Contacts of the strand formed by residues 279 - 283 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F SER* 3.8 7.9 - - - -
277F GLU 3.6 0.2 + - - -
278F CYS* 1.3 71.4 - - - +
280F CYS* 1.3 59.0 + - - +
281F TYR* 4.4 3.5 + - - -
288F THR 3.8 1.2 - - - +
289F CYS* 3.3 0.9 - - - -
290F VAL* 2.8 35.6 + - - +
350F LYS* 3.2 14.2 + - - -
351F GLY 2.7 28.1 + - - -
352F PHE* 3.6 19.9 - - - +
408F GLY* 3.8 6.6 - - - -
409F SER* 3.8 15.8 + - - -
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Residues in contact with CYS 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F GLN* 3.7 23.6 + - - +
228F SER* 4.5 0.2 + - - -
229F GLU* 4.1 19.6 + - - +
230F CYS 4.5 1.4 - - - +
231F ALA* 4.0 16.4 + - + +
238F PHE 5.4 1.8 - - - +
239F THR* 5.5 2.0 - - - -
240F VAL* 4.1 8.1 - - - -
278F CYS* 3.7 12.3 + - - -
279F SER* 1.3 74.6 - - - +
281F TYR* 1.3 62.4 + - - +
282F PRO* 4.9 0.2 - - - +
287F ILE* 3.8 10.5 - - + -
288F THR 3.3 3.8 - - - -
289F CYS* 2.0 46.9 - - - -
305F PHE* 5.5 0.4 - - - -
409F SER* 4.3 5.9 + - - +
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Residues in contact with TYR 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 3.7 27.4 - - + -
231F ALA* 3.9 5.4 - - - -
279F SER 4.8 2.7 - - - -
280F CYS* 1.3 76.3 - - - +
282F PRO* 1.3 81.8 - - + +
283F ASN* 3.9 14.1 - - + -
287F ILE* 3.6 1.9 - - - -
288F THR* 3.1 65.6 + - + +
290F VAL* 5.2 2.2 - - + -
353F SER 3.6 20.4 + - - -
354F PHE* 3.7 23.8 - + + -
355F LYS* 3.2 30.8 + - - +
409F SER* 4.5 8.3 - - - +
411F VAL* 3.6 17.5 - - + -
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Residues in contact with PRO 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F GLY 5.0 1.6 - - - +
91F LEU* 4.3 0.5 - - - +
229F GLU* 5.7 0.4 - - - +
231F ALA* 3.9 16.4 - - + -
232F CYS 4.0 4.5 - - - +
233F VAL* 3.8 27.1 - - + -
281F TYR* 1.3 88.6 - - - +
283F ASN* 1.3 63.1 + - - +
286F GLU 3.5 6.7 - - - +
287F ILE* 4.7 0.4 - - - -
411F VAL* 3.5 21.5 - - + -
412F HIS* 3.7 31.2 - - - +
418F ILE* 3.8 23.6 - - + +
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Residues in contact with ASN 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F SER 4.0 3.6 - - - -
90F SER* 3.9 4.8 + - - +
91F LEU* 3.0 48.8 - - - +
281F TYR* 3.9 18.4 - - + +
282F PRO* 1.3 76.3 - - - +
284F ALA* 1.3 81.7 + - - +
285F GLY 3.3 0.8 - - - +
286F GLU* 2.8 27.1 + - - +
288F THR* 5.2 4.7 - - - +
355F LYS 5.4 3.0 + - - -
418F ILE* 4.5 0.9 - - - -
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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
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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