Contacts of the strand formed by residues 279 - 283 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C SER* 3.8 5.7 + - - -
277C GLU 3.7 0.2 + - - -
278C CYS* 1.3 70.9 - - - +
280C CYS* 1.3 61.4 + - - +
281C TYR* 4.6 3.3 - - - -
288C THR 3.5 2.1 - - - +
289C CYS* 3.2 1.0 - - - -
290C VAL* 2.8 34.1 + - - +
350C LYS* 3.2 14.4 + - - -
351C GLY 2.9 23.9 + - - -
352C PHE* 3.6 15.6 - - - +
408C GLY* 3.6 9.9 - - - -
409C SER* 3.5 21.9 + - - -
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Residues in contact with CYS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C GLN* 3.7 23.9 + - - +
229C GLU* 3.8 23.3 + - - +
231C ALA* 4.4 12.2 - - + +
238C PHE 5.5 1.6 - - - +
239C THR* 5.4 2.2 - - - -
240C VAL* 4.1 9.2 - - - -
278C CYS* 3.8 10.2 - - - -
279C SER* 1.3 74.4 - - - +
281C TYR* 1.3 62.3 + - - +
282C PRO* 4.7 0.2 - - - +
287C ILE* 3.6 13.0 - - + -
288C THR 3.1 4.5 - - - -
289C CYS* 2.0 46.2 - - - -
305C PHE* 5.4 0.7 - - - -
409C SER* 4.0 6.0 + - - +
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Residues in contact with TYR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.8 27.4 - - + -
231C ALA* 4.2 4.0 - - - -
279C SER 4.6 2.9 - - - -
280C CYS* 1.3 77.7 - - - +
282C PRO* 1.3 80.7 - - + +
283C ASN* 3.8 12.7 + - + -
287C ILE* 3.5 0.8 - - - +
288C THR* 2.9 63.3 + - + +
290C VAL* 5.0 1.3 - - + -
353C SER 3.5 21.5 - - - -
354C PHE* 4.1 15.3 - + + -
355C LYS* 2.9 39.4 + - - +
383C TRP* 5.6 0.2 - - - -
409C SER* 4.5 10.3 - - - +
411C VAL* 3.9 15.7 - - + -
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Residues in contact with PRO 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLY 5.0 0.9 - - - +
91C LEU* 4.1 0.7 - - - +
229C GLU* 5.3 1.6 - - - +
230C CYS 5.7 0.2 - - - +
231C ALA* 3.8 17.2 - - + -
232C CYS 4.3 5.4 - - - +
233C VAL* 3.8 26.0 - - + -
280C CYS 4.7 0.4 - - - +
281C TYR* 1.3 90.1 - - + +
283C ASN* 1.3 65.5 + - - +
286C GLU 3.4 7.2 - - - +
287C ILE* 4.5 1.3 - - - -
411C VAL* 3.8 15.5 - - + -
412C HIS* 3.6 32.8 - - - +
418C ILE* 3.6 23.6 - - + +
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Residues in contact with ASN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLY 4.6 0.2 + - - -
89C SER 4.0 4.7 - - - -
90C SER* 3.9 5.1 + - - +
91C LEU* 3.0 47.3 - - - +
281C TYR* 4.0 15.9 - - + +
282C PRO* 1.3 75.6 - - - +
284C ALA* 1.3 82.3 + - - +
285C GLY 3.1 1.4 - - - +
286C GLU* 2.7 27.9 + - - +
288C THR* 5.2 4.7 - - - +
355C LYS 5.3 3.0 + - - -
418C ILE* 4.5 0.6 - - - +
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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