* 1.3 55.9 + - - +
131C LEU 3.1 6.3 - - - -
132C THR* 2.8 35.9 + - - +
136C GLY* 3.6 19.3 + - - -
140C LEU* 4.0 1.6 - - - -
166C VAL* 3.4 18.9 - - - +
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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