Contacts of the strand formed by residues 277 - 282 (chain A) in PDB entry 4XDO
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 TYR 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A TRP* 3.8 16.2 - - + -
190A HIS* 3.3 37.2 - - - -
191A THR* 3.5 22.5 + - + +
212A ALA* 3.3 2.8 - - - +
213A ILE* 3.0 40.5 + - + -
218A GLY* 3.7 28.3 - - - -
221A LEU* 3.9 16.6 - - + -
222A GLU* 2.7 39.9 + - + +
240A LEU* 3.6 26.9 - - + +
275A TYR* 3.4 12.8 + + - -
276A GLY* 1.3 73.3 - - - +
278A HIS* 1.3 60.9 + - - +
306A LYS* 5.7 0.5 - - - -
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 5.9 0.7 - - - +
46A LEU* 5.1 1.1 - - + -
187A PHE* 4.1 2.9 - + - -
189A TRP* 3.5 5.3 - - - -
190A HIS* 2.9 60.4 + + - -
191A THR* 4.6 0.7 - - - -
192A GLU* 2.9 14.6 - - + -
210A TRP* 3.6 25.8 - + + -
211A TYR 3.1 16.4 - - - +
212A ALA* 4.5 5.2 - - + -
272A THR* 3.6 24.1 - - + +
276A GLY 3.0 20.6 + - - +
277A TYR* 1.3 75.5 - - - +
279A ALA* 1.3 61.0 + - - +
402A FE 2.1 31.8 - - - -
403A OGA 2.9 14.1 + - - -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE* 3.3 29.5 - - - +
188A ALA* 4.4 0.4 - - - -
189A TRP* 3.6 41.2 - - + +
210A TRP* 3.3 4.5 - - - +
211A TYR* 2.7 33.4 + - + +
278A HIS* 1.3 76.5 - - - +
280A GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TYR* 4.0 5.7 + - - -
186A THR* 3.6 3.6 - - - +
187A PHE* 3.0 36.9 + - - +
209A SER 3.1 11.7 - - - -
211A TYR* 4.1 13.2 - - - -
279A ALA* 1.3 81.8 - - - +
281A PHE* 1.3 66.7 + - - +
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Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR 5.5 1.1 - - - -
119A LEU* 4.8 1.8 - - + -
120A GLU* 3.8 28.9 - - + -
123A TYR* 3.4 56.8 - + + -
183A TRP* 4.2 9.6 - + - -
185A THR 3.3 7.4 - - - +
187A PHE* 3.6 3.4 - - - -
208A LYS* 3.5 3.9 - - - -
209A SER* 2.9 54.5 + - - -
211A TYR* 3.7 27.1 - + - -
280A GLY* 1.3 78.6 - - - +
282A ASN* 1.3 74.0 + - - +
283A HIS* 3.6 20.4 - + - -
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.2 29.5 + - - -
181A GLY* 4.1 0.4 - - - -
182A MET 3.5 7.9 - - - +
183A TRP* 3.5 4.5 - - - -
184A LYS 3.1 25.3 + - - -
185A THR* 2.8 36.3 + - - +
187A PHE* 5.2 2.4 - - - -
207A PRO 3.8 2.2 - - - -
208A LYS* 2.8 31.8 + - - +
281A PHE* 1.3 77.7 - - - +
283A HIS* 1.3 61.3 + - - +
284A GLY 4.0 4.9 - - - +
286A ASN* 2.9 25.4 + - - +
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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