Contacts of the strand formed by residues 215 - 222 (chain A) in PDB entry 2HTE
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 LYS 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A PHE 3.2 0.4 - - - -
214A LYS* 1.3 82.9 - - + +
216A VAL* 1.3 66.2 + - - +
217A GLU* 3.6 28.6 + - - +
235A CYS 3.5 3.3 - - - +
236A CYS* 3.6 1.0 - - - -
237A SER* 2.9 36.0 + - - +
239A THR 3.5 18.8 - - - +
240A ASP* 3.2 31.6 + - - +
241A THR 4.5 0.4 - - - -
242A GLY* 3.6 19.7 - - - -
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 4.1 18.6 - - + +
209A ALA* 3.7 42.0 - - + +
210A LYS* 3.8 30.2 - - + +
213A PHE* 3.9 11.2 - - + +
214A LYS 4.3 0.4 + - - -
215A LYS* 1.3 81.0 - - - +
217A GLU* 1.3 68.4 + - - +
234A LEU* 3.7 28.7 - - + -
235A CYS 3.2 6.7 - - - +
236A CYS* 4.7 1.3 - - - -
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 5.8 1.3 - - - -
215A LYS* 3.6 35.7 + - + +
216A VAL* 1.3 80.8 - - - +
218A TYR* 1.3 59.3 + - - +
234A LEU* 3.6 4.1 - - - +
235A CYS* 2.6 44.0 + - + +
237A SER* 4.8 0.7 + - - -
241A THR 4.5 2.3 - - - +
242A GLY* 3.5 6.6 - - - -
243A LEU* 2.8 31.5 + - - +
244A THR* 3.4 24.3 + - + +
270A PHE* 4.0 16.3 - - + -
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Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A CYS* 3.2 30.6 + - + -
193A GLU 2.9 24.4 + - - -
195A LEU* 3.8 12.8 + - + +
202A ILE* 3.5 37.8 - - + +
206A ILE* 4.4 14.1 - - + -
217A GLU* 1.3 76.6 - - - +
219A ALA* 1.3 70.7 + - - +
220A ASN* 4.6 1.6 + - + -
232A GLY* 3.3 12.0 + - - -
233A ILE 3.4 9.9 - - - -
234A LEU* 4.6 6.5 - - + -
270A PHE* 3.6 15.1 - - - +
272A LEU* 3.6 40.6 - - + +
276A LEU* 3.8 22.0 - - + -
280A ILE* 5.1 3.3 - - + +
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A TYR* 1.3 81.2 - - - +
220A ASN* 1.3 60.7 + - - +
232A GLY* 2.9 6.6 - - - -
233A ILE* 2.9 52.2 + - + +
269A ALA* 3.3 18.8 - - + +
270A PHE* 3.7 29.4 - - + -
272A LEU* 4.5 0.4 - - - -
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Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET* 5.3 0.3 - - - +
195A LEU* 3.9 28.5 + - + +
196A TRP* 6.0 0.2 - - - +
218A TYR* 4.6 3.2 + - + -
219A ALA* 1.3 76.3 - - - +
221A ILE* 1.3 65.0 + - - +
222A SER* 4.4 1.5 + - - +
230A CYS* 3.6 35.6 - - - +
231A ILE 3.5 15.9 - - - +
232A GLY* 4.0 2.3 + - - -
260A TYR* 4.6 3.6 + - - -
269A ALA* 2.9 31.3 + - - +
272A LEU* 4.6 6.1 - - + -
273A PRO* 6.0 0.6 - - + +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA 3.7 25.4 - - - +
64A TYR* 4.0 28.9 - - + +
67A MET* 3.7 30.1 - - + -
68A MET* 4.2 5.8 - - + -
220A ASN* 1.3 78.6 - - - +
222A SER* 1.3 71.6 + - - +
223A ILE* 3.7 5.7 + - + +
230A CYS* 3.1 9.4 - - - +
231A ILE* 2.9 39.7 + - + +
232A GLY 5.1 0.7 - - - -
233A ILE* 3.6 29.6 - - + -
260A TYR* 3.9 7.2 - - + +
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 3.7 6.9 - - - +
220A ASN* 4.4 1.5 + - - +
221A ILE* 1.3 72.2 - - - +
223A ILE* 1.3 62.3 + - - +
224A PRO* 4.7 3.4 - - - +
229A GLY 3.7 7.1 + - - -
230A CYS* 4.5 2.9 - - - -
260A TYR* 3.1 35.1 + - - -
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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