Contacts of the strand formed by residues 251 - 258 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D TRP* 2.9 33.9 + - - -
219D ARG* 3.8 15.8 + - - -
242D THR* 3.4 5.0 - - - -
243D ASP 2.9 40.2 + - - -
250D ALA* 1.3 73.1 - - - +
252D TYR* 1.3 60.8 + - - +
267D GLU* 2.6 31.1 + - - -
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Residues in contact with TYR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D VAL* 5.1 3.6 - - + -
241D MET 3.5 5.8 - - - +
242D THR* 4.0 5.8 - - + +
249D GLN* 3.9 1.7 + - - -
250D ALA* 3.2 48.1 + - + -
251D SER* 1.3 78.3 + - - +
253D LYS* 1.3 62.0 + - - +
267D GLU* 3.2 10.1 + - - +
268D LEU* 2.9 47.4 + - + -
270D ALA* 4.1 24.0 - - + -
273D TYR 2.6 29.0 + - - -
274D HIS* 3.1 9.2 - + - -
275D TYR* 3.2 58.1 - + + -
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Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D TRP* 3.6 53.8 - - + +
240D VAL* 3.4 6.8 - - - +
241D MET 3.1 31.8 + - - -
251D SER 4.4 0.2 + - - -
252D TYR* 1.3 79.6 - - - +
254D ILE* 1.3 66.1 + - - +
255D PHE* 3.6 26.4 - - + -
265D SER* 5.3 7.5 + - - +
266D VAL 3.1 16.4 - - - +
267D GLU* 3.7 29.6 - - + +
268D LEU* 4.6 0.7 - - - +
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Residues in contact with ILE 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D THR 3.6 8.1 - - - +
240D VAL* 4.6 9.2 - - + -
253D LYS* 1.3 75.2 - - - +
255D PHE* 1.3 68.3 + - - +
265D SER* 3.4 3.3 - - - -
266D VAL* 2.9 33.4 + - + +
268D LEU* 3.4 34.1 - - + -
303D VAL* 4.2 7.2 - - + -
305D PHE* 3.2 63.7 - - + -
310D LEU* 3.7 21.3 - - + +
312D TYR* 4.4 6.7 - - + -
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Residues in contact with PHE 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ILE* 3.8 35.0 - - + -
218D TRP* 3.8 23.8 - + - -
238D PHE* 3.3 28.8 - - - +
239D THR* 3.2 24.8 + - + +
241D MET* 3.8 28.5 - - + -
253D LYS* 3.6 33.2 - - + -
254D ILE* 1.3 79.6 - - - +
256D LYS* 1.3 61.7 + - - +
257D MET* 4.4 9.9 - - - -
262D VAL* 4.2 13.0 - - + -
264D LYS 3.7 2.9 - - - +
265D SER* 3.6 23.1 - - - -
310D LEU* 4.6 0.4 - - - -
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Residues in contact with LYS 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D SER* 3.7 15.8 + - - -
237D CYS 3.6 3.8 - - - -
238D PHE* 3.7 14.6 - - + -
255D PHE* 1.3 73.8 - - - +
257D MET* 1.3 64.2 + - - +
258D GLU* 3.5 23.8 + - - -
262D VAL* 3.6 2.9 - - - -
263D VAL* 3.0 38.7 + - + +
264D LYS* 2.9 27.3 + - + +
308D GLN* 2.7 33.7 + - - +
309D ASN* 4.2 8.5 + - - -
310D LEU* 3.8 19.1 - - + -
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Residues in contact with MET 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D LEU* 3.6 22.2 - - + -
192D ILE* 3.4 19.3 - - + -
205D LEU* 3.7 22.0 - - - -
215D ILE* 5.8 0.9 - - - -
230D CYS* 4.8 1.8 - - - -
235D GLY 4.4 0.2 - - - +
236D SER* 3.5 0.9 - - - -
237D CYS* 2.9 44.3 + - + +
238D PHE 4.3 2.2 - - - -
239D THR* 3.3 42.8 - - + +
255D PHE* 4.4 12.6 - - - -
256D LYS* 1.3 74.9 - - - +
258D GLU* 1.3 70.1 + - - +
259D LYS 4.2 0.2 - - - -
260D GLY* 4.4 7.0 - - - -
261D LYS 3.2 21.8 - - - +
262D VAL* 4.3 3.6 - - - -
263D VAL* 4.5 0.2 - - - -
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Residues in contact with GLU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D GLY 4.1 11.2 - - - +
236D SER* 3.0 25.5 + - - +
256D LYS* 3.5 14.0 + - - -
257D MET* 1.3 79.9 - - - +
259D LYS* 1.3 75.5 + - + +
260D GLY 3.1 0.2 - - - -
261D LYS* 2.9 24.9 + - - +
263D VAL* 3.7 29.5 - - + +
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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