Contacts of the helix formed by residues 124 - 134 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ALA 3.3 0.4 + - - -
121B GLU* 3.2 10.8 + - - -
122B GLU 3.2 5.1 + - - -
123B ARG* 1.3 79.0 - - - +
125B ILE* 1.3 62.7 + - - +
126B ARG 3.4 2.5 - - - -
127B GLN* 3.5 27.1 + - - +
128B PHE* 3.1 23.8 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 3.1 38.5 + - + +
123B ARG* 4.5 8.3 - - + +
124B GLY* 1.3 73.8 - - - +
126B ARG* 1.3 60.2 + - - +
128B PHE* 3.2 4.8 + - + +
129B VAL* 2.9 45.5 + - + +
360B PHE* 5.2 0.9 - - + -
371B LEU* 4.0 21.1 - - + -
551B LEU* 5.3 2.0 - - + -
552B VAL* 4.0 22.0 - - + +
555B ALA* 3.5 31.9 - - + -
556B ILE* 4.0 20.2 - - + +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA 4.8 0.6 + - - -
124B GLY 3.4 0.2 - - - -
125B ILE* 1.3 78.9 - - - +
127B GLN* 1.3 99.2 + - - +
129B VAL* 3.4 6.8 + - - +
130B GLN* 3.2 39.3 + - + +
361B ALA 5.9 2.5 - - - +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU* 4.9 4.4 + - - +
124B GLY* 3.5 28.2 - - - +
125B ILE 3.3 0.2 - - - -
126B ARG* 1.3 114.3 + - - +
128B PHE* 1.3 60.5 + - - +
130B GLN* 3.5 8.1 + - - +
131B SER* 3.0 31.3 + - - +
134B ARG* 4.9 0.9 + - - -
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG 5.6 0.9 - - - +
124B GLY 3.1 17.5 + - - +
125B ILE* 3.5 8.3 - - + +
127B GLN* 1.3 73.4 - - - +
129B VAL* 1.3 60.4 + - - +
131B SER* 3.2 7.9 + - - -
132B VAL* 2.9 50.2 + - + +
138B VAL* 4.1 21.3 - - + -
419B ARG* 3.7 41.3 - - - -
551B LEU* 3.7 31.4 - - + -
555B ALA* 3.7 26.5 - - + -
559B ILE 5.7 4.0 - - - -
562B TYR* 4.7 11.7 - + - -
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ILE* 2.9 28.7 + - + +
126B ARG* 3.6 7.9 - - - +
128B PHE* 1.3 75.7 - - - +
130B GLN* 1.3 61.0 + - - +
132B VAL* 3.2 7.6 + - - +
133B PHE* 2.9 49.9 + - + -
360B PHE* 3.6 46.0 - - + +
361B ALA* 4.4 18.2 - - + -
551B LEU* 4.0 11.9 - - + -
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ARG* 3.2 28.8 + - + +
127B GLN* 3.8 8.1 - - - +
129B VAL* 1.3 78.9 - - - +
131B SER* 1.3 56.7 - - - +
133B PHE* 3.5 7.9 + - - +
134B ARG* 3.0 56.4 + - - +
361B ALA* 3.7 34.8 + - - +
362B ASN* 5.0 2.6 + - - -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLN* 3.0 15.9 + - - +
128B PHE* 3.4 12.7 - - - -
129B VAL 3.2 0.2 - - - -
130B GLN* 1.3 73.5 - - - +
132B VAL* 1.3 61.9 + - - +
134B ARG* 3.6 12.8 + - - +
135B GLY 3.4 3.1 + - - -
136B GLU* 3.0 57.7 + - - +
138B VAL* 4.1 12.6 - - - -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE* 2.9 45.0 + - + +
129B VAL* 3.2 7.6 + - - +
131B SER* 1.3 75.7 - - - +
133B PHE* 1.3 70.9 + - + +
135B GLY* 3.2 12.5 + - - -
136B GLU 4.5 1.4 + - - +
138B VAL* 3.9 22.2 - - + -
146B VAL* 3.4 33.2 + - + +
147B LEU* 3.4 12.8 - - - +
148B HIS* 5.5 3.1 - - + -
149B ILE* 5.6 3.8 - - + -
551B LEU* 4.2 20.9 - - + -
562B TYR* 5.2 1.6 - - - +
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B VAL* 2.9 36.7 + - + +
130B GLN* 3.9 10.1 - - - +
132B VAL* 1.3 89.6 - - + +
134B ARG* 1.3 59.0 + - - +
135B GLY 3.3 0.6 + - - -
147B LEU* 3.9 0.3 - - - +
149B ILE* 3.8 50.9 - - + +
159B ILE* 3.7 18.2 - - - +
357B ASP* 3.6 37.0 - - + -
358B GLU* 5.2 5.6 - - - -
360B PHE* 4.1 8.3 - + - -
361B ALA* 4.0 14.4 - - + -
548B HIS* 4.0 19.7 - + - -
551B LEU* 5.0 2.0 - - + -
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLN 4.9 0.6 + - - -
130B GLN* 3.0 44.5 + - - +
131B SER* 3.6 24.5 + - - +
133B PHE* 1.3 75.1 - - - +
135B GLY* 1.3 58.0 + - - +
136B GLU* 2.7 42.9 + - + -
159B ILE* 4.2 10.1 - - - +
160B TYR* 3.6 17.0 + - - +
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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