Contacts of the strand formed by residues 251 - 258 (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 251 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C TRP* 2.9 31.9 + - - -
219C ARG* 3.9 15.8 - - - +
242C THR* 3.4 5.0 - - - +
243C ASP 2.9 37.9 + - - -
250C ALA* 1.3 71.9 - - - +
252C TYR* 1.3 62.3 + - - +
267C GLU* 2.9 32.1 - - - +
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Residues in contact with TYR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C VAL* 5.0 3.6 - - + -
241C MET 3.5 5.8 - - - +
242C THR* 3.6 15.0 - - + +
249C GLN* 4.0 2.1 + - - -
250C ALA* 3.0 48.1 + - + -
251C SER* 1.3 77.7 + - - +
253C LYS* 1.3 63.5 + - - +
267C GLU* 3.3 8.7 - - - +
268C LEU* 2.8 52.5 + - + -
270C ALA* 4.2 20.0 - - + -
273C TYR 2.7 28.8 + - - -
274C HIS* 3.2 10.3 - + - -
275C TYR* 3.3 50.9 - + + -
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C TRP* 3.4 55.3 - - + +
240C VAL* 3.3 7.9 - - - +
241C MET 2.9 33.4 + - - -
252C TYR* 1.3 79.7 - - - +
254C ILE* 1.3 63.9 + - - +
255C PHE* 3.6 27.9 - - + -
265C SER* 5.1 6.3 - - - +
266C VAL 3.3 8.3 - - - +
267C GLU* 3.4 37.7 + - + +
268C LEU* 4.7 0.7 - - - +
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Residues in contact with ILE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C THR 3.4 8.7 - - - +
240C VAL* 4.6 7.0 - - + +
253C LYS* 1.3 74.1 - - - +
255C PHE* 1.3 68.2 + - - +
265C SER* 3.1 6.4 - - - -
266C VAL* 3.0 31.6 + - + +
268C LEU* 3.8 34.8 - - + -
303C VAL* 4.5 2.9 - - + -
305C PHE* 3.5 63.5 - - + -
310C LEU* 3.9 19.9 - - + +
312C TYR* 4.3 10.1 - - + -
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Residues in contact with PHE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ILE* 3.7 35.2 - - + -
218C TRP* 4.0 17.5 - + - -
238C PHE* 3.1 28.1 - - - +
239C THR* 2.9 27.9 + - + +
241C MET* 3.6 34.3 - - + -
253C LYS* 3.6 35.0 - - + -
254C ILE* 1.3 79.4 - - - +
256C LYS* 1.3 59.7 + - - +
257C MET* 4.1 10.9 - - - +
262C VAL* 4.1 14.1 - - + -
264C LYS 3.7 2.7 - - - +
265C SER* 3.6 22.9 - - - -
310C LEU* 4.7 0.4 - - - -
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C SER* 3.4 27.7 + - - -
237C CYS 3.6 2.7 - - - -
238C PHE* 3.4 22.7 - - + -
255C PHE* 1.3 72.6 - - - +
257C MET* 1.3 62.2 + - - +
258C GLU* 3.7 11.9 + - - -
262C VAL* 3.6 2.3 - - - -
263C VAL* 3.0 38.2 + - + +
264C LYS* 2.8 28.2 + - + +
308C GLN* 2.8 35.0 + - - +
309C ASN* 4.6 7.5 + - - +
310C LEU* 3.7 13.7 - - + +
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Residues in contact with MET 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LEU* 3.8 24.0 - - + -
192C ILE* 3.4 17.7 - - + -
205C LEU* 3.6 25.4 - - + -
215C ILE* 5.7 0.9 - - - -
230C CYS* 5.1 1.6 - - + -
235C GLY 4.1 0.2 - - - +
236C SER* 3.3 7.4 - - - -
237C CYS* 2.7 55.9 + - - +
238C PHE* 4.3 1.8 - - - -
239C THR* 3.1 41.5 - - + +
255C PHE* 4.6 7.2 - - - +
256C LYS* 1.3 73.6 - - - +
258C GLU* 1.3 65.1 + - - +
260C GLY* 4.3 3.6 - - - -
261C LYS 3.3 22.7 - - - +
262C VAL* 4.2 8.7 - - - +
263C VAL* 4.4 0.7 - - - -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C GLY 3.8 14.1 - - - +
236C SER* 2.9 23.9 + - - +
237C CYS* 6.4 0.2 - - - -
256C LYS* 3.7 13.5 + - - -
257C MET* 1.3 80.5 - - - +
259C LYS* 1.3 77.6 + - + +
260C GLY 3.0 0.7 - - - -
261C LYS* 2.8 21.0 + - - +
263C VAL* 3.9 27.7 - - + +
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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