Contacts of the strand formed by residues 133 - 137 (chain B) in PDB entry 1OJ7
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 MET 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.9 6.7 - - - -
89B LEU* 3.0 21.8 - - + +
91B ALA* 4.1 13.2 - - + -
98B LEU* 3.7 22.0 - - + +
101B THR* 3.7 23.3 - - + +
102B LYS* 3.6 35.4 - - + -
105B ALA* 4.7 4.5 - - + -
131B ILE 4.2 4.5 - - - +
132B PRO* 1.3 76.2 - - - +
134B GLY* 1.3 64.7 + - - +
135B CYS* 5.1 0.2 - - + -
168B VAL* 4.0 10.5 - - - +
169B GLN 4.9 1.9 + - - +
170B PRO* 4.1 22.7 - - + -
171B VAL* 2.8 31.4 + - - +
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Residues in contact with GLY 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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88B PHE* 3.6 4.6 - - - -
89B LEU 2.9 7.3 + - - +
90B LEU* 3.5 7.3 - - - -
91B ALA* 3.0 22.9 + - - +
133B MET* 1.3 81.0 - - - +
135B CYS* 1.3 63.1 + - - +
170B PRO* 4.6 1.3 - - - -
172B PHE* 3.3 32.1 - - - -
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Residues in contact with CYS 135 (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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90B LEU* 3.8 4.0 - - - +
91B ALA* 3.1 12.8 - - + +
98B LEU* 3.8 38.1 - - + -
133B MET* 5.1 2.0 - - + -
134B GLY* 1.3 76.0 - - - +
136B VAL* 1.3 64.9 + - - +
137B LEU 5.0 2.9 - - - -
145B GLU* 3.8 12.8 - - - -
170B PRO* 4.5 4.5 - - - -
172B PHE* 3.1 12.6 + - - -
173B ALA* 3.5 27.9 - - - -
174B VAL* 2.8 31.0 + - - +
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Residues in contact with VAL 136 (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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19B ILE* 5.0 2.7 - - + -
22B LEU* 4.7 7.2 - - + -
46B VAL* 4.6 4.3 - - + -
50B VAL* 4.2 19.7 - - + -
90B LEU* 4.3 15.5 - - + -
91B ALA 2.8 6.9 + - - +
92B VAL* 3.4 19.1 - - + -
93B GLY 3.1 25.6 + - - +
135B CYS* 1.3 78.3 - - - +
137B LEU* 1.3 60.5 + - - +
138B THR* 3.7 2.1 + - + +
174B VAL* 3.6 24.0 - - + +
179B TYR* 3.7 35.2 - - + -
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Residues in contact with LEU 137 (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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93B GLY 3.4 13.9 - - - +
94B GLY* 4.3 6.5 - - - -
95B GLY* 4.5 2.0 - - - +
98B LEU* 3.9 24.7 - - + -
135B CYS* 4.0 1.7 - - - -
136B VAL* 1.3 72.5 - - - +
138B THR* 1.3 60.7 + - - +
139B LEU 3.4 26.5 - - - +
140B PRO* 4.2 12.3 - - + -
141B ALA 5.5 0.2 - - - +
142B THR* 5.7 1.3 - - - +
145B GLU* 3.4 39.3 - - + +
174B VAL 3.2 16.4 + - - +
175B LEU* 4.4 11.0 - - + -
176B ASP 4.7 0.7 + - - +
179B TYR* 4.3 12.5 - - - +
245B MET* 3.8 29.4 - - + +
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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