Contacts of the helix formed by residues 123 - 135 (chain C) in PDB entry 2Y05
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 GLY 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C ALA 3.4 17.5 - - - -
120C GLY 3.1 7.8 + - - -
121C THR 3.3 0.8 + - - -
122C VAL* 1.3 79.0 - - - +
124C MET* 1.3 66.2 + - - -
126C GLY 3.0 2.4 + - - -
127C LEU* 3.0 28.5 + - - +
284C LEU* 3.9 4.8 - - - +
1331C EDO 3.4 8.5 - - - -
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Residues in contact with MET 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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47C ASP* 4.1 16.8 - - + +
49C TYR* 4.0 26.5 - - + -
66C GLN* 4.9 12.6 + - - +
118C ALA 4.5 2.4 + - - -
119C LEU* 4.7 1.2 - - - +
123C GLY* 1.3 70.0 - - - -
125C PRO* 1.3 78.0 - - + +
127C LEU* 3.3 11.6 + - - +
128C THR* 2.9 27.7 + - - -
272C VAL* 3.7 19.5 - - + +
273C TYR* 3.8 27.1 - - + +
701C NAP 3.6 32.1 - - + -
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Residues in contact with PRO 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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47C ASP* 4.5 6.1 - - - +
119C LEU 3.3 25.8 - - - +
120C GLY* 3.6 13.0 - - - +
124C MET* 1.3 104.2 - - + +
126C GLY* 1.3 62.6 + - - +
128C THR* 3.3 5.1 + - - +
129C ALA* 3.1 22.2 + - - +
153C ALA* 3.8 23.1 - - + +
154C VAL* 3.8 22.1 - - + +
324C LYS* 4.0 15.3 - - + -
701C NAP 4.7 4.7 - - - +
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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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120C GLY 3.0 12.1 + - - -
121C THR* 3.4 26.2 - - - -
123C GLY 3.0 0.8 + - - -
125C PRO* 1.3 76.5 - - - +
127C LEU* 1.3 57.7 + - - +
129C ALA* 3.4 2.8 + - - +
130C TYR* 3.0 27.7 + - - +
157C VAL* 4.3 13.2 - - - -
287C LEU* 3.7 12.3 - - - +
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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
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123C GLY 3.0 20.1 + - - +
124C MET* 3.7 6.5 - - - +
126C GLY* 1.3 74.3 - - - +
128C THR* 1.3 59.1 + - - +
130C TYR* 3.1 3.7 + - - +
131C PHE* 2.8 46.9 + - + +
272C VAL* 3.6 19.5 - - + -
275C TRP 5.9 0.2 - - - +
280C ARG* 4.0 33.2 - - + +
283C ALA* 3.5 32.1 - - + -
284C LEU* 3.8 32.1 - - + +
287C LEU* 3.9 6.2 - - + +
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Residues in contact with THR 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 MET* 2.9 16.2 + - - -
125C PRO 3.3 10.1 - - - -
127C LEU* 1.3 75.7 - - - +
129C ALA* 1.3 62.3 + - - +
131C PHE* 5.4 0.4 - - - -
132C GLY* 3.0 19.9 + - - -
154C VAL* 3.9 10.5 - - + -
215C PHE* 4.0 0.6 - - + -
239C CYS* 3.3 33.4 - - - -
270C PHE* 3.5 14.4 - - + -
272C VAL* 3.4 16.3 - - - +
701C NAP 3.1 33.4 - - + -
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Residues in contact with ALA 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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125C PRO 3.1 6.4 + - - +
126C GLY 3.6 8.1 - - - +
128C THR* 1.3 79.2 - - - +
130C TYR* 1.3 64.6 + - - +
133C LEU* 2.9 30.0 + - - +
154C VAL* 3.6 14.3 - - + +
157C VAL* 3.7 13.2 - - + -
158C VAL* 3.4 37.2 - - + +
161C ILE* 4.6 2.2 - - + -
215C PHE* 3.9 3.7 - - - -
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Residues in contact with TYR 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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126C GLY 3.0 18.4 + - - +
127C LEU* 3.5 7.6 - - - +
129C ALA* 1.3 76.9 - - - +
131C PHE* 1.3 80.2 + + - +
134C LEU* 2.9 56.0 + - + +
135C GLU* 5.9 1.1 - - + -
161C ILE* 4.1 11.4 - - + +
279C ALA 5.6 0.2 - - - -
282C LYS* 5.1 5.0 - - - +
283C ALA* 3.6 30.7 + - + -
286C ASP* 2.6 43.8 + - + -
287C LEU* 4.2 14.1 - - + -
290C TRP* 3.7 24.9 - + - -
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Residues in contact with PHE 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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127C LEU* 2.8 41.1 + - + +
128C THR* 4.6 1.6 - - - +
130C TYR* 1.3 89.0 - + - +
132C GLY* 1.3 58.9 + - - +
135C GLU* 2.9 43.9 + - + +
136C ILE* 3.0 14.7 + - - +
270C PHE* 5.3 0.7 - - + -
272C VAL* 5.0 3.1 - - + -
275C TRP* 3.4 76.1 - + + -
279C ALA* 3.6 27.6 - - + -
280C ARG* 4.6 3.1 - - + -
283C ALA* 3.7 19.5 - - + -
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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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128C THR 3.0 12.4 + - - -
131C PHE* 1.3 79.2 - - - +
133C LEU* 1.3 56.3 + - - +
136C ILE* 3.5 7.9 - - - +
137C CYS* 2.9 24.4 + - - +
215C PHE* 3.7 9.6 - - - -
237C ALA* 3.6 11.1 - - - +
270C PHE* 3.5 29.7 - - - -
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Residues in contact with LEU 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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129C ALA 2.9 17.3 + - - +
130C TYR* 4.3 0.9 - - - +
132C GLY* 1.3 77.7 - - - +
134C LEU* 1.3 61.7 + - + +
135C GLU 3.5 0.2 - - - -
137C CYS* 3.2 16.7 - - + +
138C GLY 2.8 24.4 + - - -
139C VAL* 3.4 39.6 + - + -
145C VAL* 4.3 15.5 - - + -
158C VAL* 3.3 40.8 - - + +
161C ILE* 4.0 15.3 - - + -
162C ALA* 3.4 23.8 - - + +
215C PHE* 3.7 7.5 - - + -
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Residues in contact with LEU 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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130C TYR* 2.9 60.8 + - + +
133C LEU* 1.3 82.0 - - + +
135C GLU* 1.3 62.3 + - + +
138C GLY* 3.4 15.6 - - - -
139C VAL* 3.9 25.9 - - + +
161C ILE* 3.8 28.9 - - + -
165C LYS* 4.0 20.4 - - + +
290C TRP* 4.5 6.5 - - + -
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Residues in contact with GLU 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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130C TYR* 5.9 0.8 - - + -
131C PHE* 2.9 35.9 + - + +
134C LEU* 1.3 84.5 - - + +
136C ILE* 1.3 66.7 + - + +
138C GLY* 3.9 7.1 + - - -
266C ARG* 4.7 2.8 + - - -
275C TRP* 3.1 34.8 + - + -
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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