Contacts of the strand formed by residues 292 - 301 (chain B) in PDB entry 5U2H
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 ASN 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B GLY 4.6 5.3 - - - +
291B TYR* 1.3 81.9 - - - +
293B PHE* 1.3 67.5 + - - +
311B LYS* 5.6 3.8 - - - +
312B VAL 2.9 19.3 - - - +
313B PHE* 3.4 37.4 - - + -
405B ATP 3.4 39.7 + - - -
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Residues in contact with PHE 293 (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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95B PHE* 5.8 3.8 - - + -
103B PHE* 3.5 43.3 - + - -
291B TYR* 3.5 35.9 - + - -
292B ASN* 1.3 76.4 - - - +
294B ARG* 1.3 69.8 + - - +
295B TYR* 4.7 9.4 - + + -
311B LYS* 4.8 1.6 - - - -
312B VAL* 2.9 48.2 + - + +
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Residues in contact with ARG 294 (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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171B GLU* 6.0 2.2 - - - +
293B PHE* 1.3 79.5 - - - +
295B TYR* 1.3 62.6 + - - +
309B LEU* 4.3 18.2 - - + -
310B ILE 3.6 6.1 - - - +
311B LYS* 4.7 3.6 - - + +
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Residues in contact with TYR 295 (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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293B PHE* 4.7 10.5 - + + -
294B ARG* 1.3 76.2 - - - +
296B ALA* 1.3 77.0 + - - +
297B LYS* 5.0 7.4 - - + +
308B THR 3.9 0.3 - - - +
309B LEU* 4.6 1.6 - - - -
310B ILE* 2.9 46.7 + - + +
312B VAL* 4.5 15.7 - - + -
404B 7S1 6.5 0.9 - - + -
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Residues in contact with ALA 296 (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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295B TYR* 1.3 96.2 - - - +
297B LYS* 1.3 61.4 + - - +
298B TYR* 4.3 31.0 - - + +
307B ARG* 5.0 3.4 - - + -
308B THR 3.0 16.8 - - - +
309B LEU* 4.2 14.6 - - + -
404B 7S1 5.4 3.9 - - + +
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Residues in contact with LYS 297 (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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295B TYR* 5.0 8.3 - - + -
296B ALA* 1.3 74.3 - - - +
298B TYR* 1.3 65.3 + - - +
299B TYR* 3.8 7.0 - - + -
307B ARG* 3.6 0.5 - - - -
308B THR* 2.9 40.7 + - + +
310B ILE* 6.3 2.2 - - + -
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Residues in contact with TYR 298 (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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167B TRP* 4.6 10.8 - + - -
296B ALA* 4.4 21.0 - - + +
297B LYS* 1.3 75.8 - - - +
299B TYR* 1.3 63.0 + - - +
305B GLU* 4.5 18.4 - - + +
306B LYS 3.4 10.1 - - - +
307B ARG* 3.6 24.9 - - + -
404B 7S1 3.3 84.5 + + + +
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Residues in contact with TYR 299 (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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112B GLU* 4.6 2.9 - - - +
113B GLY* 3.4 29.0 + - - -
297B LYS* 3.8 12.1 - - + -
298B TYR* 1.3 73.8 - - - +
300B LYS* 1.3 66.8 - - - +
301B GLU* 4.5 11.7 - - + -
305B GLU* 5.2 2.9 - - - -
306B LYS* 2.9 48.0 + - + +
307B ARG 4.5 1.3 - - - -
308B THR* 2.9 28.6 + - - -
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Residues in contact with LYS 300 (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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299B TYR* 1.3 75.5 - - - +
301B GLU* 1.3 61.1 + - - +
303B ASN* 5.3 2.7 - - - -
304B VAL 3.3 14.6 - - - +
305B GLU* 4.4 13.9 - - - +
306B LYS 4.5 0.4 - - - +
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Residues in contact with GLU 301 (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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299B TYR* 4.1 18.8 + - + -
300B LYS* 1.3 74.8 - - - +
302B ASN* 1.3 74.1 + - + +
303B ASN 3.2 0.9 - - - -
304B VAL* 2.9 26.4 + - - +
306B LYS* 5.2 2.7 - - + +
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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