Contacts of the helix formed by residues 123 - 131 (chain B) in PDB entry 1OFY
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 ASP 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ASP* 6.5 0.7 - - + -
1303A GOL 3.9 14.4 - - - -
121B LYS* 3.3 38.4 + - + +
122B ARG* 1.3 78.2 + - - +
124B GLU* 1.3 60.1 + - + +
125B ALA* 4.0 12.6 - - - +
126B TRP* 3.0 20.3 + - - +
127B CYS* 3.0 24.9 + - - -
220B LYS* 4.6 8.5 + - - -
1296B HEC 4.8 3.9 - - - +
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Residues in contact with GLU 124 (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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121A LYS* 6.1 1.1 - - - -
220A LYS* 6.0 1.0 - - - +
232A SER 4.8 0.2 - - - +
233A PRO* 3.4 24.5 - - + +
234A LEU* 2.9 34.6 + - - +
1303A GOL 3.5 26.3 + - - +
123B ASP* 1.3 76.4 - - + +
125B ALA* 1.3 57.3 + - - +
127B CYS* 3.3 5.6 + - - +
128B ALA* 2.8 31.5 + - - +
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Residues in contact with ALA 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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123B ASP* 3.2 8.0 + - - +
124B GLU* 1.3 76.2 - - - +
126B TRP* 1.3 62.8 + - - +
128B ALA* 4.0 6.0 - - - +
129B THR* 2.8 26.5 + - - -
219B ASN* 3.3 16.7 + - - +
220B LYS* 3.9 29.8 - - + +
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Residues in contact with TRP 126 (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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98B VAL* 3.9 28.3 - - + -
122B ARG* 3.1 55.4 - - + +
123B ASP* 3.0 24.6 + - - +
125B ALA* 1.3 76.0 - - - +
127B CYS* 1.3 67.5 + - - +
129B THR* 3.1 21.3 + - - -
217B PHE* 3.5 26.0 - + - -
219B ASN* 4.8 2.0 - - - +
1296B HEC 3.1 42.2 + - + +
1297B HEC 3.6 64.9 - - + +
1302B GOL 4.2 11.4 - - - -
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Residues in contact with CYS 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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233A PRO* 4.1 13.5 - - + -
1303A GOL 3.4 21.5 - - - -
30B MET* 4.1 4.7 - - + -
123B ASP 3.0 14.1 + - - -
124B GLU 3.3 5.1 + - - +
126B TRP* 1.3 75.7 - - - +
128B ALA* 1.3 59.1 - - - +
130B CYS* 3.1 6.4 + - - +
131B HIS* 3.0 29.6 + - + -
1297B HEC 1.8 82.9 - - + -
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Residues in contact with ALA 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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233A PRO* 5.6 2.2 - - + +
124B GLU 2.8 18.2 + - - +
125B ALA* 4.0 7.4 - - - +
126B TRP 3.2 0.4 - - - -
127B CYS* 1.3 73.1 - - - +
129B THR* 1.3 66.2 + - - +
130B CYS 3.1 0.8 + - - -
131B HIS* 3.3 24.8 - - - +
132B ASN* 3.5 11.1 - - - +
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Residues in contact with THR 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 ALA 2.8 18.6 + - - -
126B TRP 3.3 10.0 + - - -
127B CYS 3.1 1.0 - - - -
128B ALA* 1.3 78.0 - - - +
130B CYS* 1.3 56.7 + - - +
132B ASN* 3.5 15.6 + - - +
216B ALA* 3.7 30.1 - - + +
217B PHE* 3.6 37.2 - - + -
219B ASN* 2.9 16.1 + - - -
1295B HEC 3.8 10.0 - - + +
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Residues in contact with CYS 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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33B VAL* 3.3 23.7 - - + +
127B CYS 3.1 2.8 + - - -
129B THR* 1.3 81.6 - - - +
131B HIS* 1.3 60.5 + - - +
132B ASN* 2.8 24.9 + - - +
217B PHE* 4.1 9.0 - - - -
1295B HEC 4.0 17.7 - - + -
1297B HEC 1.8 74.3 - - + -
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Residues in contact with HIS 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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233A PRO* 6.3 0.2 - - + -
30B MET* 3.4 28.1 - - + +
31B LYS* 2.9 48.6 + - + +
32B PRO 3.9 1.6 - - - -
33B VAL* 3.4 8.2 - - + +
127B CYS 3.0 25.2 + - - +
128B ALA* 3.3 18.1 - - - +
130B CYS* 1.3 70.6 - - - +
132B ASN* 1.3 57.3 + - - +
1297B HEC 1.9 89.9 + + + -
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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