Contacts of the strand formed by residues 210 - 216 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206E LYS* 4.0 1.6 - - - -
207E TYR* 2.9 40.8 + - + +
208E ASN* 4.1 10.5 - - + +
209E GLY* 1.3 83.3 - - - +
211E ILE* 1.3 67.8 + - - +
212E THR* 3.2 10.8 + - + +
100H TYR* 4.5 8.3 - - - +
129H CYS* 6.1 1.8 - - - -
412H GLN* 3.8 44.2 - - + +
413H THR* 3.7 37.9 - - + +
419H ARG* 5.1 2.7 - - - +
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Residues in contact with ILE 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E VAL* 3.9 22.4 - - + -
205E LEU 3.3 13.5 - - - +
206E LYS* 3.8 6.9 - - - +
209E GLY 4.2 0.2 + - - -
210E ILE* 1.3 72.3 - - - +
212E THR* 1.3 64.3 + - - +
213E ASP 4.0 10.5 - - - +
214E THR* 5.2 0.4 - - - +
98H ALA* 3.8 32.8 - - + +
99H VAL 4.1 2.7 - - - +
100H TYR* 3.8 31.0 - - + -
412H GLN* 5.6 0.2 + - - -
413H THR* 5.5 1.7 - - - +
419H ARG* 2.9 37.4 + - - +
447H CYS* 4.1 13.7 - - + -
449H VAL* 3.8 22.7 - - + -
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Residues in contact with THR 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E LEU 2.9 11.4 + - - -
207E TYR* 3.6 19.0 + - + -
210E ILE* 3.3 20.4 - - + +
211E ILE* 1.3 74.8 - - - +
213E ASP* 1.3 64.9 + - - +
259E LYS 3.6 17.7 - - - +
260E GLY* 2.8 27.7 + - - -
261E LYS* 3.2 24.8 + - - +
413H THR* 6.5 0.4 - - + -
415H LEU* 6.4 1.6 - - + -
419H ARG* 5.3 3.1 - - - +
449H VAL* 6.3 0.2 - - - -
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Residues in contact with ASP 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E VAL* 3.9 1.2 - - - -
205E LEU* 3.0 34.0 + - + +
211E ILE* 3.9 8.0 - - - +
212E THR* 1.3 81.9 + - - +
214E THR* 1.3 90.6 + - - +
260E GLY 3.4 15.5 + - - +
261E LYS* 3.8 11.0 - - - +
262E VAL* 3.1 35.0 + - - +
449H VAL* 6.1 0.9 - - - -
451H SER* 3.9 15.2 - - - -
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Residues in contact with THR 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E VAL* 3.3 21.3 - - + +
203E ALA 3.2 8.2 + - - -
204E VAL* 4.6 2.9 - - - -
205E LEU 4.9 0.2 - - - +
211E ILE* 5.2 0.5 - - - +
213E ASP* 1.3 91.9 + - - +
215E ILE* 1.3 80.5 + - - +
216E LYS* 4.1 4.3 - - - +
262E VAL* 5.1 0.3 - - - +
98H ALA* 4.5 12.5 - - - +
449H VAL* 4.5 6.8 - - - +
451H SER* 2.8 27.6 + - - +
452H ASP 2.7 29.6 + - - +
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Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E ALA* 2.8 38.9 + - + +
205E LEU* 4.1 21.5 - - + -
214E THR* 1.3 86.6 - - - +
216E LYS* 1.3 65.2 + - - +
218E TRP* 4.9 3.4 - - + -
223E LEU* 3.3 12.8 - - + +
239E THR* 6.1 0.7 - - + -
241E MET* 4.4 17.9 - - + -
255E PHE* 3.7 46.9 - - + -
257E MET* 5.4 1.6 - - - -
262E VAL* 3.7 23.3 - - + -
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Residues in contact with LYS 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E GLY 5.7 0.4 - - - +
201E ALA 3.8 6.5 - - - +
202E VAL* 4.3 8.3 - - + +
214E THR* 4.1 5.2 - - + +
215E ILE* 1.3 78.0 - - - +
217E SER* 1.3 72.0 - - - +
218E TRP* 3.4 12.3 + - - +
223E LEU* 4.2 1.1 - - - -
451H SER* 5.5 1.0 - - - -
452H ASP* 2.7 56.2 - - + +
454H VAL* 5.4 7.2 - - + -
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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