Contacts of the strand formed by residues 134 - 141 (chain B) in PDB entry 3OMA
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 VAL 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA* 3.6 4.8 - - - +
133B ASP* 1.3 87.7 - - + +
135B THR* 1.3 67.1 + - - +
136B VAL* 4.1 20.2 - - + -
149B TYR* 4.4 6.5 - - + -
151B ASP* 5.3 1.6 - - - -
200B VAL* 4.8 4.7 - - + -
201B PRO* 3.8 30.7 - - + -
204B LYS* 5.0 0.9 - - + -
205B THR 3.1 3.4 + - - -
206B VAL* 3.5 19.0 - - + +
207B VAL 2.9 26.0 + - - -
275B TYR* 3.6 26.9 - - + +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 3.5 21.3 - - - +
134B VAL* 1.3 72.0 - - - +
136B VAL* 1.3 69.7 + - - +
149B TYR* 3.7 9.9 - - - +
150B PRO* 3.3 36.2 - - + +
151B ASP* 4.6 17.9 + - - +
207B VAL* 3.4 10.0 - - + +
209B GLN* 3.5 33.7 - - - +
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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
----------------------------------------------------------
134B VAL* 4.1 10.3 - - + -
135B THR* 1.3 82.8 - - - +
137B LYS* 1.3 64.7 - - - +
138B VAL* 4.0 5.2 - - + -
147B TYR* 3.8 29.4 - - + -
148B GLU 3.4 9.4 - - - +
149B TYR* 3.7 35.0 - - + -
198B MET* 4.0 23.6 - - + -
200B VAL* 4.9 0.9 - - + -
206B VAL* 4.4 4.7 - - + -
207B VAL 3.0 5.9 + - - -
208B VAL* 3.2 11.1 - - + +
209B GLN* 2.8 25.6 + - - +
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR 4.3 0.2 - - - -
136B VAL* 1.3 72.4 - - - +
138B VAL* 1.3 62.0 + - - +
139B THR* 3.9 17.4 + - - +
146B GLY 3.7 1.0 - - - +
147B TYR* 3.5 3.5 - - - -
148B GLU* 2.8 71.2 + - + +
150B PRO* 4.4 8.9 - - + +
209B GLN* 3.3 27.8 - - + +
211B THR* 4.2 11.7 - - - +
235B LEU* 4.1 23.8 - - + -
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 4.0 4.9 - - + -
137B LYS* 1.3 74.9 - - - +
139B THR* 1.3 66.6 + - - +
145B TRP* 3.6 15.9 - - + -
146B GLY 3.3 5.6 - - - +
147B TYR* 3.7 30.7 - - + -
208B VAL* 3.3 29.8 - - + -
209B GLN 2.7 12.9 + - - +
210B VAL* 3.5 6.0 - - + +
211B THR* 3.0 26.2 + - - +
219B TRP* 3.5 33.9 - - + +
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Residues in contact with THR 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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137B LYS* 3.9 13.7 + - - +
138B VAL* 1.3 76.4 + - - +
140B GLY* 1.3 60.6 + - - +
141B TYR* 3.4 37.3 + - + +
145B TRP* 3.5 6.7 - - - -
146B GLY 2.8 39.6 + - - -
148B GLU* 4.1 9.2 + - - -
211B THR* 3.3 24.1 - - + +
213B ALA* 3.7 21.3 - - + +
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Residues in contact with GLY 140 (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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139B THR* 1.3 71.5 - - - +
141B TYR* 1.3 59.5 + - - -
144B TYR 3.9 0.4 - - - -
145B TRP* 3.5 26.5 - - - -
211B THR 2.9 14.0 + - - -
213B ALA* 2.9 29.6 + - - +
214B ASP* 3.9 0.2 - - - +
217B HIS* 3.4 20.7 + - - -
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Residues in contact with TYR 141 (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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139B THR* 3.4 41.1 + - + +
140B GLY* 1.3 72.3 - - - -
142B GLN* 1.3 60.5 + - - +
143B TRP* 3.1 2.1 - - - -
144B TYR* 2.9 80.6 + + + +
146B GLY* 4.0 11.3 - - - -
148B GLU* 5.7 0.9 + - - -
157B GLU* 5.5 1.6 - - + -
213B ALA* 3.5 24.5 - - + -
214B ASP* 3.5 9.2 - - - +
217B HIS* 3.1 17.5 - - - -
263B MET* 3.4 1.9 - - - +
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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