Contacts of the strand formed by residues 286 - 292 (chain A) in PDB entry 4MJV
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 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ILE* 3.7 4.2 - - - +
282A PRO* 3.2 6.2 - - - +
283A ASN 2.9 32.0 + - - +
284A ASP* 4.2 9.0 - - + +
285A GLY* 1.3 85.0 - - - +
287A VAL* 1.3 65.1 + - - +
288A GLU* 4.0 1.8 - - + -
304A VAL* 4.0 27.2 - - + +
305A ILE 3.2 13.2 - - - +
306A SER* 3.7 26.6 + - - +
308A PRO* 4.8 2.5 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A THR* 3.7 29.2 - - + +
233A ILE* 3.9 10.5 - - + -
238A TYR* 4.0 27.6 - - + +
280A CYS* 3.6 28.5 - - + -
281A TYR 3.4 5.8 - - - +
286A LYS* 1.3 76.7 - - - +
288A GLU* 1.3 60.9 + - - +
289A CYS* 3.7 9.2 - - - -
303A LEU 3.5 1.6 - - - +
304A VAL* 3.4 3.8 - - - -
305A ILE* 2.8 53.2 + - + +
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Residues in contact with GLU 288 (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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280A CYS* 3.1 3.8 - - - +
281A TYR* 2.6 74.7 + - + +
283A ASN* 3.0 34.3 + - + +
286A LYS* 5.1 0.9 - - + -
287A VAL* 1.3 77.4 - - - +
289A CYS* 1.3 60.0 + - - +
303A LEU 3.4 4.5 - - - +
304A VAL* 4.5 18.2 - - + +
355A ARG* 2.9 41.1 + - - +
383A TRP* 3.9 13.2 + - + -
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Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 4.3 7.2 - - - -
278A CYS* 4.1 1.1 - - + -
279A SER 3.4 3.6 - - - -
280A CYS* 2.0 46.9 - - - -
287A VAL* 3.7 12.1 - - - -
288A GLU* 1.3 75.8 - - - +
290A VAL* 1.3 64.0 + - - +
291A CYS* 4.0 12.0 - - - -
301A PRO 3.9 0.2 - - - +
302A VAL* 3.3 8.4 - - - +
303A LEU* 2.7 50.7 + - + +
305A ILE* 4.2 15.3 - - - -
383A TRP* 5.6 0.2 - - - -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A SER 2.9 28.2 + - - +
281A TYR* 4.9 2.2 - - + -
289A CYS* 1.3 76.2 - - - +
291A CYS* 1.3 62.0 + - - +
300A ARG* 3.5 35.2 - - + -
301A PRO 3.6 3.8 - - - +
302A VAL* 4.2 14.4 - - + -
317A LEU* 4.8 7.6 - - + -
351A GLY 3.5 10.7 - - - +
352A PHE 4.0 12.1 - - - +
353A GLY* 3.7 34.5 - - - +
383A TRP* 4.4 15.0 - - + -
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Residues in contact with CYS 291 (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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275A ILE* 3.9 15.5 - - + -
276A GLU 3.3 10.1 - - - +
277A GLU 4.5 2.2 - - - -
278A CYS* 2.0 49.8 - - - +
289A CYS* 4.0 13.2 - - - -
290A VAL* 1.3 75.9 - - - +
292A ARG* 1.3 63.9 + - - +
300A ARG* 2.8 33.1 + - - +
301A PRO* 3.0 23.9 + - + -
303A LEU* 5.0 4.7 - - - -
351A GLY 5.1 1.6 - - - -
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Residues in contact with ARG 292 (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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274A HIS 3.3 4.9 - - - +
275A ILE 3.7 0.2 - - - -
276A GLU* 2.9 46.0 + - + +
277A GLU* 2.7 39.4 + - - +
291A CYS* 1.3 82.7 - - - +
293A ASP* 1.3 68.7 + - - +
294A ASN* 2.7 30.3 + - - -
300A ARG* 3.6 13.0 - - - +
301A PRO* 3.8 3.8 - - - -
324A ASP* 4.5 1.8 - - - +
347A TYR* 3.6 17.4 - - - -
348A GLY 3.0 22.1 + - - -
349A VAL* 3.7 18.6 - - - +
350A LYS* 3.8 7.1 - - - +
406A TYR* 2.9 22.2 + - - -
501A 27V 3.6 21.9 + - - +
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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
------------------------------------------------------------
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