Contacts of the strand formed by residues 210 - 216 (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 ILE 210 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F TYR* 4.6 8.1 - - + +
129F CYS* 5.7 1.8 - - - -
412F GLN* 3.6 55.4 - - + +
413F THR* 3.7 29.8 - - + +
419F ARG* 4.9 6.5 - - - +
206H LYS* 4.2 1.3 - - - -
207H TYR* 3.1 32.8 + - + +
208H ASN* 3.3 9.4 - - + +
209H GLY* 1.3 82.2 - - - +
211H ILE* 1.3 67.5 + - - +
212H THR* 3.2 9.5 + - + +
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Residues in contact with ILE 211 (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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98F ALA* 4.0 15.7 - - + +
99F VAL 4.0 9.6 - - - +
100F TYR* 3.8 21.9 - - + -
412F GLN* 6.1 0.6 - - - +
413F THR* 5.4 1.9 - - - +
415F LEU* 6.2 0.2 - - - +
419F ARG* 3.1 34.0 + - - +
447F CYS* 4.1 17.0 - - + -
449F VAL* 3.9 20.0 - - + -
204H VAL* 3.8 28.5 - - + -
205H LEU 3.3 13.2 - - - +
206H LYS* 3.9 13.8 - - - +
210H ILE* 1.3 72.5 - - - +
212H THR* 1.3 63.0 + - - +
213H ASP 3.8 13.2 - - - +
214H THR* 4.7 2.0 - - - +
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Residues in contact with THR 212 (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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419F ARG* 5.5 1.6 - - - +
449F VAL* 6.5 0.2 - - - -
205H LEU 2.9 11.6 + - - -
207H TYR* 3.7 15.4 + - + -
210H ILE* 3.2 19.7 + - + +
211H ILE* 1.3 74.6 - - - +
213H ASP* 1.3 62.9 + - - +
259H LYS 3.4 16.4 - - - +
260H GLY* 2.4 35.3 + - - -
261H LYS* 2.9 33.2 + - - +
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Residues in contact with ASP 213 (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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449F VAL* 6.2 0.9 - - - -
451F SER* 4.1 12.6 + - - -
204H VAL 3.9 0.2 - - - -
205H LEU* 3.0 35.1 + - + +
211H ILE* 3.8 7.5 - - - +
212H THR* 1.3 82.0 + - - +
214H THR* 1.3 91.0 + - - +
260H GLY 3.5 13.9 - - - +
261H LYS* 3.9 9.0 - - - +
262H VAL* 3.0 36.9 + - - +
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Residues in contact with THR 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ALA* 4.4 13.0 - - - +
449F VAL* 4.1 9.7 - - - +
451F SER* 2.9 27.2 + - - -
452F ASP 2.6 32.4 + - - +
453F THR* 5.4 0.4 - - + -
202H VAL* 3.3 19.7 - - + +
203H ALA 3.3 6.4 + - - -
204H VAL* 4.5 3.1 - - - -
211H ILE* 4.7 0.3 - - - +
213H ASP* 1.3 94.2 + - - +
215H ILE* 1.3 74.0 + - - +
216H LYS* 4.5 3.5 + - - +
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Residues in contact with ILE 215 (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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202H VAL* 3.5 0.5 - - - -
203H ALA* 2.8 43.8 + - + +
205H LEU* 4.3 19.7 - - + -
214H THR* 1.3 82.2 - - - +
216H LYS* 1.3 69.5 + - - +
218H TRP* 4.9 5.2 - - + -
223H LEU* 3.6 11.3 - - + +
239H THR* 6.5 0.4 - - + -
241H MET* 4.6 11.2 - - + -
255H PHE* 3.6 45.1 - - + -
257H MET* 5.7 1.1 - - - -
262H VAL* 3.7 25.8 - - + -
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Residues in contact with LYS 216 (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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451F SER* 5.0 2.0 - - - +
452F ASP* 2.7 60.6 - - + +
454F VAL* 5.4 4.7 - - + -
200H GLY 5.2 3.4 - - - +
201H ALA 3.8 6.7 - - - +
202H VAL* 4.3 8.7 - - + +
214H THR* 4.3 3.6 + - - +
215H ILE* 1.3 78.8 - - - +
217H SER* 1.3 71.1 + - - +
218H TRP* 3.4 12.8 + - - +
223H LEU* 4.1 2.0 - - - -
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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