Contacts of the strand formed by residues 135 - 139 (chain B) in PDB entry 2OAT
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 LYS 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR 3.4 7.6 + - - -
49A LYS* 2.8 24.9 + - - +
50A TYR 3.3 11.0 - - - +
51A GLY 3.3 23.8 - - - +
53A HIS* 3.4 23.5 + - - -
128B THR* 3.5 4.9 - - - -
133B TYR* 3.3 1.5 - - - +
134B HIS* 1.3 85.5 + - + +
136B VAL* 1.4 62.9 + - - +
305B LEU* 3.5 8.1 - - - +
306B CYS 3.2 28.9 + - - +
308B ASP* 2.7 34.1 + - - +
311B MET* 3.4 23.3 - - + +
312B LEU* 3.9 18.2 - - + +
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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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50A TYR 3.1 6.5 + - - +
51A GLY* 3.5 2.3 - - - -
52A ALA 3.0 21.3 + - - -
123B TYR* 4.8 6.3 - - + +
124B GLU* 3.7 29.6 - - + +
127B ILE* 3.8 22.7 - - + -
128B THR* 4.0 1.6 - - + -
135B LYS* 1.4 77.9 - - - +
137B LEU* 1.3 67.8 + - - +
138B PRO* 3.9 5.2 - - + +
303B ALA* 3.7 28.3 - - + -
304B VAL 3.3 11.4 - - - +
305B LEU* 3.8 17.7 - - + -
311B MET* 3.6 2.7 - - - -
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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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52A ALA* 3.4 25.6 - - + -
54A ASN* 3.8 30.3 - - + +
136B VAL* 1.3 75.0 - - - +
138B PRO* 1.3 81.8 - - + +
139B MET* 3.7 18.9 + - + +
148B THR* 3.9 15.7 - - + -
152B LEU* 5.1 0.7 - - + -
303B ALA* 3.7 1.6 - - - -
304B VAL* 2.8 39.8 + - + +
311B MET* 3.9 15.3 - - + -
314B ILE* 5.0 11.9 - - + -
319B HIS* 4.1 14.1 - - + +
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Residues in contact with PRO 138 (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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52A ALA 5.4 1.6 - - - +
54A ASN* 5.2 3.6 - - - +
113B ARG* 3.8 20.4 + - - +
120B LEU* 4.3 13.7 - - + -
123B TYR* 4.8 13.0 - - + -
124B GLU* 4.4 7.6 - - - +
136B VAL* 3.9 10.7 - - + +
137B LEU* 1.3 90.8 - - + +
139B MET* 1.3 73.3 - - - +
301B VAL* 6.4 0.9 - - + -
302B SER 3.9 6.7 - - - +
303B ALA* 4.8 1.8 - - + -
321B SER* 5.1 0.2 - - - -
324B GLY* 3.8 8.6 - - - -
325B GLY* 3.7 31.4 - - - +
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Residues in contact with MET 139 (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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180A ARG* 5.6 1.8 - - + -
137B LEU* 3.7 16.0 + - + +
138B PRO* 1.3 86.5 - - - +
140B ASN* 1.3 65.0 + - - +
144B GLU* 3.8 32.8 - - + +
145B ALA* 4.5 2.5 - - - +
147B GLU* 6.4 0.4 - - + -
148B THR* 3.5 25.8 - - + +
301B VAL* 3.9 6.4 - - - +
302B SER* 3.0 38.0 + - - +
304B VAL* 5.0 0.9 - - + -
319B HIS* 3.7 19.5 - - + +
320B GLY* 3.7 20.0 - - - +
321B SER* 3.8 20.0 - - - -
324B GLY* 4.3 6.5 - - - -
325B GLY 4.9 1.2 + - - -
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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