Contacts of the strand formed by residues 279 - 283 (chain B) 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 SER 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B SER* 3.5 6.7 - - - -
277B GLU 3.7 0.2 + - - -
278B CYS* 1.3 70.7 - - - +
280B CYS* 1.3 60.2 + - - +
281B TYR* 4.3 4.3 + - - -
288B THR 3.7 1.4 - - - +
289B CYS* 3.4 1.4 - - - -
290B VAL* 2.9 30.2 + - - +
350B LYS* 3.3 13.9 + - - -
351B GLY 2.6 27.8 + - - -
352B PHE* 3.5 14.1 - - - +
353B SER 5.7 0.2 - - - +
408B GLY* 3.8 7.1 - - - -
409B SER* 3.5 23.6 + - - -
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Residues in contact with CYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLN* 3.6 25.2 + - - +
229B GLU* 3.8 23.4 + - - +
230B CYS 4.5 0.3 - - - +
231B ALA* 4.2 12.8 - - + +
238B PHE 5.3 1.6 - - - +
239B THR* 5.4 1.6 - - - -
240B VAL* 4.1 10.3 - - - -
278B CYS* 3.9 9.4 - - - -
279B SER* 1.3 74.3 - - - +
281B TYR* 1.3 62.8 + - - +
282B PRO* 4.7 0.2 - - - +
287B ILE* 3.8 10.5 - - + -
288B THR 3.2 3.8 - - - -
289B CYS* 2.0 46.7 - - - -
305B PHE* 5.4 0.9 - - - -
409B SER* 4.2 5.9 + - - -
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Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.7 26.9 - - + -
231B ALA* 4.1 4.0 - - - -
279B SER 4.6 4.9 - - - -
280B CYS* 1.3 76.7 - - - +
282B PRO* 1.3 80.8 - - + +
283B ASN* 4.1 11.2 - - + -
287B ILE* 3.4 3.1 - - - -
288B THR* 3.0 70.0 + - + +
290B VAL* 5.1 2.7 - - + -
353B SER 3.5 20.6 + - - -
354B PHE* 3.8 22.4 - + + -
355B LYS* 3.0 32.2 + - - +
383B TRP* 5.3 0.2 - - - -
409B SER* 4.6 7.6 - - - +
411B VAL* 3.7 16.8 - - + -
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Residues in contact with PRO 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY 5.0 0.2 - - - +
91B LEU* 4.4 0.3 - - - +
229B GLU* 5.6 1.3 - - - +
231B ALA* 3.8 16.4 - - + -
232B CYS 3.9 5.8 - - - +
233B VAL* 3.7 28.3 - - + -
280B CYS 4.7 0.2 - - - +
281B TYR* 1.3 90.4 - - + +
283B ASN* 1.3 62.7 + - - +
286B GLU 3.5 6.3 - - - +
287B ILE* 4.5 1.1 - - - -
411B VAL* 3.8 15.3 - - + -
412B HIS* 3.7 29.4 - - - +
418B ILE* 3.5 28.0 - - + +
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Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER 4.1 2.9 - - - -
90B SER* 3.6 5.6 + - - +
91B LEU* 2.7 52.6 - - - +
281B TYR* 4.0 17.7 + - + +
282B PRO* 1.3 75.4 - - - +
284B ALA* 1.3 82.3 + - - +
285B GLY 3.2 1.1 - - - +
286B GLU* 2.7 27.8 + - - +
288B THR* 5.2 4.7 - - - +
355B LYS 5.5 1.7 + - - -
418B ILE* 4.7 0.2 - - - -
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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