Contacts of the strand formed by residues 251 - 258 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218H TRP* 3.1 28.1 + - - -
219H ARG* 4.0 13.8 + - - -
242H THR* 3.2 8.8 - - - +
243H ASP 2.9 40.5 + - - -
250H ALA* 1.3 75.9 - - - +
252H TYR* 1.3 63.0 + - - +
253H LYS 4.3 0.2 - - - -
267H GLU* 3.1 30.7 + - - +
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Residues in contact with TYR 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H VAL* 5.1 4.9 - - + -
241H MET 3.5 6.3 - - - +
242H THR* 3.7 4.7 - - + +
249H GLN* 3.9 2.0 + - - -
250H ALA* 3.2 48.2 + - + -
251H SER* 1.3 79.6 + - - +
253H LYS* 1.3 58.6 + - - +
267H GLU* 3.3 6.5 - - - +
268H LEU* 2.6 60.7 + - + -
270H ALA* 4.2 15.7 - - + -
273H TYR 2.6 28.2 + - - -
274H HIS* 3.2 9.4 - + - -
275H TYR* 3.2 61.0 - + + -
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Residues in contact with LYS 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H TRP* 3.6 58.7 - - + +
240H VAL* 3.4 6.7 - - - +
241H MET 2.9 33.5 + - - -
252H TYR* 1.3 76.3 - - - +
254H ILE* 1.3 63.5 + - - +
255H PHE* 3.6 26.6 - - + -
265H SER* 5.1 10.2 + - - +
266H VAL 3.3 7.0 - - - +
267H GLU* 3.8 32.3 - - + +
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Residues in contact with ILE 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H THR 3.6 6.3 - - - +
240H VAL* 4.5 10.3 - - + -
253H LYS* 1.3 77.8 - - - +
255H PHE* 1.3 65.3 + - - +
265H SER* 3.3 7.1 - - - -
266H VAL* 2.9 34.6 + - + +
268H LEU* 3.5 34.8 - - + -
303H VAL* 4.0 5.4 - - + -
305H PHE* 3.6 58.3 - - + -
310H LEU* 3.9 24.0 - - + +
312H TYR* 4.4 8.7 - - + -
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Residues in contact with PHE 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215H ILE* 3.6 37.9 - - + -
218H TRP* 4.0 12.6 - + - -
238H PHE* 3.2 9.0 - - - +
239H THR* 2.8 47.4 + - + +
241H MET* 3.7 33.0 - - + -
253H LYS* 3.6 38.1 - - + -
254H ILE* 1.3 80.2 - - - +
256H LYS* 1.3 62.4 + - - +
257H MET* 4.3 10.5 - - - +
262H VAL* 4.2 11.9 - - + -
264H LYS 3.9 2.7 - - - -
265H SER* 3.7 23.1 - - - -
310H LEU* 5.0 0.4 - - - -
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Residues in contact with LYS 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H SER* 3.6 28.3 - - - -
237H CYS 3.4 4.0 - - - +
238H PHE* 3.4 21.3 - - + -
255H PHE* 1.3 73.2 - - - +
257H MET* 1.3 65.6 + - - +
258H GLU* 4.1 5.9 + - - -
262H VAL* 3.5 4.5 - - - +
263H VAL* 3.0 42.2 + - + +
264H LYS* 3.0 26.0 + - + +
308H GLN* 2.8 33.5 + - - +
309H ASN* 4.5 9.6 + - - +
310H LEU* 3.9 10.3 - - + -
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Residues in contact with MET 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H LEU* 3.9 26.0 - - + -
192H ILE* 3.7 17.3 - - + -
205H LEU* 4.0 22.2 - - + -
215H ILE* 5.7 1.3 - - - -
230H CYS* 5.1 1.3 - - - -
236H SER* 3.7 0.7 - - - -
237H CYS* 2.7 53.9 + - + +
238H PHE 4.1 2.0 - - - -
239H THR* 3.2 42.2 - - + +
255H PHE* 4.3 9.9 - - - +
256H LYS* 1.3 76.5 - - - +
258H GLU* 1.3 64.8 + - - +
259H LYS 4.3 0.2 - - - -
260H GLY* 4.4 1.8 - - - -
261H LYS 3.0 30.1 - - - +
262H VAL* 3.9 3.1 - - - +
263H VAL* 4.2 1.3 - - - +
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Residues in contact with GLU 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H GLY 4.1 13.0 - - - +
236H SER* 3.1 25.8 + - - +
237H CYS* 6.4 0.2 - - - -
256H LYS* 4.1 10.7 + - - -
257H MET* 1.3 79.0 - - - +
259H LYS* 1.3 77.8 + - + +
260H GLY 3.0 0.4 - - - -
261H LYS* 2.8 24.6 + - - +
263H VAL* 3.8 26.6 - - + +
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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
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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