Contacts of the strand formed by residues 149 - 154 (chain B) in PDB entry 3OX4
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 PHE 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASP* 4.2 0.3 - - - +
105B LYS* 2.8 29.8 + - - +
147B THR* 3.2 7.7 - - - -
148B ARG* 1.3 115.2 - - - +
150B CYS* 1.3 61.5 + - - +
151B ILE* 4.7 10.5 - - + -
163B ILE 3.4 2.7 - - - +
164B VAL* 4.1 24.2 - - + -
168B VAL* 4.3 0.9 - - - -
254B PHE* 3.5 29.8 - + - -
255B ASN* 3.6 20.9 - - - -
258B SER* 4.7 13.9 - - - -
259B LEU* 5.7 1.3 - - + -
1385B NAD 3.0 39.6 - - - +
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Residues in contact with CYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASP* 3.4 30.7 - - - -
105B LYS* 4.0 11.9 - - + -
106B ALA* 3.8 13.5 - - - -
149B PHE* 1.3 75.9 - - - +
151B ILE* 1.3 60.3 + - - +
152B ILE* 3.8 25.0 + - - -
161B MET 3.5 2.3 - - - +
163B ILE* 2.8 60.9 + - + +
168B VAL* 4.4 6.5 - - + -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 3.5 22.3 - - - +
102B ASP* 2.8 21.8 + - - +
149B PHE* 4.7 9.6 - - + -
150B CYS* 1.3 78.1 - - - +
152B ILE* 1.3 61.9 + - - +
153B THR 4.4 0.2 + - - -
160B LYS* 4.0 41.0 + - + +
161B MET 3.3 7.9 - - - +
162B ALA* 3.4 31.6 - - + -
163B ILE 4.5 0.4 - - - +
164B VAL* 6.3 0.2 - - + -
267B HIS* 5.1 18.2 - - + +
1385B NAD 4.4 24.2 + - + +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 3.7 7.0 - - + +
73B THR 3.6 29.2 - - - +
74B VAL* 3.6 17.5 - - + +
77B VAL* 3.8 7.6 - - + -
102B ASP 4.7 4.7 - - - +
106B ALA* 3.0 35.9 - - + -
117B VAL* 3.2 29.2 - - + -
150B CYS* 3.8 15.9 + - - +
151B ILE* 1.3 79.1 - - - +
153B THR* 1.3 63.5 + - - +
160B LYS* 4.6 0.7 - - - -
161B MET* 2.7 44.2 + - - +
163B ILE* 4.4 2.2 - - + -
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 4.2 15.0 - - + +
72B PRO* 2.8 19.3 + - - +
73B THR* 3.1 9.8 - - + -
74B VAL* 3.0 24.5 + - - -
151B ILE 5.5 0.2 + - - -
152B ILE* 1.3 73.7 - - - +
154B ASP* 1.3 71.6 + - - +
155B GLU* 3.4 10.1 + - + +
158B HIS* 5.2 3.8 - - - +
159B VAL 3.7 12.1 - - - +
160B LYS* 3.6 31.0 + - + +
271B GLY* 5.5 8.5 - - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.0 18.7 - - + +
118B LYS* 5.6 3.6 - - - +
152B ILE 3.9 0.4 + - - -
153B THR* 1.3 71.7 - - - +
155B GLU* 1.3 53.1 + - - +
156B VAL* 3.1 17.2 + - - +
157B ARG* 3.1 55.1 + - + +
158B HIS* 2.7 32.2 + - - -
159B VAL* 2.7 25.0 + - + +
161B MET* 4.5 8.1 - - - +
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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