Contacts of the strand formed by residues 286 - 292 (chain E) in PDB entry 2HU4
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 GLU 286 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E VAL* 5.3 0.7 - - - -
281E TYR 4.0 0.2 - - - +
282E PRO* 3.7 1.6 - - - -
283E ASN* 2.9 34.9 + - - +
284E ALA* 3.8 9.3 - - + +
285E GLY* 1.3 84.4 - - - +
287E ILE* 1.3 68.0 + - - +
288E THR* 4.0 2.7 + - - +
304E SER* 6.0 1.6 - - - -
305E PHE* 3.5 11.6 + - - +
306E ASN* 3.6 35.1 + - - +
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Residues in contact with ILE 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ALA* 4.1 16.6 - - + -
233E VAL* 4.6 10.3 - - + -
238E PHE* 3.3 48.9 - - + -
280E CYS* 3.7 28.7 - - + -
281E TYR 3.6 7.0 - - - +
282E PRO* 5.0 0.9 - - + -
285E GLY 5.0 2.2 - - - +
286E GLU* 1.3 80.9 - - - +
288E THR* 1.3 64.7 + - - +
289E CYS* 3.9 9.4 - - - -
303E VAL 4.7 0.2 - - - -
304E SER* 3.1 7.8 - - - -
305E PHE* 3.1 56.3 + - + +
306E ASN 5.0 2.7 - - - +
308E GLN* 5.3 0.4 - - + -
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Residues in contact with THR 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E CYS* 3.3 1.0 - - - -
281E TYR* 2.9 71.8 + - + +
283E ASN* 5.3 3.1 - - - +
286E GLU* 4.6 3.9 + - - +
287E ILE* 1.3 80.7 + - - +
289E CYS* 1.3 67.0 + - - +
290E VAL* 5.0 1.6 - - + -
302E TRP* 5.7 0.9 - - + -
303E VAL 3.7 3.8 - - - -
304E SER* 3.8 13.9 - - - -
355E LYS* 5.4 5.0 - - + +
383E TRP* 4.5 21.5 - - + -
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Residues in contact with CYS 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E VAL* 3.9 13.2 - - - -
278E CYS* 3.9 13.2 - - + -
279E SER 3.2 5.4 - - - +
280E CYS* 2.0 48.5 - - - -
287E ILE* 3.9 8.1 - - - -
288E THR* 1.3 76.9 - - - +
290E VAL* 1.3 65.3 + - - +
291E CYS* 3.9 4.5 - - - -
302E TRP* 3.1 29.6 - - - +
303E VAL* 2.8 22.6 + - + +
305E PHE* 4.2 6.5 - - - -
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Residues in contact with VAL 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E SER* 3.1 16.9 + - - +
281E TYR* 5.1 1.1 - - + -
288E THR* 5.0 5.2 - - + -
289E CYS* 1.3 76.5 - - - +
291E CYS* 1.3 60.4 + - - +
300E ARG* 3.8 22.7 - - + -
301E PRO 3.6 4.7 - - - +
302E TRP* 4.6 1.1 - - + -
317E ILE* 3.8 16.2 - - + -
351E GLY 3.2 21.0 - - - +
352E PHE* 3.9 4.3 - - + -
353E SER* 3.5 50.9 - - - +
383E TRP* 4.2 21.8 - - + -
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Residues in contact with CYS 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E TYR* 3.5 28.5 - - + -
276E GLU 3.5 12.1 - - - +
277E GLU 4.2 2.5 - - - -
278E CYS* 2.0 52.9 - - - +
289E CYS* 4.0 12.3 - - - -
290E VAL* 1.3 74.9 - - - +
292E ARG* 1.3 61.9 + - - +
300E ARG* 2.9 28.3 + - - +
301E PRO* 3.0 19.0 + - + +
302E TRP* 4.9 0.2 - - - -
303E VAL* 5.1 1.1 - - - -
351E GLY 5.2 0.4 - - - -
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Residues in contact with ARG 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E HIS* 3.3 7.4 + - - +
275E TYR 3.8 0.5 - - - -
276E GLU* 3.0 36.4 + - - +
277E GLU* 2.8 37.5 + - - +
291E CYS* 1.3 80.6 - - - +
293E ASP* 1.3 69.9 + - - +
294E ASN* 2.8 31.8 + - + +
300E ARG* 3.5 14.4 - - - +
301E PRO* 4.1 1.3 - - - -
324E ASP* 4.5 1.6 - - - +
347E TYR* 3.5 11.1 - - - -
348E GLY 2.8 28.1 + - - -
349E VAL* 3.6 18.6 - - - +
350E LYS* 3.8 8.0 - - - +
406E TYR* 3.0 18.2 + - - -
804E G39 3.2 34.5 + - - +
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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