Contacts of the strand formed by residues 286 - 290 (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 GLU 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C VAL* 4.7 0.8 - - - +
281C TYR 3.8 0.2 - - - +
282C PRO* 3.4 2.6 - - - +
283C ASN* 2.7 36.1 + - - +
284C ALA* 4.2 9.2 - - - +
285C GLY* 1.3 84.7 - - - +
287C ILE* 1.3 70.8 + - - +
288C THR* 5.3 0.9 - - - +
304C SER* 5.7 2.2 - - - -
305C PHE* 3.5 14.1 + - - +
306C ASN* 3.9 30.5 + - - +
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Residues in contact with ILE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ALA* 3.8 22.4 - - + +
233C VAL* 4.4 11.0 - - + -
238C PHE* 3.6 37.2 - - + +
280C CYS* 3.6 28.7 - - + -
281C TYR 3.5 8.7 - - - +
282C PRO* 4.8 0.2 - - + -
285C GLY 5.2 1.1 - - - +
286C GLU* 1.3 85.7 - - - +
288C THR* 1.3 66.6 + - - +
289C CYS* 4.0 2.2 - - - -
303C VAL 4.6 0.2 - - - -
304C SER* 3.0 25.5 - - - -
305C PHE* 3.1 45.6 + - + +
306C ASN 5.3 1.1 - - - +
308C GLN* 5.3 2.0 - - + -
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Residues in contact with THR 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C CYS* 3.1 1.4 - - - -
281C TYR* 2.9 70.9 + - + +
283C ASN* 5.2 4.7 - - - +
286C GLU* 5.2 1.0 + - - +
287C ILE* 1.3 81.0 + - - +
289C CYS* 1.3 67.8 + - - +
290C VAL* 4.8 1.8 - - + -
302C TRP* 5.5 0.7 - - + -
303C VAL 3.6 4.9 - - - +
304C SER* 4.0 12.8 - - - +
355C LYS* 5.1 5.1 - - + +
383C TRP* 4.3 24.2 - - + -
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Residues in contact with CYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C VAL* 4.0 9.4 - - - -
278C CYS* 4.0 1.6 - - + -
279C SER 3.2 4.7 - - - +
280C CYS* 2.0 46.4 - - - -
287C ILE* 4.0 0.7 - - - -
288C THR* 1.3 76.4 - - - +
290C VAL* 1.3 61.5 + - - +
291C CYS* 4.0 14.9 - - - -
302C TRP* 3.0 9.4 - - - +
303C VAL* 2.7 41.6 + - + +
305C PHE* 3.9 26.5 - - - -
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Residues in contact with VAL 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C SER* 2.8 34.4 + - - +
281C TYR* 5.0 0.7 - - + -
288C THR* 4.8 6.1 - - + -
289C CYS* 1.3 75.7 - - - +
291C CYS* 1.3 63.5 + - - +
300C ARG* 3.7 33.2 - - + -
301C PRO 3.6 4.5 - - - +
302C TRP* 4.7 1.1 - - + -
317C ILE* 4.1 6.7 - - + -
351C GLY 3.6 4.3 - - - +
352C PHE* 4.0 4.9 - - - -
353C SER* 3.5 50.0 - - - +
383C TRP* 4.4 21.3 - - + -
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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
------------------------------------------------------------
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