Contacts of the helix formed by residues 124 - 135 (chain C) in PDB entry 2O2C
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 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C ALA 3.4 0.4 + - - -
121C GLU 3.2 10.8 + - - -
122C GLU 3.2 5.5 + - - -
123C ARG* 1.3 80.4 - - - +
125C ILE* 1.3 64.7 + - - +
127C GLN* 3.2 26.2 - - - +
128C PHE* 3.1 23.1 + - - +
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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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120C ALA* 3.1 36.7 + - + +
123C ARG* 4.4 7.9 - - + +
124C GLY* 1.3 73.7 - - - +
126C ARG* 1.3 66.6 + - - +
128C PHE* 3.1 5.1 + - - +
129C VAL* 2.9 43.1 + - + +
360C PHE* 5.1 1.8 - - + -
371C LEU* 4.1 11.2 - - + -
551C LEU* 5.3 1.3 - - + -
552C VAL* 4.1 29.6 - - + +
555C ALA* 3.6 31.4 - - + -
556C ILE* 4.1 19.3 - - + +
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Residues in contact with ARG 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 ALA 4.9 0.6 + - - -
121C GLU* 4.3 23.0 + - - +
124C GLY 3.4 0.4 - - - -
125C ILE* 1.3 78.5 - - - +
127C GLN* 1.3 90.4 + - - +
129C VAL* 3.5 6.8 + - - +
130C GLN* 3.2 36.3 + - + +
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Residues in contact with GLN 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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121C GLU* 4.6 11.4 + - - +
124C GLY* 3.2 29.6 - - - +
126C ARG* 1.3 104.6 + - - +
128C PHE* 1.3 65.6 + - - +
130C GLN* 3.4 7.7 + - - +
131C SER* 3.1 27.2 + - - +
134C ARG* 5.0 1.2 + - - -
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Residues in contact with PHE 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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123C ARG 5.7 0.7 - - - +
124C GLY 3.1 14.4 + - - +
125C ILE* 3.1 11.0 + - + +
127C GLN* 1.3 75.5 - - - +
129C VAL* 1.3 56.8 + - - +
131C SER* 3.2 8.2 + - - -
132C VAL* 3.0 45.0 + - + +
138C VAL* 4.0 27.6 - - + -
419C ARG* 3.5 41.3 - - - -
551C LEU* 3.7 32.1 - - + -
555C ALA* 3.8 27.8 - - + -
559C ILE 5.6 4.3 - - - -
562C TYR* 4.6 11.0 - + - -
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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
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125C ILE* 2.9 29.0 + - + +
126C ARG* 3.7 7.2 - - - +
128C PHE* 1.3 77.2 - - - +
130C GLN* 1.3 60.0 + - - +
132C VAL* 3.2 7.1 + - - +
133C PHE* 2.9 50.1 + - + -
360C PHE* 3.7 46.2 - - + +
361C ALA* 4.5 17.5 - - + -
551C LEU* 4.0 11.9 - - + -
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Residues in contact with GLN 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 ARG* 3.2 25.1 + - + +
127C GLN* 3.8 7.0 - - - +
128C PHE 3.4 0.2 - - - -
129C VAL* 1.3 79.9 - - - +
131C SER* 1.3 58.2 + - - +
133C PHE* 3.5 8.6 + - - +
134C ARG* 3.0 48.7 + - - +
361C ALA* 3.6 33.9 + - - +
362C ASN* 5.4 1.2 + - - -
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Residues in contact with SER 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 GLN 3.1 15.3 + - - -
128C PHE* 3.4 13.2 - - - -
129C VAL 3.2 0.2 - - - -
130C GLN* 1.3 74.6 - - - +
132C VAL* 1.3 61.4 + - - +
134C ARG* 3.4 18.3 + - - +
135C GLY 3.5 3.3 + - - -
136C GLU* 2.9 54.9 + - - +
138C VAL* 4.1 13.0 - - - -
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Residues in contact with VAL 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 PHE* 3.0 38.9 + - + +
129C VAL* 3.5 8.3 - - - +
131C SER* 1.3 74.6 - - - +
133C PHE* 1.3 70.1 + - + +
135C GLY* 3.3 12.0 + - - -
136C GLU 4.9 2.3 - - - +
138C VAL* 3.9 27.1 - - + -
146C VAL* 3.4 33.7 - - + +
147C LEU* 3.3 14.0 - - - +
148C HIS* 5.4 3.4 - - + -
149C ILE* 5.6 4.3 - - + -
551C LEU* 4.3 19.5 - - + -
562C TYR* 5.2 2.2 - - - +
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Residues in contact with PHE 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 VAL* 2.9 39.9 + - + +
130C GLN* 3.9 10.5 - - - +
132C VAL* 1.3 88.1 - - + +
134C ARG* 1.3 57.1 + - - +
135C GLY 3.7 0.2 + - - -
147C LEU* 3.8 4.9 - - - +
149C ILE* 3.7 54.9 - - + +
159C ILE* 3.9 12.1 - - - +
357C ASP* 3.5 37.9 - - + -
358C GLU* 5.0 6.7 - - - -
360C PHE* 4.2 8.3 - + - -
361C ALA* 3.8 16.2 - - + -
548C HIS* 4.1 19.1 - + - -
551C LEU* 5.0 1.6 - - + -
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Residues in contact with ARG 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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127C GLN 5.0 1.4 + - - -
130C GLN* 3.0 41.7 + - - +
131C SER* 3.4 24.1 + - - +
132C VAL 3.3 0.2 - - - -
133C PHE* 1.3 75.7 - - - +
135C GLY* 1.3 58.8 + - - +
136C GLU* 2.6 36.7 + - + -
159C ILE* 4.3 8.1 - - - +
160C TYR* 3.8 19.4 + - - +
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Residues in contact with GLY 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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132C VAL 3.3 8.1 + - - -
133C PHE 3.4 1.4 + - - -
134C ARG* 1.3 79.8 - - - +
136C GLU* 1.3 64.5 + - - +
137C ARG* 3.8 1.7 + - - +
145C PRO* 3.5 18.5 - - - +
147C LEU* 3.8 28.2 - - - +
160C TYR 4.2 10.9 - - - +
161C VAL* 5.1 0.5 - - - +
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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