Contacts of the strand formed by residues 276 - 283 (chain A) 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 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 2.4 51.6 + - + +
242A THR* 4.2 9.2 - - - +
246A SER* 3.9 3.8 - - - -
274A HIS* 2.7 31.6 + - - -
275A TYR* 1.3 78.1 - - - +
277A GLU* 1.3 79.3 + - + +
278A CYS* 3.2 3.7 + - - -
291A CYS* 3.5 2.9 - - - +
292A ARG* 2.8 38.7 + - + +
294A ASN* 3.6 11.6 - - - +
800A G39 3.7 18.2 - - + +
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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
----------------------------------------------------------
224A ARG* 6.5 0.4 - - - -
225A THR 3.8 13.8 + - - +
226A GLN 3.3 15.7 - - - +
227A GLU* 4.2 14.9 - - + +
276A GLU* 1.3 82.9 - - + +
278A CYS* 1.3 61.4 + - - +
279A SER* 3.8 1.6 + - - -
291A CYS* 4.3 4.2 - - - -
292A ARG* 2.9 31.2 + - - -
350A LYS* 3.0 43.5 + - + +
351A GLY 4.5 1.0 - - - +
406A TYR* 2.5 31.6 + - - -
800A G39 3.6 24.9 + - + +
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Residues in contact with CYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 3.1 21.1 + - + +
228A SER* 3.0 15.6 + - - -
240A VAL* 4.0 31.4 - - + -
275A TYR* 4.2 10.5 - - - -
276A GLU* 3.2 4.7 + - - -
277A GLU* 1.3 76.0 - - - +
279A SER* 1.3 59.4 + - - +
280A CYS* 3.9 18.6 - - - -
289A CYS* 4.0 3.4 - - + -
290A VAL 3.8 0.2 - - - -
291A CYS* 2.0 50.3 - - - -
303A VAL* 5.6 1.1 - - - -
350A LYS* 3.2 2.3 + - - -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 3.7 6.7 + - - -
278A CYS* 1.3 70.5 - - - +
280A CYS* 1.3 60.6 + - - +
281A TYR* 4.8 3.5 - - - -
288A THR 3.6 1.7 - - - +
289A CYS* 3.2 1.6 - - - -
290A VAL* 3.0 28.8 + - - +
350A LYS* 3.1 15.9 + - - -
351A GLY 2.9 24.0 + - - -
352A PHE* 3.7 14.8 - - - +
353A SER 5.8 0.3 - - - +
408A GLY* 3.8 6.9 - - - -
409A SER* 3.7 22.2 + - - -
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 3.7 24.6 + - - +
229A GLU* 3.8 24.5 + - - +
231A ALA* 3.9 15.3 + - + +
238A PHE 5.2 3.4 - - - +
240A VAL* 4.0 10.5 - - - -
278A CYS* 4.0 9.2 - - - -
279A SER* 1.3 73.1 - - - +
281A TYR* 1.3 60.4 + - - +
287A ILE* 3.7 12.8 - - + -
288A THR 3.2 3.6 - - - -
289A CYS* 2.0 46.7 - - - -
305A PHE* 5.4 0.9 - - - -
409A SER* 4.3 4.4 + - - -
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.5 26.2 - - + -
229A GLU* 5.4 0.2 - - - +
231A ALA* 4.2 3.8 - - - -
279A SER 4.8 3.6 - - - -
280A CYS* 1.3 75.8 - - - +
282A PRO* 1.3 80.0 - - + +
283A ASN* 3.9 15.4 + - + -
287A ILE* 3.6 0.7 - - - -
288A THR* 2.9 62.6 + - + +
290A VAL* 5.4 1.1 - - + -
353A SER 3.5 22.2 - - - -
354A PHE* 3.8 23.6 - + + -
355A LYS* 3.1 34.7 + - - +
383A TRP* 5.7 0.2 - - - -
409A SER* 4.5 8.5 - - - +
411A VAL* 4.0 17.7 - - + -
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Residues in contact with PRO 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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87A GLY 5.2 0.9 - - - +
91A LEU* 4.2 0.7 - - - +
229A GLU* 5.3 2.9 - - - +
231A ALA* 3.8 17.5 - - + -
232A CYS 4.2 5.6 - - - +
233A VAL* 3.8 26.0 - - + -
280A CYS 4.5 0.4 - - - +
281A TYR* 1.3 93.7 - - + +
283A ASN* 1.3 65.0 + - - +
286A GLU 3.4 7.0 - - - +
287A ILE* 4.5 1.6 - - - -
411A VAL* 4.2 10.3 - - + -
412A HIS* 3.7 30.3 - - - +
418A ILE* 3.9 27.0 - - + +
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Residues in contact with ASN 283 (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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87A GLY 4.8 0.2 + - - -
89A SER 4.1 4.3 - - - -
90A SER* 3.8 5.1 + - - +
91A LEU* 3.0 49.1 - - - +
281A TYR* 3.9 16.2 - - + +
282A PRO* 1.3 76.0 - - - +
284A ALA* 1.3 82.4 + - - +
285A GLY 3.2 1.7 - - - +
286A GLU* 2.8 26.9 + - - +
288A THR* 5.0 5.8 - - - +
355A LYS 5.4 2.5 + - - -
418A ILE* 4.7 1.3 - - - +
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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