Contacts of the strand formed by residues 214 - 223 (chain A) in PDB entry 3IEU
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 VAL 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LYS 3.5 3.6 + - - +
33A ILE* 3.3 29.0 - - + -
34A SER* 3.0 21.5 + - - -
202A LEU* 4.3 8.7 - - + -
206A LEU* 5.8 4.3 - - + -
210A LEU* 5.0 4.3 - - + -
211A PRO* 3.6 41.7 - - + +
212A TYR 3.3 0.8 - - - +
213A SER* 1.3 80.5 - - - +
215A THR* 1.3 67.7 + - - +
235A ILE* 4.1 22.0 - - + -
236A LEU 3.3 11.9 - - - +
237A VAL* 4.5 11.7 - - + +
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Residues in contact with THR 215 (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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26A ASN* 5.2 1.6 - - - +
34A SER* 3.2 24.5 - - - -
36A THR* 4.5 19.4 - - + +
213A SER* 4.5 2.0 - - - +
214A VAL* 1.3 81.0 - - - +
216A VAL* 1.3 64.5 + - - +
234A LEU 3.9 0.5 - - - +
235A ILE* 3.7 1.7 - - - -
236A LEU* 2.8 59.5 + - - +
282A LYS* 4.0 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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33A ILE* 3.9 13.5 - - + -
34A SER 2.8 10.3 + - - +
35A ILE* 3.4 9.1 - - + +
36A THR* 3.0 24.6 + - - +
195A SER* 4.1 21.1 - - - +
198A ILE* 3.9 35.9 - - + -
199A ARG* 4.1 9.2 - - + +
202A LEU* 3.9 27.8 - - + -
215A THR* 1.3 76.5 - - - +
217A GLU* 1.3 70.1 + - - +
218A ILE* 5.3 0.2 - - + -
234A LEU 3.7 7.6 - - - +
235A ILE* 4.8 2.0 - - + -
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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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36A THR* 3.1 34.1 + - - +
37A SER* 4.4 3.1 - - - +
38A ARG* 2.6 48.7 + - - +
195A SER* 5.1 1.1 - - - -
216A VAL* 1.3 81.6 - - - +
218A ILE* 1.3 71.5 + - - +
219A GLU* 3.5 12.8 + - + +
233A GLY* 3.9 1.6 - - - -
234A LEU* 2.9 49.3 + - + +
236A LEU* 4.0 16.9 - - + +
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Residues in contact with ILE 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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36A THR 4.3 2.4 + - - -
37A SER* 5.9 2.0 - - - +
38A ARG 5.9 0.9 + - - -
191A ARG* 3.1 49.7 + - + +
194A ALA* 3.5 23.6 - - + -
195A SER* 3.3 27.9 + - - +
198A ILE* 4.0 20.4 - - + -
217A GLU* 1.3 79.7 - - - +
219A GLU* 1.3 57.4 + - - +
220A ARG 3.7 24.2 - - - +
221A PHE* 4.3 6.1 - - + -
231A ILE* 3.9 17.0 - - + -
232A ASN 3.7 5.6 - - - +
233A GLY* 4.7 0.7 - - - -
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLU* 4.5 10.8 - - - +
218A ILE* 1.3 72.6 - - - +
220A ARG* 1.3 60.6 + - + +
232A ASN* 3.0 28.5 + - + +
234A LEU* 3.2 45.1 - - + +
278A TRP* 4.7 2.8 - - - -
293A ARG* 3.1 38.6 + - - -
303A SO4 4.3 3.3 + - - -
307A SO4 3.2 18.9 + - - -
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ARG* 4.8 0.2 - - - -
218A ILE* 3.3 8.1 + - - +
219A GLU* 1.3 83.1 - - + +
221A PHE* 1.3 63.1 + - - +
222A VAL* 3.2 29.5 - - + +
230A ASP* 3.8 30.1 + - - +
231A ILE* 3.3 5.4 - - - -
232A ASN* 2.9 55.7 + - + +
307A SO4 3.6 16.9 + - - +
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Residues in contact with PHE 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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190A GLN* 3.9 35.0 - - + -
191A ARG* 3.6 39.9 + - + +
194A ALA* 4.4 3.6 - - + -
218A ILE* 4.3 10.1 - - + -
220A ARG* 1.3 74.8 - - - +
222A VAL* 1.3 68.7 + - - +
229A TYR* 3.9 30.1 - + - -
230A ASP 3.8 2.0 - - - -
231A ILE* 3.7 29.8 - - + -
269A PHE* 3.8 24.9 - + - -
307A SO4 3.1 14.3 + - - -
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Residues in contact with VAL 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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220A ARG* 3.2 42.6 - - + +
221A PHE* 1.3 83.1 - - - +
223A SER* 1.3 71.4 + - - +
224A ASN* 4.5 1.6 - - - +
229A TYR* 3.3 12.9 - - - +
230A ASP* 2.8 56.7 + - + +
307A SO4 4.7 3.6 - - - +
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Residues in contact with SER 223 (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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222A VAL* 1.3 81.1 - - - +
224A ASN* 1.3 67.3 + - - +
227A GLY* 5.5 3.1 - - - -
228A GLY 3.1 13.2 - - - -
229A TYR* 3.7 18.1 - - - -
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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