Contacts of the strand formed by residues 273 - 279 (chain A) in PDB entry 5JQ1
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 ARG 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A SER* 3.4 19.7 - - - +
169A ARG* 3.5 46.1 + - - +
170A SER 3.4 17.5 - - - +
171A GLY* 4.0 0.6 - - - +
204A ILE 5.5 2.2 + - - -
207A VAL* 3.9 30.1 - - + +
208A ASN 3.7 10.8 + - - +
209A THR* 3.2 12.9 - - + +
210A TRP* 2.8 22.3 + - - -
272A TYR* 1.3 79.7 - - - +
274A TRP* 1.3 59.6 + - - +
246B HIS 5.4 0.2 + - - -
247B GLY* 3.0 39.1 + - - +
248B LEU* 4.4 6.1 - - + +
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Residues in contact with TRP 274 (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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166A TRP* 3.5 25.8 - + - -
168A SER* 3.0 47.0 + - - +
170A SER* 3.2 33.2 - - - -
172A LYS* 3.7 43.5 - - + -
177A ALA* 3.6 15.8 + - + -
180A TYR* 3.5 30.1 - + + -
181A CYS* 3.7 21.7 - - - -
188A LEU* 3.8 17.7 - - + -
209A THR* 3.7 6.7 - - - +
210A TRP* 3.7 9.0 - - + -
272A TYR 3.8 9.0 - - - -
273A ARG* 1.3 75.8 - - - +
275A VAL* 1.3 70.8 + - - +
276A CYS* 3.5 19.0 - - - -
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Residues in contact with VAL 275 (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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165A TYR* 4.2 9.9 - - + -
166A TRP 3.3 11.9 - - - +
167A PHE* 3.6 38.6 - - + -
188A LEU* 3.4 10.0 - - - +
189A VAL* 2.9 48.5 + - + +
200A VAL* 4.3 9.2 - - + -
204A ILE* 3.9 5.8 - - + -
209A THR* 3.7 18.2 - - + -
210A TRP 3.6 4.8 + - - -
257A PHE* 4.8 0.2 - - + -
274A TRP* 1.3 84.4 - - - +
276A CYS* 1.3 68.3 + - - +
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Residues in contact with CYS 276 (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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157A TRP* 3.7 24.0 - - + -
165A TYR* 3.2 6.1 - - - -
166A TRP* 2.9 37.2 + - + +
180A TYR* 3.7 14.4 - - - -
181A CYS* 2.1 55.2 - - + -
184A GLU* 5.3 0.9 - - - -
186A ALA* 4.1 1.8 - - + -
187A HIS 3.5 0.4 - - - -
274A TRP* 3.5 16.6 - - - -
275A VAL* 1.3 75.6 - - - +
277A GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 277 (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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157A TRP* 4.3 0.4 - - - -
163A SER* 2.7 27.3 + - - +
164A CYS 3.2 8.3 - - - +
165A TYR* 3.6 16.4 - - + -
186A ALA* 3.4 4.4 - - - +
187A HIS* 2.8 47.3 + - + -
189A VAL* 3.7 11.0 - - - +
190A VAL 3.1 20.4 + - - +
196A GLU* 3.2 10.4 - - - +
276A CYS* 1.3 77.2 - - - +
278A THR* 1.3 62.9 + - - +
279A GLU* 3.6 12.6 - - - +
1003A CA 2.4 29.9 - - - -
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Residues in contact with THR 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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154A PRO* 5.2 7.0 - - + -
157A TRP* 4.1 12.3 - - + -
163A SER* 3.4 5.0 + - - -
164A CYS* 2.8 55.8 + - + +
184A GLU 5.8 1.3 - - - +
185A ASP 3.5 21.2 + - - -
186A ALA* 4.2 4.9 - - - -
187A HIS* 4.6 1.5 - - - -
277A GLU* 1.3 74.6 - - - +
279A GLU* 1.3 73.7 + - - +
280A LEU* 6.0 0.7 - - + -
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Residues in contact with GLU 279 (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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162A ARG 3.8 5.6 - - - +
163A SER* 3.8 10.1 - - - +
187A HIS* 2.8 38.3 + - - -
224A ASP* 4.9 6.7 - - - +
277A GLU* 3.6 15.6 - - - +
278A THR* 1.3 81.3 + - - +
280A LEU* 1.3 65.8 + - - +
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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